HEADER LYASE 26-APR-07 2YXG TITLE CRYSTAL STRUCTURE OF DIHYRODIPICOLINATE SYNTHASE (DAPA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDRODIPICOLINATE SYNTHASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: DHDPS; COMPND 5 EC: 4.2.1.52; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METHANOCALDOCOCCUS JANNASCHII DSM SOURCE 3 2661; SOURCE 4 ORGANISM_TAXID: 243232; SOURCE 5 STRAIN: DSM2661; SOURCE 6 GENE: DAPA; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET-21A KEYWDS MJ0244, DIHYDRODIPICOLINATE SYNTHASE, TIM BETA/ALPHA-BARREL KEYWDS 2 FOLD, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON KEYWDS 3 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN KEYWDS 4 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR B.PADMANABHAN,Y.BESSHO,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-FEB-10 2YXG 1 JRNL REVDAT 2 24-FEB-09 2YXG 1 VERSN REVDAT 1 30-OCT-07 2YXG 0 JRNL AUTH B.PADMANABHAN,R.W.STRANGE,S.V.ANTONYUK,M.J.ELLIS, JRNL AUTH 2 S.S.HASNAIN,H.IINO,Y.AGARI,Y.BESSHO,S.YOKOYAMA JRNL TITL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM JRNL TITL 2 METHANOCALDOCOCCUS JANNASCHII. JRNL REF ACTA CRYSTALLOGR.,SECT.F V. 65 1222 2009 JRNL REFN ESSN 1744-3091 JRNL PMID 20054116 JRNL DOI 10.1107/S174430910904651X REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 55463 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2965 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.26 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3321 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.64 REMARK 3 BIN R VALUE (WORKING SET) : 0.1810 REMARK 3 BIN FREE R VALUE SET COUNT : 161 REMARK 3 BIN FREE R VALUE : 0.2580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 8849 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 700 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.97000 REMARK 3 B22 (A**2) : 0.98000 REMARK 3 B33 (A**2) : 0.47000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.90000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.265 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.211 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.147 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.776 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 9001 ; 0.022 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 12211 ; 1.825 ; 1.988 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1149 ; 6.852 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 364 ;38.514 ;26.154 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1624 ;16.061 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 24 ;19.352 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1453 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6612 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 4758 ; 0.246 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 6288 ; 0.311 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 647 ; 0.160 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 26 ; 0.229 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 14 ; 0.128 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 5948 ; 1.164 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 9347 ; 1.721 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3425 ; 3.374 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2864 ; 5.369 ; 4.500 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2YXG COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUL-07. REMARK 100 THE RCSB ID CODE IS RCSB027256. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX10.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 WITH SAGITTAL FOCUSSING REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58517 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 82.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.21100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1O5K REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% PEG 8000, 0.1M CACODYLATE, 0.2M REMARK 280 CA ACETATE, PH 6.5, OIL-BATCH, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 38.26600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9300 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET B 1 REMARK 465 MET C 1 REMARK 465 MET D 1 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS(M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CG SD CE REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR C 106 OG1 THR D 43 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 32 CG GLU A 32 CD 0.111 REMARK 500 LYS C 178 CB LYS C 178 CG 0.169 REMARK 500 GLU D 86 CB GLU D 86 CG 0.225 REMARK 500 GLU D 86 CG GLU D 86 CD 0.116 REMARK 500 GLU D 86 CD GLU D 86 OE2 0.163 REMARK 500 GLU D 263 CB GLU D 263 CG 0.132 REMARK 500 GLU D 263 CG GLU D 263 CD 0.122 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 228 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 GLY B 77 C - N - CA ANGL. DEV. = -18.8 DEGREES REMARK 500 ARG B 137 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 137 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG D 137 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES REMARK 500 ARG D 137 NE - CZ - NH2 ANGL. DEV. = -5.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 76 24.55 -152.32 REMARK 500 TYR A 106 -51.64 68.31 REMARK 500 VAL A 134 74.23 -150.95 REMARK 500 ASP A 223 79.04 -100.33 REMARK 500 ALA A 261 -56.69 -156.98 REMARK 500 ALA B 76 -152.51 -142.74 REMARK 500 SER B 78 156.43 177.55 REMARK 500 PRO B 104 130.59 -39.37 REMARK 500 TYR B 106 -50.67 76.58 REMARK 500 ALA B 261 -59.96 -167.52 REMARK 500 ALA C 76 16.30 -149.47 REMARK 500 PRO C 104 124.32 -37.61 REMARK 500 TYR C 106 -51.33 74.00 REMARK 500 ILE C 157 98.81 -69.93 REMARK 500 ALA C 261 -63.05 -163.46 REMARK 500 GLU C 270 137.72 -37.52 REMARK 500 SER C 272 146.45 -32.17 REMARK 500 ALA D 76 16.68 -144.24 REMARK 500 TYR D 106 -47.51 73.07 REMARK 500 ALA D 261 -59.14 -168.82 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ILE D 157 SER D 158 -149.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 ASN A 107 24.4 L L OUTSIDE RANGE REMARK 500 SER A 171 24.7 L L OUTSIDE RANGE REMARK 500 VAL A 282 24.8 L L OUTSIDE RANGE REMARK 500 THR B 44 19.9 L L OUTSIDE RANGE REMARK 500 ILE B 248 21.6 L L OUTSIDE RANGE REMARK 500 VAL D 18 21.5 L L OUTSIDE RANGE REMARK 500 THR D 44 23.0 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MJA001000244.1 RELATED DB: TARGETDB DBREF 2YXG A 1 289 UNP Q57695 DAPA_METJA 1 289 DBREF 2YXG B 1 289 UNP Q57695 DAPA_METJA 1 289 DBREF 2YXG C 1 289 UNP Q57695 DAPA_METJA 1 289 DBREF 2YXG D 1 289 UNP Q57695 DAPA_METJA 1 289 SEQRES 1 A 289 MET PHE LYS GLY VAL TYR PRO ALA ILE ILE THR PRO PHE SEQRES 2 A 289 LYS ASN LYS GLU VAL ASP PHE ASP GLY LEU GLU GLU ASN SEQRES 3 A 289 ILE ASN PHE LEU ILE GLU ASN GLY VAL SER GLY ILE VAL SEQRES 4 A 289 ALA VAL GLY THR THR GLY GLU SER PRO THR LEU SER HIS SEQRES 5 A 289 GLU GLU HIS LYS LYS VAL ILE GLU LYS VAL VAL ASP VAL SEQRES 6 A 289 VAL ASN GLY ARG VAL GLN VAL ILE ALA GLY ALA GLY SER SEQRES 7 A 289 ASN CYS THR GLU GLU ALA ILE GLU LEU SER VAL PHE ALA SEQRES 8 A 289 GLU ASP VAL GLY ALA ASP ALA VAL LEU SER ILE THR PRO SEQRES 9 A 289 TYR TYR ASN LYS PRO THR GLN GLU GLY LEU ARG LYS HIS SEQRES 10 A 289 PHE GLY LYS VAL ALA GLU SER ILE ASN LEU PRO ILE VAL SEQRES 11 A 289 LEU TYR ASN VAL PRO SER ARG THR ALA VAL ASN LEU GLU SEQRES 12 A 289 PRO LYS THR VAL LYS LEU LEU ALA GLU GLU TYR SER ASN SEQRES 13 A 289 ILE SER ALA VAL LYS GLU ALA ASN PRO ASN LEU SER GLN SEQRES 14 A 289 VAL SER GLU LEU ILE HIS ASP ALA LYS ILE THR VAL LEU SEQRES 15 A 289 SER GLY ASN ASP GLU LEU THR LEU PRO ILE ILE ALA LEU SEQRES 16 A 289 GLY GLY LYS GLY VAL ILE SER VAL VAL ALA ASN ILE VAL SEQRES 17 A 289 PRO LYS GLU PHE VAL GLU MET VAL ASN TYR ALA LEU GLU SEQRES 18 A 289 GLY ASP PHE GLU LYS ALA ARG GLU ILE HIS TYR LYS LEU SEQRES 19 A 289 PHE PRO LEU MET LYS ALA MET PHE ILE GLU THR ASN PRO SEQRES 20 A 289 ILE PRO VAL LYS THR ALA LEU ASN MET MET GLY ARG PRO SEQRES 21 A 289 ALA GLY GLU LEU ARG LEU PRO LEU CYS GLU MET SER GLU SEQRES 22 A 289 GLU HIS LYS LYS ILE LEU GLU ASN VAL LEU LYS ASP LEU SEQRES 23 A 289 GLY LEU ILE SEQRES 1 B 289 MET PHE LYS GLY VAL TYR PRO ALA ILE ILE THR PRO PHE SEQRES 2 B 289 LYS ASN LYS GLU VAL ASP PHE ASP GLY LEU GLU GLU ASN SEQRES 3 B 289 ILE ASN PHE LEU ILE GLU ASN GLY VAL SER GLY ILE VAL SEQRES 4 B 289 ALA VAL GLY THR THR GLY GLU SER PRO THR LEU SER HIS SEQRES 5 B 289 GLU GLU HIS LYS LYS VAL ILE GLU LYS VAL VAL ASP VAL SEQRES 6 B 289 VAL ASN GLY ARG VAL GLN VAL ILE ALA GLY ALA GLY SER SEQRES 7 B 289 ASN CYS THR GLU GLU ALA ILE GLU LEU SER VAL PHE ALA SEQRES 8 B 289 GLU ASP VAL GLY ALA ASP ALA VAL LEU SER ILE THR PRO SEQRES 9 B 289 TYR TYR ASN LYS PRO THR GLN GLU GLY LEU ARG LYS HIS SEQRES 10 B 289 PHE GLY LYS VAL ALA GLU SER ILE ASN LEU PRO ILE VAL SEQRES 11 B 289 LEU TYR ASN VAL PRO SER ARG THR ALA VAL ASN LEU GLU SEQRES 12 B 289 PRO LYS THR VAL LYS LEU LEU ALA GLU GLU TYR SER ASN SEQRES 13 B 289 ILE SER ALA VAL LYS GLU ALA ASN PRO ASN LEU SER GLN SEQRES 14 B 289 VAL SER GLU LEU ILE HIS ASP ALA LYS ILE THR VAL LEU SEQRES 15 B 289 SER GLY ASN ASP GLU LEU THR LEU PRO ILE ILE ALA LEU SEQRES 16 B 289 GLY GLY LYS GLY VAL ILE SER VAL VAL ALA ASN ILE VAL SEQRES 17 B 289 PRO LYS GLU PHE VAL GLU MET VAL ASN TYR ALA LEU GLU SEQRES 18 B 289 GLY ASP PHE GLU LYS ALA ARG GLU ILE HIS TYR LYS LEU SEQRES 19 B 289 PHE PRO LEU MET LYS ALA MET PHE ILE GLU THR ASN PRO SEQRES 20 B 289 ILE PRO VAL LYS THR ALA LEU ASN MET MET GLY ARG PRO SEQRES 21 B 289 ALA GLY GLU LEU ARG LEU PRO LEU CYS GLU MET SER GLU SEQRES 22 B 289 GLU HIS LYS LYS ILE LEU GLU ASN VAL LEU LYS ASP LEU SEQRES 23 B 289 GLY LEU ILE SEQRES 1 C 289 MET PHE LYS GLY VAL TYR PRO ALA ILE ILE THR PRO PHE SEQRES 2 C 289 LYS ASN LYS GLU VAL ASP PHE ASP GLY LEU GLU GLU ASN SEQRES 3 C 289 ILE ASN PHE LEU ILE GLU ASN GLY VAL SER GLY ILE VAL SEQRES 4 C 289 ALA VAL GLY THR THR GLY GLU SER PRO THR LEU SER HIS SEQRES 5 C 289 GLU GLU HIS LYS LYS VAL ILE GLU LYS VAL VAL ASP VAL SEQRES 6 C 289 VAL ASN GLY ARG VAL GLN VAL ILE ALA GLY ALA GLY SER SEQRES 7 C 289 ASN CYS THR GLU GLU ALA ILE GLU LEU SER VAL PHE ALA SEQRES 8 C 289 GLU ASP VAL GLY ALA ASP ALA VAL LEU SER ILE THR PRO SEQRES 9 C 289 TYR TYR ASN LYS PRO THR GLN GLU GLY LEU ARG LYS HIS SEQRES 10 C 289 PHE GLY LYS VAL ALA GLU SER ILE ASN LEU PRO ILE VAL SEQRES 11 C 289 LEU TYR ASN VAL PRO SER ARG THR ALA VAL ASN LEU GLU SEQRES 12 C 289 PRO LYS THR VAL LYS LEU LEU ALA GLU GLU TYR SER ASN SEQRES 13 C 289 ILE SER ALA VAL LYS GLU ALA ASN PRO ASN LEU SER GLN SEQRES 14 C 289 VAL SER GLU LEU ILE HIS ASP ALA LYS ILE THR VAL LEU SEQRES 15 C 289 SER GLY ASN ASP GLU LEU THR LEU PRO ILE ILE ALA LEU SEQRES 16 C 289 GLY GLY LYS GLY VAL ILE SER VAL VAL ALA ASN ILE VAL SEQRES 17 C 289 PRO LYS GLU PHE VAL GLU MET VAL ASN TYR ALA LEU GLU SEQRES 18 C 289 GLY ASP PHE GLU LYS ALA ARG GLU ILE HIS TYR LYS LEU SEQRES 19 C 289 PHE PRO LEU MET LYS ALA MET PHE ILE GLU THR ASN PRO SEQRES 20 C 289 ILE PRO VAL LYS THR ALA LEU ASN MET MET GLY ARG PRO SEQRES 21 C 289 ALA GLY GLU LEU ARG LEU PRO LEU CYS GLU MET SER GLU SEQRES 22 C 289 GLU HIS LYS LYS ILE LEU GLU ASN VAL LEU LYS ASP LEU SEQRES 23 C 289 GLY LEU ILE SEQRES 1 D 289 MET PHE LYS GLY VAL TYR PRO ALA ILE ILE THR PRO PHE SEQRES 2 D 289 LYS ASN LYS GLU VAL ASP PHE ASP GLY LEU GLU GLU ASN SEQRES 3 D 289 ILE ASN PHE LEU ILE GLU ASN GLY VAL SER GLY ILE VAL SEQRES 4 D 289 ALA VAL GLY THR THR GLY GLU SER PRO THR LEU SER HIS SEQRES 5 D 289 GLU GLU HIS LYS LYS VAL ILE GLU LYS VAL VAL ASP VAL SEQRES 6 D 289 VAL ASN GLY ARG VAL GLN VAL ILE ALA GLY ALA GLY SER SEQRES 7 D 289 ASN CYS THR GLU GLU ALA ILE GLU LEU SER VAL PHE ALA SEQRES 8 D 289 GLU ASP VAL GLY ALA ASP ALA VAL LEU SER ILE THR PRO SEQRES 9 D 289 TYR TYR ASN LYS PRO THR GLN GLU GLY LEU ARG LYS HIS SEQRES 10 D 289 PHE GLY LYS VAL ALA GLU SER ILE ASN LEU PRO ILE VAL SEQRES 11 D 289 LEU TYR ASN VAL PRO SER ARG THR ALA VAL ASN LEU GLU SEQRES 12 D 289 PRO LYS THR VAL LYS LEU LEU ALA GLU GLU TYR SER ASN SEQRES 13 D 289 ILE SER ALA VAL LYS GLU ALA ASN PRO ASN LEU SER GLN SEQRES 14 D 289 VAL SER GLU LEU ILE HIS ASP ALA LYS ILE THR VAL LEU SEQRES 15 D 289 SER GLY ASN ASP GLU LEU THR LEU PRO ILE ILE ALA LEU SEQRES 16 D 289 GLY GLY LYS GLY VAL ILE SER VAL VAL ALA ASN ILE VAL SEQRES 17 D 289 PRO LYS GLU PHE VAL GLU MET VAL ASN TYR ALA LEU GLU SEQRES 18 D 289 GLY ASP PHE GLU LYS ALA ARG GLU ILE HIS TYR LYS LEU SEQRES 19 D 289 PHE PRO LEU MET LYS ALA MET PHE ILE GLU THR ASN PRO SEQRES 20 D 289 ILE PRO VAL LYS THR ALA LEU ASN MET MET GLY ARG PRO SEQRES 21 D 289 ALA GLY GLU LEU ARG LEU PRO LEU CYS GLU MET SER GLU SEQRES 22 D 289 GLU HIS LYS LYS ILE LEU GLU ASN VAL LEU LYS ASP LEU SEQRES 23 D 289 GLY LEU ILE FORMUL 5 HOH *700(H2 O) HELIX 1 1 ASP A 19 ASN A 33 1 15 HELIX 2 2 GLU A 46 LEU A 50 5 5 HELIX 3 3 SER A 51 ASN A 67 1 17 HELIX 4 4 CYS A 80 GLY A 95 1 16 HELIX 5 5 THR A 110 ILE A 125 1 16 HELIX 6 6 VAL A 134 ALA A 139 1 6 HELIX 7 7 GLU A 143 TYR A 154 1 12 HELIX 8 8 LEU A 167 ALA A 177 1 11 HELIX 9 9 ASN A 185 GLU A 187 5 3 HELIX 10 10 LEU A 188 LEU A 195 1 8 HELIX 11 11 VAL A 203 ILE A 207 5 5 HELIX 12 12 VAL A 208 GLY A 222 1 15 HELIX 13 13 ASP A 223 MET A 241 1 19 HELIX 14 14 PRO A 247 MET A 257 1 11 HELIX 15 15 SER A 272 LEU A 286 1 15 HELIX 16 16 ASP B 19 ASN B 33 1 15 HELIX 17 17 GLU B 46 LEU B 50 5 5 HELIX 18 18 SER B 51 ASN B 67 1 17 HELIX 19 19 CYS B 80 VAL B 94 1 15 HELIX 20 20 THR B 110 ILE B 125 1 16 HELIX 21 21 VAL B 134 ALA B 139 1 6 HELIX 22 22 GLU B 143 TYR B 154 1 12 HELIX 23 23 LEU B 167 ALA B 177 1 11 HELIX 24 24 ASN B 185 GLU B 187 5 3 HELIX 25 25 LEU B 188 LEU B 195 1 8 HELIX 26 26 VAL B 203 ILE B 207 5 5 HELIX 27 27 VAL B 208 GLU B 221 1 14 HELIX 28 28 ASP B 223 MET B 241 1 19 HELIX 29 29 PRO B 247 MET B 257 1 11 HELIX 30 30 SER B 272 LEU B 286 1 15 HELIX 31 31 ASP C 19 ASN C 33 1 15 HELIX 32 32 GLY C 42 LEU C 50 5 9 HELIX 33 33 SER C 51 ASN C 67 1 17 HELIX 34 34 CYS C 80 VAL C 94 1 15 HELIX 35 35 THR C 110 ILE C 125 1 16 HELIX 36 36 VAL C 134 ALA C 139 1 6 HELIX 37 37 GLU C 143 TYR C 154 1 12 HELIX 38 38 ASN C 166 ASP C 176 1 11 HELIX 39 39 ASN C 185 GLU C 187 5 3 HELIX 40 40 LEU C 188 LEU C 195 1 8 HELIX 41 41 VAL C 203 ILE C 207 5 5 HELIX 42 42 VAL C 208 GLY C 222 1 15 HELIX 43 43 ASP C 223 MET C 241 1 19 HELIX 44 44 PRO C 247 MET C 257 1 11 HELIX 45 45 SER C 272 LEU C 286 1 15 HELIX 46 46 ASP D 19 ASN D 33 1 15 HELIX 47 47 GLU D 46 LEU D 50 5 5 HELIX 48 48 SER D 51 ASN D 67 1 17 HELIX 49 49 CYS D 80 GLY D 95 1 16 HELIX 50 50 THR D 110 ILE D 125 1 16 HELIX 51 51 VAL D 134 ALA D 139 1 6 HELIX 52 52 GLU D 143 TYR D 154 1 12 HELIX 53 53 ASN D 166 ALA D 177 1 12 HELIX 54 54 ASN D 185 GLU D 187 5 3 HELIX 55 55 LEU D 188 GLY D 196 1 9 HELIX 56 56 VAL D 203 ILE D 207 5 5 HELIX 57 57 VAL D 208 GLY D 222 1 15 HELIX 58 58 ASP D 223 MET D 241 1 19 HELIX 59 59 PRO D 247 MET D 257 1 11 HELIX 60 60 SER D 272 LEU D 286 1 15 SHEET 1 A 8 GLY A 4 PRO A 7 0 SHEET 2 A 8 GLY A 199 SER A 202 1 O VAL A 200 N TYR A 6 SHEET 3 A 8 THR A 180 SER A 183 1 N SER A 183 O GLY A 199 SHEET 4 A 8 ILE A 157 GLU A 162 1 N VAL A 160 O LEU A 182 SHEET 5 A 8 ILE A 129 ASN A 133 1 N LEU A 131 O LYS A 161 SHEET 6 A 8 ALA A 98 ILE A 102 1 N VAL A 99 O VAL A 130 SHEET 7 A 8 GLN A 71 GLY A 75 1 N ALA A 74 O ALA A 98 SHEET 8 A 8 GLY A 37 ALA A 40 1 N ILE A 38 O ILE A 73 SHEET 1 B 2 PHE A 13 LYS A 14 0 SHEET 2 B 2 GLU A 17 VAL A 18 -1 O GLU A 17 N LYS A 14 SHEET 1 C 8 GLY B 4 PRO B 7 0 SHEET 2 C 8 GLY B 199 SER B 202 1 O VAL B 200 N TYR B 6 SHEET 3 C 8 THR B 180 SER B 183 1 N SER B 183 O GLY B 199 SHEET 4 C 8 ILE B 157 GLU B 162 1 N GLU B 162 O LEU B 182 SHEET 5 C 8 ILE B 129 ASN B 133 1 N LEU B 131 O LYS B 161 SHEET 6 C 8 ALA B 98 ILE B 102 1 N SER B 101 O VAL B 130 SHEET 7 C 8 GLN B 71 ALA B 76 1 N ALA B 74 O ALA B 98 SHEET 8 C 8 GLY B 37 ALA B 40 1 N ILE B 38 O ILE B 73 SHEET 1 D 2 PHE B 13 LYS B 14 0 SHEET 2 D 2 GLU B 17 VAL B 18 -1 O GLU B 17 N LYS B 14 SHEET 1 E 8 GLY C 4 PRO C 7 0 SHEET 2 E 8 GLY C 199 SER C 202 1 O VAL C 200 N TYR C 6 SHEET 3 E 8 THR C 180 SER C 183 1 N SER C 183 O ILE C 201 SHEET 4 E 8 ILE C 157 GLU C 162 1 N VAL C 160 O LEU C 182 SHEET 5 E 8 ILE C 129 ASN C 133 1 N LEU C 131 O LYS C 161 SHEET 6 E 8 ALA C 98 ILE C 102 1 N SER C 101 O VAL C 130 SHEET 7 E 8 GLN C 71 GLY C 75 1 N ALA C 74 O ALA C 98 SHEET 8 E 8 GLY C 37 ALA C 40 1 N ILE C 38 O ILE C 73 SHEET 1 F 2 PHE C 13 LYS C 14 0 SHEET 2 F 2 GLU C 17 VAL C 18 -1 O GLU C 17 N LYS C 14 SHEET 1 G 8 GLY D 4 PRO D 7 0 SHEET 2 G 8 GLY D 199 SER D 202 1 O VAL D 200 N TYR D 6 SHEET 3 G 8 THR D 180 SER D 183 1 N SER D 183 O GLY D 199 SHEET 4 G 8 ILE D 157 GLU D 162 1 N VAL D 160 O LEU D 182 SHEET 5 G 8 ILE D 129 ASN D 133 1 N LEU D 131 O LYS D 161 SHEET 6 G 8 ALA D 98 ILE D 102 1 N VAL D 99 O VAL D 130 SHEET 7 G 8 GLN D 71 GLY D 75 1 N ALA D 74 O ALA D 98 SHEET 8 G 8 GLY D 37 ALA D 40 1 N ILE D 38 O ILE D 73 SHEET 1 H 2 PHE D 13 LYS D 14 0 SHEET 2 H 2 GLU D 17 VAL D 18 -1 O GLU D 17 N LYS D 14 CISPEP 1 ASN A 246 PRO A 247 0 -1.15 CISPEP 2 LEU A 266 PRO A 267 0 11.71 CISPEP 3 ASN B 246 PRO B 247 0 4.66 CISPEP 4 LEU B 266 PRO B 267 0 10.39 CISPEP 5 ASN C 246 PRO C 247 0 2.93 CISPEP 6 LEU C 266 PRO C 267 0 9.80 CISPEP 7 ASN D 246 PRO D 247 0 4.69 CISPEP 8 LEU D 266 PRO D 267 0 9.58 CRYST1 80.469 76.532 101.863 90.00 106.87 90.00 P 1 21 1 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.012427 0.000000 0.003769 0.00000 SCALE2 0.000000 0.013066 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010259 0.00000