HEADER ANTIBIOTIC/ANTIBIOTIC INHIBITOR 09-MAY-06 2GYK TITLE CRYSTAL STRUCTURE OF THE COMPLEX OF THE COLICIN E9 DNASE DOMAIN WITH A TITLE 2 MUTANT IMMUNITY PROTEIN, IMME9 (D51A) COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLICIN-E9 IMMUNITY PROTEIN; COMPND 3 CHAIN: A, E; COMPND 4 SYNONYM: IMME9, MICROCIN-E9 IMMUNITY PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: COLICIN-E9; COMPND 9 CHAIN: B, F; COMPND 10 FRAGMENT: C-TERMINAL DOMAIN, DNASE DOMAIN; COMPND 11 EC: 3.1.21.1; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: IMM9_ECOLI; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21D; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K12; SOURCE 13 ORGANISM_TAXID: 83333; SOURCE 14 STRAIN: K-12; SOURCE 15 GENE: COL, CEI; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: JM105; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PTRC99A KEYWDS PROTEIN-PROTEIN COMPLEX, 4-HELIX BUNDLE, DNASE DOMAIN, HNH-MOTIF, KEYWDS 2 ANTIBIOTIC-ANTIBIOTIC INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.S.SANTI,O.O.KOLADE,U.C.KUHLMANN,A.M.HEMMINGS REVDAT 5 20-OCT-21 2GYK 1 REMARK SEQADV LINK REVDAT 4 18-OCT-17 2GYK 1 REMARK REVDAT 3 06-OCT-10 2GYK 1 REMARK REVDAT 2 24-FEB-09 2GYK 1 VERSN REVDAT 1 15-MAY-07 2GYK 0 JRNL AUTH U.C.KUHLMANN,P.S.SANTI,O.O.KOLADE,G.R.MOORE,R.JAMES, JRNL AUTH 2 C.KLEANTHOUS,A.M.HEMMINGS JRNL TITL CRYSTAL STRUCTURES OF THE COMPLEXES OF THE COLICIN E9 DNASE JRNL TITL 2 DOMAIN WITH MUTANT IMMUNITY PROTEINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.KLEANTHOUS,U.C.KUHLMANN,A.J.POMMER,N.FERGUSON,S.E.RADFORD, REMARK 1 AUTH 2 G.R.MOORE,R.JAMES,A.M.HEMMINGS REMARK 1 TITL STRUCTURAL AND MECHANISTIC BASIS OF IMMUNITY TOWARDS REMARK 1 TITL 2 ENDONUCLEASE COLICINS REMARK 1 REF NAT.STRUCT.BIOL. V. 6 243 1999 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 10074943 REMARK 1 DOI 10.1038/6683 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 51228 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2598 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.64 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2893 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.1990 REMARK 3 BIN FREE R VALUE SET COUNT : 160 REMARK 3 BIN FREE R VALUE : 0.2330 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3373 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 686 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.109 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.065 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.390 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3499 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4721 ; 1.229 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 428 ; 5.806 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;35.306 ;24.878 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 646 ;13.353 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;17.686 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 498 ; 0.090 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2653 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1678 ; 0.200 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2372 ; 0.297 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 463 ; 0.147 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 4 ; 0.113 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 61 ; 0.190 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 71 ; 0.146 ; 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): 2220 ; 0.805 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3484 ; 1.248 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1452 ; 2.149 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1235 ; 3.309 ; 4.500 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 : 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2GYK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037706. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUN-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : SILICON(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51260 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.02700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.04500 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: PDB ENTRY 1EMV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% (W/V) PEG 4K, 100MM SODIUM ACETATE REMARK 280 BUFFER PH 5.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 44.12400 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS A DIMER OF REMARK 300 THE BIOLOGICAL UNIT 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1890 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11150 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1920 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F 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 A 1 REMARK 465 GLU A 2 REMARK 465 GLY A 86 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 SER B 3 REMARK 465 LYS B 134 REMARK 465 MET E 1 REMARK 465 GLU E 2 REMARK 465 GLY E 86 REMARK 465 MET F 1 REMARK 465 LYS F 134 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 60 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 25 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP B 52 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP B 117 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP F 24 CB - CG - OD2 ANGL. DEV. = 6.8 DEGREES REMARK 500 ASP F 25 CB - CG - OD2 ANGL. DEV. = 6.5 DEGREES REMARK 500 ASP F 115 CB - CG - OD2 ANGL. DEV. = 5.5 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 LYS A 4 38.95 -141.80 REMARK 500 GLU A 45 18.52 58.14 REMARK 500 ASP B 29 -128.52 55.99 REMARK 500 ASP B 44 -5.99 77.74 REMARK 500 LYS E 4 -4.85 -141.34 REMARK 500 ASP F 29 -130.96 50.17 REMARK 500 ASP F 44 -2.57 73.54 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 LYS A 84 GLN A 85 139.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 102 ND1 REMARK 620 2 HIS B 127 NE2 100.3 REMARK 620 3 HIS B 131 NE2 105.5 102.0 REMARK 620 4 PO4 B 703 O3 106.0 116.0 124.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS F 102 ND1 REMARK 620 2 HIS F 127 NE2 102.0 REMARK 620 3 HIS F 131 NE2 112.2 102.0 REMARK 620 4 PO4 F 704 O2 102.4 116.8 120.3 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 F 704 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1EMV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITS COGNATE REMARK 900 IMMUNITY PROTEIN IM9 (1.7 ANGSTROMS) REMARK 900 RELATED ID: 1BXI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASE DOMAIN REMARK 900 WITH ITS COGNATE IMMUNITY PROTEIN IM9 REMARK 900 RELATED ID: 2GZE RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF THE COLICIN E9 DNASE DOMAIN REMARK 900 WITH A MUTANT IMMUNITY PROTEIN, IM9 (Y55A) REMARK 900 RELATED ID: 2GZF RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF THE COLICIN E9 DNASE DOMAIN REMARK 900 WITH A MUTANT IMMUNITY PROTEIN, IM9 (Y54F) REMARK 900 RELATED ID: 2GZG RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF THE COLICIN E9 DNASE DOMAIN REMARK 900 WITH A MUTANT IMMUNITY PROTEIN, IM9 (Y55F) REMARK 900 RELATED ID: 2GZI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF THE COLICIN E9 DNASE DOMAIN REMARK 900 WITH A MUTANT IMMUNITY PROTEIN, IM9 (V34A) REMARK 900 RELATED ID: 2GZJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COMPLEX OF THE COLICIN E9 DNASE DOMAIN REMARK 900 WITH A MUTANT IMMUNITY PROTEIN, IM9 (D51A) DBREF 2GYK A 1 86 UNP P13479 IMM9_ECOLI 1 86 DBREF 2GYK E 1 86 UNP P13479 IMM9_ECOLI 1 86 DBREF 2GYK B 1 134 UNP P09883 CEA9_ECOLI 450 582 DBREF 2GYK F 1 134 UNP P09883 CEA9_ECOLI 450 582 SEQADV 2GYK ALA A 51 UNP P13479 ASP 51 ENGINEERED MUTATION SEQADV 2GYK ALA E 51 UNP P13479 ASP 51 ENGINEERED MUTATION SEQADV 2GYK MET B 1 UNP P09883 INITIATING METHIONINE SEQADV 2GYK MET F 1 UNP P09883 INITIATING METHIONINE SEQRES 1 A 86 MET GLU LEU LYS HIS SER ILE SER ASP TYR THR GLU ALA SEQRES 2 A 86 GLU PHE LEU GLN LEU VAL THR THR ILE CYS ASN ALA ASP SEQRES 3 A 86 THR SER SER GLU GLU GLU LEU VAL LYS LEU VAL THR HIS SEQRES 4 A 86 PHE GLU GLU MET THR GLU HIS PRO SER GLY SER ALA LEU SEQRES 5 A 86 ILE TYR TYR PRO LYS GLU GLY ASP ASP ASP SER PRO SER SEQRES 6 A 86 GLY ILE VAL ASN THR VAL LYS GLN TRP ARG ALA ALA ASN SEQRES 7 A 86 GLY LYS SER GLY PHE LYS GLN GLY SEQRES 1 B 134 MET GLU SER LYS ARG ASN LYS PRO GLY LYS ALA THR GLY SEQRES 2 B 134 LYS GLY LYS PRO VAL GLY ASP LYS TRP LEU ASP ASP ALA SEQRES 3 B 134 GLY LYS ASP SER GLY ALA PRO ILE PRO ASP ARG ILE ALA SEQRES 4 B 134 ASP LYS LEU ARG ASP LYS GLU PHE LYS SER PHE ASP ASP SEQRES 5 B 134 PHE ARG LYS ALA VAL TRP GLU GLU VAL SER LYS ASP PRO SEQRES 6 B 134 GLU LEU SER LYS ASN LEU ASN PRO SER ASN LYS SER SER SEQRES 7 B 134 VAL SER LYS GLY TYR SER PRO PHE THR PRO LYS ASN GLN SEQRES 8 B 134 GLN VAL GLY GLY ARG LYS VAL TYR GLU LEU HIS HIS ASP SEQRES 9 B 134 LYS PRO ILE SER GLN GLY GLY GLU VAL TYR ASP MET ASP SEQRES 10 B 134 ASN ILE ARG VAL THR THR PRO LYS ARG HIS ILE ASP ILE SEQRES 11 B 134 HIS ARG GLY LYS SEQRES 1 E 86 MET GLU LEU LYS HIS SER ILE SER ASP TYR THR GLU ALA SEQRES 2 E 86 GLU PHE LEU GLN LEU VAL THR THR ILE CYS ASN ALA ASP SEQRES 3 E 86 THR SER SER GLU GLU GLU LEU VAL LYS LEU VAL THR HIS SEQRES 4 E 86 PHE GLU GLU MET THR GLU HIS PRO SER GLY SER ALA LEU SEQRES 5 E 86 ILE TYR TYR PRO LYS GLU GLY ASP ASP ASP SER PRO SER SEQRES 6 E 86 GLY ILE VAL ASN THR VAL LYS GLN TRP ARG ALA ALA ASN SEQRES 7 E 86 GLY LYS SER GLY PHE LYS GLN GLY SEQRES 1 F 134 MET GLU SER LYS ARG ASN LYS PRO GLY LYS ALA THR GLY SEQRES 2 F 134 LYS GLY LYS PRO VAL GLY ASP LYS TRP LEU ASP ASP ALA SEQRES 3 F 134 GLY LYS ASP SER GLY ALA PRO ILE PRO ASP ARG ILE ALA SEQRES 4 F 134 ASP LYS LEU ARG ASP LYS GLU PHE LYS SER PHE ASP ASP SEQRES 5 F 134 PHE ARG LYS ALA VAL TRP GLU GLU VAL SER LYS ASP PRO SEQRES 6 F 134 GLU LEU SER LYS ASN LEU ASN PRO SER ASN LYS SER SER SEQRES 7 F 134 VAL SER LYS GLY TYR SER PRO PHE THR PRO LYS ASN GLN SEQRES 8 F 134 GLN VAL GLY GLY ARG LYS VAL TYR GLU LEU HIS HIS ASP SEQRES 9 F 134 LYS PRO ILE SER GLN GLY GLY GLU VAL TYR ASP MET ASP SEQRES 10 F 134 ASN ILE ARG VAL THR THR PRO LYS ARG HIS ILE ASP ILE SEQRES 11 F 134 HIS ARG GLY LYS HET ZN B 301 1 HET PO4 B 703 5 HET ZN F 301 1 HET PO4 F 704 5 HETNAM ZN ZINC ION HETNAM PO4 PHOSPHATE ION FORMUL 5 ZN 2(ZN 2+) FORMUL 6 PO4 2(O4 P 3-) FORMUL 9 HOH *686(H2 O) HELIX 1 1 SER A 6 TYR A 10 5 5 HELIX 2 2 THR A 11 ASN A 24 1 14 HELIX 3 3 SER A 29 GLU A 45 1 17 HELIX 4 4 SER A 50 TYR A 55 1 6 HELIX 5 5 SER A 63 ASN A 78 1 16 HELIX 6 6 LYS B 21 LYS B 28 5 8 HELIX 7 7 PRO B 35 ARG B 43 1 9 HELIX 8 8 SER B 49 ASP B 64 1 16 HELIX 9 9 LEU B 67 LEU B 71 5 5 HELIX 10 10 ASN B 72 LYS B 81 1 10 HELIX 11 11 PRO B 88 GLN B 92 5 5 HELIX 12 12 PRO B 106 GLY B 110 5 5 HELIX 13 13 ASP B 115 ASP B 117 5 3 HELIX 14 14 THR B 123 ARG B 132 1 10 HELIX 15 15 SER E 6 TYR E 10 5 5 HELIX 16 16 THR E 11 ASN E 24 1 14 HELIX 17 17 SER E 29 GLU E 45 1 17 HELIX 18 18 SER E 50 TYR E 55 1 6 HELIX 19 19 SER E 63 ASN E 78 1 16 HELIX 20 20 SER F 3 LYS F 7 5 5 HELIX 21 21 LYS F 21 ALA F 26 1 6 HELIX 22 22 PRO F 35 ARG F 43 1 9 HELIX 23 23 SER F 49 ASP F 64 1 16 HELIX 24 24 ASP F 64 LYS F 69 1 6 HELIX 25 25 ASN F 72 LYS F 81 1 10 HELIX 26 26 PRO F 88 GLN F 92 5 5 HELIX 27 27 PRO F 106 GLY F 110 5 5 HELIX 28 28 ASP F 115 ASP F 117 5 3 HELIX 29 29 THR F 123 ARG F 132 1 10 SHEET 1 A 2 GLY B 9 LYS B 10 0 SHEET 2 A 2 GLU B 46 PHE B 47 -1 O PHE B 47 N GLY B 9 SHEET 1 B 3 ALA B 32 PRO B 33 0 SHEET 2 B 3 ILE B 119 THR B 122 -1 O VAL B 121 N ALA B 32 SHEET 3 B 3 GLU B 100 HIS B 103 -1 N GLU B 100 O THR B 122 SHEET 1 C 2 GLY F 9 LYS F 10 0 SHEET 2 C 2 GLU F 46 PHE F 47 -1 O PHE F 47 N GLY F 9 SHEET 1 D 3 ALA F 32 PRO F 33 0 SHEET 2 D 3 ILE F 119 THR F 122 -1 O VAL F 121 N ALA F 32 SHEET 3 D 3 GLU F 100 HIS F 103 -1 N GLU F 100 O THR F 122 LINK ND1 HIS B 102 ZN ZN B 301 1555 1555 2.06 LINK NE2 HIS B 127 ZN ZN B 301 1555 1555 2.06 LINK NE2 HIS B 131 ZN ZN B 301 1555 1555 2.08 LINK ZN ZN B 301 O3 PO4 B 703 1555 1555 1.83 LINK ND1 HIS F 102 ZN ZN F 301 1555 1555 2.06 LINK NE2 HIS F 127 ZN ZN F 301 1555 1555 2.13 LINK NE2 HIS F 131 ZN ZN F 301 1555 1555 2.11 LINK ZN ZN F 301 O2 PO4 F 704 1555 1555 1.90 SITE 1 AC1 4 HIS B 102 HIS B 127 HIS B 131 PO4 B 703 SITE 1 AC2 10 ARG B 5 LEU B 101 HIS B 102 HIS B 103 SITE 2 AC2 10 HIS B 127 HIS B 131 ZN B 301 HOH B 714 SITE 3 AC2 10 HOH B 878 SER E 28 SITE 1 AC3 4 HIS F 102 HIS F 127 HIS F 131 PO4 F 704 SITE 1 AC4 9 SER A 28 HOH A 139 ARG F 5 LEU F 101 SITE 2 AC4 9 HIS F 102 HIS F 103 HIS F 127 HIS F 131 SITE 3 AC4 9 ZN F 301 CRYST1 44.903 88.248 52.235 90.00 91.92 90.00 P 1 21 1 4 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 0.022270 0.000000 0.000750 0.00000 SCALE2 0.000000 0.011330 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019150 0.00000