PDB Short entry for 1V13 HEADER HYDROLASE 06-APR-04 1V13 TITLE CRYSTAL STRUCTURE OF THE MUTANT HIS103ALA OF THE COLICIN E9 DNASE TITLE 2 DOMAIN IN COMPLEX WITH ZN+2 (2.0 ANGSTROMS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLICIN E9; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.1.-.-; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR: PET; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PTRC 99A (PRJ352) KEYWDS HOMING ENDONUCLEASES, COLICINS, BETA-BETA-ALPHA METAL ANTIBIOTIC, KEYWDS 2 BACTERIOCIN, HYDROLASE, ENDONUCLEASE MOTIF, H-N-H MOTIF EXPDTA X-RAY DIFFRACTION AUTHOR M.J.MATE,C.KLEANTHOUS REVDAT 7 13-DEC-23 1V13 1 REMARK LINK REVDAT 6 13-JUL-11 1V13 1 VERSN REVDAT 5 02-JUN-09 1V13 1 CAVEAT REMARK REVDAT 4 24-FEB-09 1V13 1 VERSN REVDAT 3 12-AUG-04 1V13 1 JRNL REVDAT 2 07-JUL-04 1V13 1 REMARK REVDAT 1 23-JUN-04 1V13 0 JRNL AUTH M.J.MATE,C.KLEANTHOUS JRNL TITL STRUCTURE-BASED ANALYSIS OF THE METAL-DEPENDENT MECHANISM OF JRNL TITL 2 H-N-H ENDONUCLEASES JRNL REF J.BIOL.CHEM. V. 279 34763 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 15190054 JRNL DOI 10.1074/JBC.M403719200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH U.C.KUHLMANN,A.J.POMMER,G.M.MOORE,R.JAMES,C.KLEANTHOUS REMARK 1 TITL SPECIFICITY IN PROTEIN-PROTEIN INTERACTIONS: THE STRUCTURAL REMARK 1 TITL 2 BASIS FOR DUAL RECOGNITION IN ENDONUCLEASE COLICIN-IMMUNITY REMARK 1 TITL 3 PROTEIN COMPLEXES REMARK 1 REF J.MOL.BIOL. V. 301 1163 2000 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 10966813 REMARK 1 DOI 10.1006/JMBI.2000.3945 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0001 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.8 REMARK 3 NUMBER OF REFLECTIONS : 18519 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) : 0.234 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.307 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1009 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.05 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1360 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 78 REMARK 3 BIN FREE R VALUE : 0.2810 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1914 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.91 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.75000 REMARK 3 B22 (A**2) : -4.14000 REMARK 3 B33 (A**2) : 1.39000 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): 0.209 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.209 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.165 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.299 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.907 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1955 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2628 ; 1.751 ; 1.943 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 241 ; 6.857 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 90 ;36.793 ;24.222 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 343 ;18.571 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;24.028 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 267 ; 0.160 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1494 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 906 ; 0.228 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 129 ; 0.294 ; 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): 16 ; 0.281 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.135 ; 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): 1256 ; 0.820 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1960 ; 1.260 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 793 ; 2.207 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 668 ; 3.181 ; 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 : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 8 A 83 REMARK 3 ORIGIN FOR THE GROUP (A): 25.0283 17.5517 35.7180 REMARK 3 T TENSOR REMARK 3 T11: 0.0913 T22: 0.2356 REMARK 3 T33: 0.2317 T12: 0.0537 REMARK 3 T13: -0.2532 T23: 0.0921 REMARK 3 L TENSOR REMARK 3 L11: 4.6843 L22: 4.4445 REMARK 3 L33: 2.3687 L12: -0.0772 REMARK 3 L13: -1.2221 L23: 0.0765 REMARK 3 S TENSOR REMARK 3 S11: 0.2522 S12: -0.4557 S13: -0.7196 REMARK 3 S21: 0.2199 S22: -0.1482 S23: -0.7454 REMARK 3 S31: 0.1568 S32: 0.4978 S33: -0.1040 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 84 A 133 REMARK 3 ORIGIN FOR THE GROUP (A): 17.6735 27.1915 33.4050 REMARK 3 T TENSOR REMARK 3 T11: -0.0817 T22: 0.0869 REMARK 3 T33: -0.1601 T12: -0.1063 REMARK 3 T13: -0.1126 T23: 0.0461 REMARK 3 L TENSOR REMARK 3 L11: 6.2571 L22: 4.8587 REMARK 3 L33: 2.2586 L12: 0.5684 REMARK 3 L13: 0.2989 L23: -0.1681 REMARK 3 S TENSOR REMARK 3 S11: 0.5397 S12: -0.4991 S13: -0.1687 REMARK 3 S21: 0.4470 S22: -0.2438 S23: -0.7336 REMARK 3 S31: -0.0187 S32: 0.3931 S33: -0.2959 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 8 B 133 REMARK 3 ORIGIN FOR THE GROUP (A): 4.5493 32.7805 20.5226 REMARK 3 T TENSOR REMARK 3 T11: -0.1699 T22: -0.2025 REMARK 3 T33: -0.2048 T12: 0.0496 REMARK 3 T13: 0.0785 T23: 0.0751 REMARK 3 L TENSOR REMARK 3 L11: 4.7339 L22: 5.3238 REMARK 3 L33: 2.9508 L12: -0.3998 REMARK 3 L13: -1.1258 L23: 0.7558 REMARK 3 S TENSOR REMARK 3 S11: 0.3119 S12: 0.2397 S13: 0.1126 REMARK 3 S21: -0.1904 S22: -0.0590 S23: 0.2147 REMARK 3 S31: -0.4402 S32: -0.0993 S33: -0.2529 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 1V13 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-04. REMARK 100 THE DEPOSITION ID IS D_1290014916. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.80 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID14-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9645 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18519 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 91.7 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1EMV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 5.80 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 26.34650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 45.55350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.72050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 45.55350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.34650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.72050 REMARK 290 SMTRY3 4 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 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: PQS 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 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 SER A 3 REMARK 465 LYS A 4 REMARK 465 ARG A 5 REMARK 465 ASN A 6 REMARK 465 LYS A 7 REMARK 465 VAL A 18 REMARK 465 GLY A 19 REMARK 465 ASP A 20 REMARK 465 GLU A 66 REMARK 465 LEU A 67 REMARK 465 ASN A 70 REMARK 465 LYS A 134 REMARK 465 MET B 1 REMARK 465 GLU B 2 REMARK 465 SER B 3 REMARK 465 LYS B 4 REMARK 465 ARG B 5 REMARK 465 ASN B 6 REMARK 465 LYS B 7 REMARK 465 LYS B 134 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 A 14 CG CD CE NZ REMARK 470 LYS A 21 CG CD CE NZ REMARK 470 LYS A 89 CG CD CE NZ REMARK 470 GLN A 109 CG CD OE1 NE2 REMARK 470 LYS B 89 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS B 28 CE NZ 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 ZN ZN A 200 O HOH A 2027 1.36 REMARK 500 O HOH B 2035 O HOH B 2065 1.85 REMARK 500 O HOH A 2026 O HOH A 2028 1.88 REMARK 500 O GLY B 15 O HOH B 2003 1.90 REMARK 500 O HOH B 2064 O HOH B 2065 1.96 REMARK 500 NH2 ARG B 54 O HOH B 2027 1.98 REMARK 500 NH1 ARG B 54 O HOH B 2027 1.98 REMARK 500 O HOH A 2026 O HOH A 2027 1.99 REMARK 500 O ILE B 128 O HIS B 131 2.05 REMARK 500 ND2 ASN A 72 O HOH A 2006 2.10 REMARK 500 O HOH B 2056 O HOH B 2057 2.14 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 24 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 ASP A 36 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 ASP A 129 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 GLY B 13 N - CA - C ANGL. DEV. = 18.8 DEGREES REMARK 500 ASP B 25 CB - CG - OD2 ANGL. DEV. = 5.9 DEGREES REMARK 500 ASP B 51 CB - CG - OD2 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG B 54 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 ASP B 104 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 129 CB - CG - OD2 ANGL. DEV. = 6.3 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 ASP A 29 -139.09 53.05 REMARK 500 ASP A 44 -15.91 84.52 REMARK 500 PRO A 106 57.10 -67.58 REMARK 500 SER A 108 4.98 -63.31 REMARK 500 TYR A 114 73.78 -115.59 REMARK 500 ARG A 132 -53.51 164.68 REMARK 500 LYS B 14 -49.50 96.42 REMARK 500 LYS B 21 14.56 81.45 REMARK 500 ASP B 29 -129.01 49.03 REMARK 500 PRO B 65 -72.28 -29.09 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 HIS A 131 ARG A 132 149.41 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 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 102 ND1 REMARK 620 2 HIS A 127 NE2 95.7 REMARK 620 3 HIS A 131 NE2 108.6 113.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 102 ND1 REMARK 620 2 HIS B 127 NE2 99.6 REMARK 620 3 HIS B 131 NE2 105.8 100.2 REMARK 620 4 HOH B2064 O 102.6 116.8 128.0 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 A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 200 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BXI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE ESCHERICHIA COLI COLICIN E9 DNASEDOMAIN REMARK 900 WITH ITS COGNATE IMMUNITY PROTEIN IM9 REMARK 900 RELATED ID: 1EMV RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITSCOGNATE REMARK 900 IMMUNITY PROTEIN IM9 (1.7 ANGSTROMS) REMARK 900 RELATED ID: 1FR2 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN WITH A MUTANTIMMUNITY REMARK 900 PROTEIN IM9(E41A) REMARK 900 RELATED ID: 1FSJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE E9 DNASE DOMAIN REMARK 900 RELATED ID: 1V14 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE COLICIN E9, MUTANT HIS103ALA, IN COMPLEX REMARK 900 WITH MG+2 AND DSDNA (RESOLUTION 2.9A) REMARK 900 RELATED ID: 1V15 RELATED DB: PDB REMARK 900 COLICIN E9, MUTANT HIS103ALA, IN COMPLEX WITH ZN+2 AND DOUBLE REMARK 900 STRAND DNA DBREF 1V13 A 1 1 PDB 1V13 1V13 1 1 DBREF 1V13 A 2 134 UNP P09883 CEA9_ECOLI 450 582 DBREF 1V13 B 1 1 PDB 1V13 1V13 1 1 DBREF 1V13 B 2 134 UNP P09883 CEA9_ECOLI 450 582 SEQADV 1V13 ALA A 103 UNP P09883 HIS 551 ENGINEERED MUTATION SEQADV 1V13 ALA B 103 UNP P09883 HIS 551 ENGINEERED MUTATION SEQRES 1 A 134 MET GLU SER LYS ARG ASN LYS PRO GLY LYS ALA THR GLY SEQRES 2 A 134 LYS GLY LYS PRO VAL GLY ASP LYS TRP LEU ASP ASP ALA SEQRES 3 A 134 GLY LYS ASP SER GLY ALA PRO ILE PRO ASP ARG ILE ALA SEQRES 4 A 134 ASP LYS LEU ARG ASP LYS GLU PHE LYS SER PHE ASP ASP SEQRES 5 A 134 PHE ARG LYS ALA VAL TRP GLU GLU VAL SER LYS ASP PRO SEQRES 6 A 134 GLU LEU SER LYS ASN LEU ASN PRO SER ASN LYS SER SER SEQRES 7 A 134 VAL SER LYS GLY TYR SER PRO PHE THR PRO LYS ASN GLN SEQRES 8 A 134 GLN VAL GLY GLY ARG LYS VAL TYR GLU LEU HIS ALA ASP SEQRES 9 A 134 LYS PRO ILE SER GLN GLY GLY GLU VAL TYR ASP MET ASP SEQRES 10 A 134 ASN ILE ARG VAL THR THR PRO LYS ARG HIS ILE ASP ILE SEQRES 11 A 134 HIS ARG GLY LYS 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 ALA 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 HET ZN A 200 1 HET ZN B 200 1 HETNAM ZN ZINC ION FORMUL 3 ZN 2(ZN 2+) FORMUL 5 HOH *93(H2 O) HELIX 1 1 LYS A 21 ASP A 25 5 5 HELIX 2 2 PRO A 35 ARG A 43 1 9 HELIX 3 3 SER A 49 LYS A 63 1 15 HELIX 4 4 ASN A 72 LYS A 81 1 10 HELIX 5 5 PRO A 88 GLN A 92 5 5 HELIX 6 6 THR A 123 ARG A 132 1 10 HELIX 7 7 LYS B 21 LYS B 28 5 8 HELIX 8 8 PRO B 35 ARG B 43 1 9 HELIX 9 9 SER B 49 LYS B 63 1 15 HELIX 10 10 ASP B 64 LYS B 69 1 6 HELIX 11 11 ASN B 72 LYS B 81 1 10 HELIX 12 12 PRO B 88 GLN B 92 5 5 HELIX 13 13 THR B 123 HIS B 131 1 9 SHEET 1 AA 3 GLU A 46 PHE A 47 0 SHEET 2 AA 3 GLY A 9 THR A 12 -1 O GLY A 9 N PHE A 47 SHEET 3 AA 3 VAL A 113 ASP A 115 1 O TYR A 114 N THR A 12 SHEET 1 AB 3 ALA A 32 PRO A 33 0 SHEET 2 AB 3 ILE A 119 THR A 122 -1 O VAL A 121 N ALA A 32 SHEET 3 AB 3 GLU A 100 ALA A 103 -1 O GLU A 100 N THR A 122 SHEET 1 BA 3 GLU B 46 PHE B 47 0 SHEET 2 BA 3 GLY B 9 THR B 12 -1 O GLY B 9 N PHE B 47 SHEET 3 BA 3 VAL B 113 ASP B 115 1 O TYR B 114 N THR B 12 SHEET 1 BB 3 ALA B 32 PRO B 33 0 SHEET 2 BB 3 ILE B 119 THR B 122 -1 O VAL B 121 N ALA B 32 SHEET 3 BB 3 GLU B 100 ALA B 103 -1 O GLU B 100 N THR B 122 LINK ND1 HIS A 102 ZN ZN A 200 1555 1555 1.95 LINK NE2 HIS A 127 ZN ZN A 200 1555 1555 2.19 LINK NE2 HIS A 131 ZN ZN A 200 1555 1555 1.87 LINK ND1 HIS B 102 ZN ZN B 200 1555 1555 2.03 LINK NE2 HIS B 127 ZN ZN B 200 1555 1555 2.05 LINK NE2 HIS B 131 ZN ZN B 200 1555 1555 2.02 LINK ZN ZN B 200 O HOH B2064 1555 1555 2.02 SITE 1 AC1 4 HIS A 102 HIS A 127 HIS A 131 HOH A2027 SITE 1 AC2 5 HIS B 102 HIS B 127 HIS B 131 HOH B2064 SITE 2 AC2 5 HOH B2065 CRYST1 52.693 61.441 91.107 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 0.018978 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016276 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010976 0.00000