HEADER SIGNALING PROTEIN 08-JUL-03 1PY4 TITLE BETA2 MICROGLOBULIN MUTANT H31Y DISPLAYS HINTS FOR AMYLOID FORMATIONS CAVEAT 1PY4 CHIRALITY ERROR IN LYS75 B AND GLU44 C COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-2-MICROGLOBULIN PRECURSOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: H31Y; COMPND 5 SYNONYM: HDCMA22P; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: B2M; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PHN1 KEYWDS AMYLOID, DIALYSIS RELATED AMYLOIDOSIS, C-TYPE IMMUNOGLOBULIN, PROTEIN KEYWDS 2 MUTANT, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.ROSANO,S.ZUCCOTTI,P.MANGIONE,S.GIORGETTI,V.BELLOTTI,F.PETTIROSSI, AUTHOR 2 A.CORAZZA,P.VIGLINO,G.ESPOSITO,M.BOLOGNESI REVDAT 3 27-OCT-21 1PY4 1 SEQADV REVDAT 2 24-FEB-09 1PY4 1 VERSN REVDAT 1 04-MAY-04 1PY4 0 JRNL AUTH C.ROSANO,S.ZUCCOTTI,P.MANGIONE,S.GIORGETTI,V.BELLOTTI, JRNL AUTH 2 F.PETTIROSSI,A.CORAZZA,P.VIGLINO,G.ESPOSITO,M.BOLOGNESI JRNL TITL BETA2-MICROGLOBULIN H31Y VARIANT 3D STRUCTURE HIGHLIGHTS THE JRNL TITL 2 PROTEIN NATURAL PROPENSITY TOWARDS INTERMOLECULAR JRNL TITL 3 AGGREGATION JRNL REF J.MOL.BIOL. V. 335 1051 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 14698299 JRNL DOI 10.1016/J.JMB.2003.11.040 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 TITL PRELIMINARY CRYSTALLOGRAPHIC CHARACTERIZATION OF THE HUMAN REMARK 1 TITL 2 BETA2 MICROGLOBULIN IN A TETRAMERIC ASSEMBLY REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 59 1270 2003 REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.19 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15528 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) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.240 REMARK 3 FREE R VALUE : 0.313 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 826 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1076 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.5820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3243 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 30 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.33000 REMARK 3 B22 (A**2) : 4.75000 REMARK 3 B33 (A**2) : -3.42000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.935 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.468 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.293 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.417 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.889 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.813 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3457 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2931 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4689 ; 1.631 ; 1.937 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6861 ; 0.925 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 397 ;10.376 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 486 ; 0.200 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3805 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 745 ; 0.005 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1082 ; 0.372 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3826 ; 0.363 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2142 ; 0.106 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 115 ; 0.318 ; 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): 19 ; 0.276 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 29 ; 0.412 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.530 ; 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): 2012 ;14.297 ; 5.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3287 ;16.232 ; 6.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1445 ;16.473 ; 6.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1402 ;18.857 ; 7.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1PY4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019690. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ELETTRA; ESRF REMARK 200 BEAMLINE : 5.2R; ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.927; 0.939 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL; NULL REMARK 200 DETECTOR MANUFACTURER : NULL; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16354 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 19.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1LDS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4K 31%, GLYCEROL 25%, AMMONIUM REMARK 280 ACETATE 0.2 M, PH 5.6, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 300K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 46.83550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 46.83550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 52.59750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 75.08300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 52.59750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 75.08300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 46.83550 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 52.59750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 75.08300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 46.83550 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 52.59750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 75.08300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ASP A 98 REMARK 465 MET A 99 REMARK 465 MET B 0 REMARK 465 ASP B 98 REMARK 465 MET B 99 REMARK 465 MET C 0 REMARK 465 ILE C 1 REMARK 465 ASP C 98 REMARK 465 MET C 99 REMARK 465 MET D 0 REMARK 465 ASP D 98 REMARK 465 MET D 99 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 ILE A 1 CD1 REMARK 470 ILE A 7 CD1 REMARK 470 ILE A 35 CD1 REMARK 470 ILE A 92 CD1 REMARK 470 ILE B 1 CG1 CG2 CD1 REMARK 470 ILE B 46 CD1 REMARK 470 ILE B 92 CD1 REMARK 470 ILE C 35 CD1 REMARK 470 ILE C 46 CD1 REMARK 470 ILE C 92 CD1 REMARK 470 ILE D 7 CD1 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 N GLN C 2 O HOH C 104 1.64 REMARK 500 NE ARG C 12 O PHE C 22 1.75 REMARK 500 CZ ARG C 12 O PHE C 22 1.93 REMARK 500 OD1 ASN A 24 CG1 ILE C 7 2.00 REMARK 500 CA GLN C 2 O HOH C 104 2.03 REMARK 500 CG ASN A 24 CG1 ILE C 7 2.04 REMARK 500 O LYS C 41 N GLU C 44 2.08 REMARK 500 ND2 ASN A 24 CG1 ILE C 7 2.09 REMARK 500 O TYR C 10 OD1 ASN C 24 2.11 REMARK 500 O PRO C 14 OD1 ASN C 21 2.13 REMARK 500 O GLN B 2 NZ LYS D 58 2.14 REMARK 500 O SER C 52 N LEU C 54 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 58 O GLN C 2 6555 1.91 REMARK 500 OD2 ASP B 53 OH TYR B 63 4555 2.10 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 ASP A 34 CB - CG - OD2 ANGL. DEV. = 7.3 DEGREES REMARK 500 ASP B 34 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP B 59 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP C 59 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP D 59 CB - CG - OD2 ANGL. DEV. = 5.8 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 ASN A 17 11.25 -60.95 REMARK 500 ASN A 21 -158.95 -135.29 REMARK 500 PRO A 32 -154.87 -65.72 REMARK 500 ASN A 42 87.65 54.43 REMARK 500 SER A 52 154.69 -36.81 REMARK 500 SER A 61 -141.21 68.41 REMARK 500 PHE A 70 99.22 -171.79 REMARK 500 THR A 71 99.06 -61.56 REMARK 500 PRO A 72 -171.11 -45.53 REMARK 500 THR A 73 161.19 175.58 REMARK 500 SER A 88 -84.15 -47.68 REMARK 500 ASP A 96 -146.34 -80.64 REMARK 500 PRO B 32 -136.23 -76.25 REMARK 500 SER B 33 -10.74 -143.42 REMARK 500 ASN B 42 41.75 36.57 REMARK 500 HIS B 51 136.36 -176.29 REMARK 500 ASP B 59 35.36 -58.29 REMARK 500 TRP B 60 85.42 37.39 REMARK 500 SER B 61 152.06 175.80 REMARK 500 GLU B 74 -38.46 -29.48 REMARK 500 LYS B 75 -89.61 -43.22 REMARK 500 THR C 4 52.31 167.43 REMARK 500 PRO C 5 -154.56 -37.91 REMARK 500 LYS C 6 105.00 -34.42 REMARK 500 ILE C 7 121.93 140.50 REMARK 500 VAL C 9 11.83 168.48 REMARK 500 SER C 11 -29.90 78.86 REMARK 500 PRO C 14 -179.40 -36.64 REMARK 500 ALA C 15 -81.73 -16.30 REMARK 500 ALA C 15 -81.73 -64.25 REMARK 500 GLU C 16 99.21 65.09 REMARK 500 PRO C 32 -157.69 -100.09 REMARK 500 ASN C 42 62.01 18.95 REMARK 500 ARG C 45 107.81 -39.29 REMARK 500 GLU C 47 -83.64 -63.40 REMARK 500 LYS C 48 53.37 -94.86 REMARK 500 HIS C 51 -143.44 -120.50 REMARK 500 ASP C 53 67.91 -50.92 REMARK 500 LEU C 54 137.34 -13.50 REMARK 500 SER C 57 172.26 174.31 REMARK 500 LYS C 58 -93.27 -54.35 REMARK 500 SER C 61 -79.10 49.41 REMARK 500 PHE C 62 125.21 -176.97 REMARK 500 LEU C 64 -164.36 168.64 REMARK 500 THR C 68 142.79 -172.69 REMARK 500 GLU C 69 157.84 -43.98 REMARK 500 GLU C 74 -65.38 -7.72 REMARK 500 SER C 88 -97.61 -77.82 REMARK 500 TRP C 95 122.11 -14.91 REMARK 500 PRO D 5 -179.24 -64.88 REMARK 500 REMARK 500 THIS ENTRY HAS 76 RAMACHANDRAN OUTLIERS. 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 GLU A 44 ARG A 45 -139.66 REMARK 500 PRO B 32 SER B 33 -149.06 REMARK 500 TYR C 10 SER C 11 -144.50 REMARK 500 VAL C 27 SER C 28 -145.12 REMARK 500 REMARK 500 REMARK: NULL DBREF 1PY4 A 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 1PY4 B 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 1PY4 C 1 99 UNP P61769 B2MG_HUMAN 21 119 DBREF 1PY4 D 1 99 UNP P61769 B2MG_HUMAN 21 119 SEQADV 1PY4 MET A 0 UNP P61769 INITIATING METHIONINE SEQADV 1PY4 TYR A 31 UNP P61769 HIS 51 ENGINEERED MUTATION SEQADV 1PY4 MET B 0 UNP P61769 INITIATING METHIONINE SEQADV 1PY4 TYR B 31 UNP P61769 HIS 51 ENGINEERED MUTATION SEQADV 1PY4 MET C 0 UNP P61769 INITIATING METHIONINE SEQADV 1PY4 TYR C 31 UNP P61769 HIS 51 ENGINEERED MUTATION SEQADV 1PY4 MET D 0 UNP P61769 INITIATING METHIONINE SEQADV 1PY4 TYR D 31 UNP P61769 HIS 51 ENGINEERED MUTATION SEQRES 1 A 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 A 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 A 100 TYR VAL SER GLY PHE TYR PRO SER ASP ILE GLU VAL ASP SEQRES 4 A 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 A 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 A 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 A 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 A 100 LYS ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 B 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 B 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 B 100 TYR VAL SER GLY PHE TYR PRO SER ASP ILE GLU VAL ASP SEQRES 4 B 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 B 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 B 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 B 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 B 100 LYS ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 C 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 C 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 C 100 TYR VAL SER GLY PHE TYR PRO SER ASP ILE GLU VAL ASP SEQRES 4 C 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 C 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 C 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 C 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 C 100 LYS ILE VAL LYS TRP ASP ARG ASP MET SEQRES 1 D 100 MET ILE GLN ARG THR PRO LYS ILE GLN VAL TYR SER ARG SEQRES 2 D 100 HIS PRO ALA GLU ASN GLY LYS SER ASN PHE LEU ASN CYS SEQRES 3 D 100 TYR VAL SER GLY PHE TYR PRO SER ASP ILE GLU VAL ASP SEQRES 4 D 100 LEU LEU LYS ASN GLY GLU ARG ILE GLU LYS VAL GLU HIS SEQRES 5 D 100 SER ASP LEU SER PHE SER LYS ASP TRP SER PHE TYR LEU SEQRES 6 D 100 LEU TYR TYR THR GLU PHE THR PRO THR GLU LYS ASP GLU SEQRES 7 D 100 TYR ALA CYS ARG VAL ASN HIS VAL THR LEU SER GLN PRO SEQRES 8 D 100 LYS ILE VAL LYS TRP ASP ARG ASP MET FORMUL 5 HOH *30(H2 O) SHEET 1 A 4 LYS A 6 SER A 11 0 SHEET 2 A 4 PHE A 22 PHE A 30 -1 O TYR A 26 N GLN A 8 SHEET 3 A 4 SER A 61 GLU A 69 -1 O THR A 68 N LEU A 23 SHEET 4 A 4 GLU A 50 HIS A 51 -1 N GLU A 50 O TYR A 67 SHEET 1 B 7 LYS A 6 SER A 11 0 SHEET 2 B 7 PHE A 22 PHE A 30 -1 O TYR A 26 N GLN A 8 SHEET 3 B 7 SER A 61 GLU A 69 -1 O THR A 68 N LEU A 23 SHEET 4 B 7 LEU A 54 SER A 57 -1 N SER A 57 O SER A 61 SHEET 5 B 7 LEU D 54 SER D 57 -1 O LEU D 54 N PHE A 56 SHEET 6 B 7 SER D 61 LEU D 64 -1 O SER D 61 N SER D 57 SHEET 7 B 7 VAL D 27 PHE D 30 -1 N PHE D 30 O PHE D 62 SHEET 1 C 3 ILE A 35 LYS A 41 0 SHEET 2 C 3 TYR A 78 HIS A 84 -1 O ALA A 79 N LEU A 40 SHEET 3 C 3 LYS A 91 LYS A 94 -1 O VAL A 93 N CYS A 80 SHEET 1 D 4 LYS B 6 SER B 11 0 SHEET 2 D 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 D 4 SER B 61 PHE B 70 -1 O TYR B 66 N CYS B 25 SHEET 4 D 4 GLU B 50 HIS B 51 -1 N GLU B 50 O TYR B 67 SHEET 1 E 4 LYS B 6 SER B 11 0 SHEET 2 E 4 ASN B 21 PHE B 30 -1 O ASN B 24 N TYR B 10 SHEET 3 E 4 SER B 61 PHE B 70 -1 O TYR B 66 N CYS B 25 SHEET 4 E 4 SER B 55 SER B 57 -1 N SER B 57 O SER B 61 SHEET 1 F 4 GLU B 44 ARG B 45 0 SHEET 2 F 4 GLU B 36 LYS B 41 -1 N LYS B 41 O GLU B 44 SHEET 3 F 4 TYR B 78 ASN B 83 -1 O ASN B 83 N GLU B 36 SHEET 4 F 4 LYS B 91 LYS B 94 -1 O VAL B 93 N CYS B 80 SHEET 1 G 4 LYS C 6 TYR C 10 0 SHEET 2 G 4 ASN C 21 SER C 28 -1 O TYR C 26 N GLN C 8 SHEET 3 G 4 PHE C 62 PHE C 70 -1 O LEU C 64 N VAL C 27 SHEET 4 G 4 SER C 55 PHE C 56 -1 N SER C 55 O TYR C 63 SHEET 1 H 4 GLU C 44 ILE C 46 0 SHEET 2 H 4 ILE C 35 LYS C 41 -1 N LYS C 41 O GLU C 44 SHEET 3 H 4 TYR C 78 HIS C 84 -1 O ALA C 79 N LEU C 40 SHEET 4 H 4 LYS C 91 VAL C 93 -1 O VAL C 93 N CYS C 80 SHEET 1 I 2 GLU D 50 HIS D 51 0 SHEET 2 I 2 TYR D 66 TYR D 67 -1 O TYR D 67 N GLU D 50 SSBOND 1 CYS A 25 CYS A 80 1555 1555 2.05 SSBOND 2 CYS B 25 CYS B 80 1555 1555 2.06 SSBOND 3 CYS C 25 CYS C 80 1555 1555 2.02 SSBOND 4 CYS D 25 CYS D 80 1555 1555 2.02 CISPEP 1 TYR A 31 PRO A 32 0 -2.47 CISPEP 2 TYR B 31 PRO B 32 0 5.96 CISPEP 3 TYR C 31 PRO C 32 0 12.81 CISPEP 4 TYR D 31 PRO D 32 0 8.94 CRYST1 105.195 150.166 93.671 90.00 90.00 90.00 C 2 2 21 32 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 0.009506 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006659 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010676 0.00000