PDB Short entry for 3GKL HEADER HYDROLASE 11-MAR-09 3GKL TITLE FOLLOWING EVOLUTIONARY PATHS TO HIGH AFFINITY AND SELECTIVITY PROTEIN- TITLE 2 PROTEIN INTERACTIONS USING COLICIN7 AND IMMUNITY PROTEINS CAVEAT 3GKL CHIRALITY ERRORS AT RESIDUES D1004 AND D1027 COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLICIN-E9 IMMUNITY PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 446-576; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: COLICIN-E7; COMPND 10 CHAIN: C, D; COMPND 11 SYNONYM: IMME9, MICROCIN-E9 IMMUNITY PROTEIN; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: COLE7, CEA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET20; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 12 ORGANISM_TAXID: 562; SOURCE 13 GENE: IMM, CEIE9; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 18 EXPRESSION_SYSTEM_PLASMID: PET20 KEYWDS PROTEIN-PROTEIN COMPLEX, STRUCTURAL GENOMICS, ISRAEL STRUCTURAL KEYWDS 2 PROTEOMICS CENTER, ISPC, BACTERIOCIN IMMUNITY, PLASMID, ANTIBIOTIC, KEYWDS 3 ANTIMICROBIAL, BACTERIOCIN, ENDONUCLEASE, HYDROLASE, METAL-BINDING, KEYWDS 4 NUCLEASE, ZINC EXPDTA X-RAY DIFFRACTION AUTHOR O.DYM,D.S.TAWFIK,ISRAEL STRUCTURAL PROTEOMICS CENTER (ISPC) REVDAT 3 06-SEP-23 3GKL 1 REMARK REVDAT 2 20-OCT-21 3GKL 1 REMARK SEQADV REVDAT 1 08-SEP-09 3GKL 0 JRNL AUTH K.BERNATH,O.DYM,S.ALBECK,S.MAGDASSI,A.KEEBLE,C.KLEANTHOUS, JRNL AUTH 2 D.S.TAWFIK JRNL TITL FOLLOWING EVOLUTIONARY PATHS TO HIGH AFFINITY AND JRNL TITL 2 SELECTIVITY PROTEIN-PROTEIN INTERACTIONS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0067 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 21366 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 : 0.277 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1147 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) : 1567 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.3610 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.3950 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3211 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.10000 REMARK 3 B22 (A**2) : 5.20000 REMARK 3 B33 (A**2) : -2.10000 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): 0.341 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.246 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.191 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.766 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.922 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3311 ; 0.048 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4448 ; 3.856 ; 1.949 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 402 ;10.270 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 165 ;42.161 ;24.848 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 612 ;23.441 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;18.978 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 462 ; 0.274 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2516 ; 0.019 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1547 ; 0.350 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2122 ; 0.360 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 139 ; 0.206 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 1 ; 0.142 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 15 ; 0.351 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.157 ; 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): 2020 ; 1.914 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3252 ; 3.198 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1291 ; 4.994 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1195 ; 7.245 ; 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 : 1.40 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. U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3GKL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-09. REMARK 100 THE DEPOSITION ID IS D_1000051977. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : HORIZONTALLY DIFFRACTING REMARK 200 OPTICS : PT COATED MIRRORS IN A REMARK 200 KIRKPATRICK-BAEZ (KB) GEOMETRY 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 : 23137 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.13000 REMARK 200 R SYM (I) : 0.12000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 8.7000 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) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.80 REMARK 200 R MERGE FOR SHELL (I) : 0.42600 REMARK 200 R SYM FOR SHELL (I) : 0.33400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3GJN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 400, 0.1 CHES PH 9.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 27.08050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.61550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.68550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.61550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.08050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.68550 REMARK 290 SMTRY3 4 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 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 APPLY THE FOLLOWING TO CHAINS: A, 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: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 A 436 REMARK 465 HIS A 437 REMARK 465 HIS A 438 REMARK 465 HIS A 439 REMARK 465 HIS A 440 REMARK 465 HIS A 441 REMARK 465 HIS A 442 REMARK 465 SER A 443 REMARK 465 MET A 444 REMARK 465 GLY A 445 REMARK 465 LYS A 446 REMARK 465 ARG A 447 REMARK 465 ASN A 448 REMARK 465 LYS A 449 REMARK 465 PRO A 548 REMARK 465 ILE A 549 REMARK 465 SER A 550 REMARK 465 GLN A 551 REMARK 465 ASN A 552 REMARK 465 GLY A 553 REMARK 465 GLY A 554 REMARK 465 MET B 436 REMARK 465 HIS B 437 REMARK 465 HIS B 438 REMARK 465 HIS B 439 REMARK 465 HIS B 440 REMARK 465 HIS B 441 REMARK 465 HIS B 442 REMARK 465 SER B 443 REMARK 465 MET B 444 REMARK 465 GLY B 445 REMARK 465 LYS B 446 REMARK 465 ARG B 447 REMARK 465 ASN B 448 REMARK 465 LYS B 449 REMARK 465 PRO B 548 REMARK 465 ILE B 549 REMARK 465 SER B 550 REMARK 465 GLN B 551 REMARK 465 ASN B 552 REMARK 465 GLY B 553 REMARK 465 GLY B 554 REMARK 465 MET C 1001 REMARK 465 GLU C 1002 REMARK 465 LEU C 1003 REMARK 465 GLY C 1086 REMARK 465 MET D 1001 REMARK 465 GLU D 1002 REMARK 465 LEU D 1003 REMARK 465 GLY D 1086 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 LYS D1072 C O CD CE NZ 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 B 576 OE2 GLU D 1058 4456 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 B 546 C LYS B 547 N 0.160 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 574 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 PRO B 459 C - N - CD ANGL. DEV. = -15.9 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 461 -155.58 -96.26 REMARK 500 TRP A 464 -62.85 -28.82 REMARK 500 ASP A 471 -130.35 64.82 REMARK 500 PRO A 507 -39.63 -34.71 REMARK 500 ASP B 471 -129.84 33.06 REMARK 500 SER B 491 175.69 179.81 REMARK 500 SER B 514 156.43 -44.52 REMARK 500 ASP B 557 93.03 -67.45 REMARK 500 ILE C1022 -36.20 -37.54 REMARK 500 GLU C1032 -78.71 -28.92 REMARK 500 GLU C1045 13.56 46.79 REMARK 500 THR D1028 125.08 -176.22 REMARK 500 GLU D1032 -71.59 -30.76 REMARK 500 GLU D1045 19.43 46.02 REMARK 500 GLU D1058 109.84 -50.31 REMARK 500 LYS D1080 162.03 -49.07 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 PRO A 450 GLY A 451 139.37 REMARK 500 VAL A 555 TYR A 556 -128.17 REMARK 500 VAL B 555 TYR B 556 -138.19 REMARK 500 GLU C 1031 GLU C 1032 139.78 REMARK 500 ASN C 1078 GLY C 1079 -116.16 REMARK 500 ALA D 1027 THR D 1028 -122.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLU B 546 -12.50 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 A 600 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 544 ND1 REMARK 620 2 HIS A 569 NE2 77.3 REMARK 620 3 HIS A 573 NE2 85.8 89.3 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 600 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3GJN RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEX, DIFFERENT MUTATIONS DBREF 3GKL A 446 576 UNP Q47112 CEA7_ECOLX 446 576 DBREF 3GKL C 1001 1086 UNP P13479 IMM9_ECOLX 1 86 DBREF 3GKL B 446 576 UNP Q47112 CEA7_ECOLX 446 576 DBREF 3GKL D 1001 1086 UNP P13479 IMM9_ECOLX 1 86 SEQADV 3GKL MET A 436 UNP Q47112 EXPRESSION TAG SEQADV 3GKL HIS A 437 UNP Q47112 EXPRESSION TAG SEQADV 3GKL HIS A 438 UNP Q47112 EXPRESSION TAG SEQADV 3GKL HIS A 439 UNP Q47112 EXPRESSION TAG SEQADV 3GKL HIS A 440 UNP Q47112 EXPRESSION TAG SEQADV 3GKL HIS A 441 UNP Q47112 EXPRESSION TAG SEQADV 3GKL HIS A 442 UNP Q47112 EXPRESSION TAG SEQADV 3GKL SER A 443 UNP Q47112 EXPRESSION TAG SEQADV 3GKL MET A 444 UNP Q47112 EXPRESSION TAG SEQADV 3GKL GLY A 445 UNP Q47112 EXPRESSION TAG SEQADV 3GKL ALA A 545 UNP Q47112 HIS 545 ENGINEERED MUTATION SEQADV 3GKL MET B 436 UNP Q47112 EXPRESSION TAG SEQADV 3GKL HIS B 437 UNP Q47112 EXPRESSION TAG SEQADV 3GKL HIS B 438 UNP Q47112 EXPRESSION TAG SEQADV 3GKL HIS B 439 UNP Q47112 EXPRESSION TAG SEQADV 3GKL HIS B 440 UNP Q47112 EXPRESSION TAG SEQADV 3GKL HIS B 441 UNP Q47112 EXPRESSION TAG SEQADV 3GKL HIS B 442 UNP Q47112 EXPRESSION TAG SEQADV 3GKL SER B 443 UNP Q47112 EXPRESSION TAG SEQADV 3GKL MET B 444 UNP Q47112 EXPRESSION TAG SEQADV 3GKL GLY B 445 UNP Q47112 EXPRESSION TAG SEQADV 3GKL ALA B 545 UNP Q47112 HIS 545 ENGINEERED MUTATION SEQADV 3GKL ALA C 1020 UNP P13479 THR 20 ENGINEERED MUTATION SEQADV 3GKL ASP C 1024 UNP P13479 ASN 24 ENGINEERED MUTATION SEQADV 3GKL ALA C 1027 UNP P13479 THR 27 ENGINEERED MUTATION SEQADV 3GKL THR C 1028 UNP P13479 SER 28 ENGINEERED MUTATION SEQADV 3GKL ASP C 1034 UNP P13479 VAL 34 ENGINEERED MUTATION SEQADV 3GKL ILE C 1037 UNP P13479 VAL 37 ENGINEERED MUTATION SEQADV 3GKL GLY C 1041 UNP P13479 GLU 41 ENGINEERED MUTATION SEQADV 3GKL GLU C 1057 UNP P13479 LYS 57 ENGINEERED MUTATION SEQADV 3GKL ALA D 1020 UNP P13479 THR 20 ENGINEERED MUTATION SEQADV 3GKL ASP D 1024 UNP P13479 ASN 24 ENGINEERED MUTATION SEQADV 3GKL ALA D 1027 UNP P13479 THR 27 ENGINEERED MUTATION SEQADV 3GKL THR D 1028 UNP P13479 SER 28 ENGINEERED MUTATION SEQADV 3GKL ASP D 1034 UNP P13479 VAL 34 ENGINEERED MUTATION SEQADV 3GKL ILE D 1037 UNP P13479 VAL 37 ENGINEERED MUTATION SEQADV 3GKL GLY D 1041 UNP P13479 GLU 41 ENGINEERED MUTATION SEQADV 3GKL GLU D 1057 UNP P13479 LYS 57 ENGINEERED MUTATION SEQRES 1 A 141 MET HIS HIS HIS HIS HIS HIS SER MET GLY LYS ARG ASN SEQRES 2 A 141 LYS PRO GLY LYS ALA THR GLY LYS GLY LYS PRO VAL ASN SEQRES 3 A 141 ASN LYS TRP LEU ASN ASN ALA GLY LYS ASP LEU GLY SER SEQRES 4 A 141 PRO VAL PRO ASP ARG ILE ALA ASN LYS LEU ARG ASP LYS SEQRES 5 A 141 GLU PHE LYS SER PHE ASP ASP PHE ARG LYS LYS PHE TRP SEQRES 6 A 141 GLU GLU VAL SER LYS ASP PRO GLU LEU SER LYS GLN PHE SEQRES 7 A 141 SER ARG ASN ASN ASN ASP ARG MET LYS VAL GLY LYS ALA SEQRES 8 A 141 PRO LYS THR ARG THR GLN ASP VAL SER GLY LYS ARG THR SEQRES 9 A 141 SER PHE GLU LEU HIS ALA GLU LYS PRO ILE SER GLN ASN SEQRES 10 A 141 GLY GLY VAL TYR ASP MET ASP ASN ILE SER VAL VAL THR SEQRES 11 A 141 PRO LYS ARG HIS ILE ASP ILE HIS ARG GLY LYS SEQRES 1 B 141 MET HIS HIS HIS HIS HIS HIS SER MET GLY LYS ARG ASN SEQRES 2 B 141 LYS PRO GLY LYS ALA THR GLY LYS GLY LYS PRO VAL ASN SEQRES 3 B 141 ASN LYS TRP LEU ASN ASN ALA GLY LYS ASP LEU GLY SER SEQRES 4 B 141 PRO VAL PRO ASP ARG ILE ALA ASN LYS LEU ARG ASP LYS SEQRES 5 B 141 GLU PHE LYS SER PHE ASP ASP PHE ARG LYS LYS PHE TRP SEQRES 6 B 141 GLU GLU VAL SER LYS ASP PRO GLU LEU SER LYS GLN PHE SEQRES 7 B 141 SER ARG ASN ASN ASN ASP ARG MET LYS VAL GLY LYS ALA SEQRES 8 B 141 PRO LYS THR ARG THR GLN ASP VAL SER GLY LYS ARG THR SEQRES 9 B 141 SER PHE GLU LEU HIS ALA GLU LYS PRO ILE SER GLN ASN SEQRES 10 B 141 GLY GLY VAL TYR ASP MET ASP ASN ILE SER VAL VAL THR SEQRES 11 B 141 PRO LYS ARG HIS ILE ASP ILE HIS ARG GLY LYS SEQRES 1 C 86 MET GLU LEU LYS HIS SER ILE SER ASP TYR THR GLU ALA SEQRES 2 C 86 GLU PHE LEU GLN LEU VAL ALA THR ILE CYS ASP ALA ASP SEQRES 3 C 86 ALA THR SER GLU GLU GLU LEU ASP LYS LEU ILE THR HIS SEQRES 4 C 86 PHE GLY GLU MET THR GLU HIS PRO SER GLY SER ASP LEU SEQRES 5 C 86 ILE TYR TYR PRO GLU GLU GLY ASP ASP ASP SER PRO SER SEQRES 6 C 86 GLY ILE VAL ASN THR VAL LYS GLN TRP ARG ALA ALA ASN SEQRES 7 C 86 GLY LYS SER GLY PHE LYS GLN GLY SEQRES 1 D 86 MET GLU LEU LYS HIS SER ILE SER ASP TYR THR GLU ALA SEQRES 2 D 86 GLU PHE LEU GLN LEU VAL ALA THR ILE CYS ASP ALA ASP SEQRES 3 D 86 ALA THR SER GLU GLU GLU LEU ASP LYS LEU ILE THR HIS SEQRES 4 D 86 PHE GLY GLU MET THR GLU HIS PRO SER GLY SER ASP LEU SEQRES 5 D 86 ILE TYR TYR PRO GLU GLU GLY ASP ASP ASP SER PRO SER SEQRES 6 D 86 GLY ILE VAL ASN THR VAL LYS GLN TRP ARG ALA ALA ASN SEQRES 7 D 86 GLY LYS SER GLY PHE LYS GLN GLY HET ZN A 600 1 HET ZN B 600 1 HETNAM ZN ZINC ION FORMUL 5 ZN 2(ZN 2+) FORMUL 7 HOH *10(H2 O) HELIX 1 1 LYS A 463 ALA A 468 5 6 HELIX 2 2 PRO A 477 ARG A 485 1 9 HELIX 3 3 SER A 491 ASP A 506 1 16 HELIX 4 4 ASP A 506 LYS A 511 1 6 HELIX 5 5 SER A 514 VAL A 523 1 10 HELIX 6 6 THR A 565 HIS A 573 1 9 HELIX 7 7 LYS B 463 LYS B 470 5 8 HELIX 8 8 PRO B 477 ARG B 485 1 9 HELIX 9 9 SER B 491 ASP B 506 1 16 HELIX 10 10 ASP B 506 LYS B 511 1 6 HELIX 11 11 SER B 514 VAL B 523 1 10 HELIX 12 12 ARG B 530 VAL B 534 5 5 HELIX 13 13 THR B 565 ARG B 574 1 10 HELIX 14 14 SER C 1006 TYR C 1010 5 5 HELIX 15 15 THR C 1011 CYS C 1023 1 13 HELIX 16 16 SER C 1029 GLU C 1045 1 17 HELIX 17 17 SER C 1050 TYR C 1055 1 6 HELIX 18 18 SER C 1063 ALA C 1077 1 15 HELIX 19 19 SER D 1006 TYR D 1010 5 5 HELIX 20 20 THR D 1011 CYS D 1023 1 13 HELIX 21 21 ASP D 1024 THR D 1028 5 5 HELIX 22 22 SER D 1029 GLU D 1045 1 17 HELIX 23 23 SER D 1050 TYR D 1055 1 6 HELIX 24 24 SER D 1063 LYS D 1072 1 10 HELIX 25 25 GLN D 1073 ASN D 1078 1 6 SHEET 1 A 2 ALA A 453 THR A 454 0 SHEET 2 A 2 TYR A 556 ASP A 557 1 O TYR A 556 N THR A 454 SHEET 1 B 3 SER A 474 PRO A 475 0 SHEET 2 B 3 ILE A 561 VAL A 564 -1 O VAL A 563 N SER A 474 SHEET 3 B 3 GLU A 542 ALA A 545 -1 N GLU A 542 O VAL A 564 SHEET 1 C 2 ALA B 453 THR B 454 0 SHEET 2 C 2 TYR B 556 ASP B 557 1 O TYR B 556 N THR B 454 SHEET 1 D 3 SER B 474 PRO B 475 0 SHEET 2 D 3 ILE B 561 VAL B 564 -1 O VAL B 563 N SER B 474 SHEET 3 D 3 GLU B 542 ALA B 545 -1 N GLU B 542 O VAL B 564 LINK ND1 HIS A 544 ZN ZN A 600 1555 1555 2.35 LINK NE2 HIS A 569 ZN ZN A 600 1555 1555 2.03 LINK NE2 HIS A 573 ZN ZN A 600 1555 1555 2.05 SITE 1 AC1 3 HIS A 544 HIS A 569 HIS A 573 SITE 1 AC2 4 HIS B 544 ALA B 545 HIS B 569 HIS B 573 CRYST1 54.161 67.371 123.231 90.00 90.00 90.00 P 21 21 21 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 0.018463 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014843 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008115 0.00000