PDB Short entry for 1OUP HEADER HYDROLASE/DNA 25-MAR-03 1OUP TITLE CRYSTAL STRUCTURE OF THE PERIPLASMIC ENDONUCLEASE VVN COMPLEXED WITH TITLE 2 OCTAMER DOUBLE STRANDED DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*GP*CP*GP*AP*TP*CP*GP*C)-3'; COMPND 3 CHAIN: C, D, F; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*CP*GP*AP*TP*C)-3'; COMPND 7 CHAIN: E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 5'-D(P*GP*C)-3'; COMPND 11 CHAIN: G; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 4; COMPND 14 MOLECULE: NUCLEASE; COMPND 15 CHAIN: A, B; COMPND 16 FRAGMENT: RESIDUES 19-231; COMPND 17 SYNONYM: VVN NUCLEASE; COMPND 18 EC: 3.1.-.-; COMPND 19 ENGINEERED: YES; COMPND 20 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 SYNTHETIC: YES; SOURCE 7 MOL_ID: 4; SOURCE 8 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 9 ORGANISM_TAXID: 672; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PTYB2 KEYWDS NON-SPECIFIC ENDONUCLEASE, BETA-BETA-ALPHA METAL MOTIF, HYDROLASE-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.S.YUAN,C.-L.LI REVDAT 7 03-APR-24 1OUP 1 REMARK REVDAT 6 10-NOV-21 1OUP 1 REMARK SEQADV LINK REVDAT 5 11-OCT-17 1OUP 1 REMARK REVDAT 4 24-FEB-09 1OUP 1 VERSN REVDAT 3 14-SEP-04 1OUP 1 REMARK REVDAT 2 03-FEB-04 1OUP 1 AUTHOR REVDAT 1 05-AUG-03 1OUP 0 JRNL AUTH C.-L.LI,L.-I.HOR,Z.-F.CHANG,L.-C.TSAI,W.-Z.YANG,H.S.YUAN JRNL TITL DNA BINDING AND CLEAVAGE BY THE PERIPLASMIC NUCLEASE VVN: A JRNL TITL 2 NOVEL STRUCTURE WITH A KNOWN ACTIVE SITE. JRNL REF EMBO J. V. 22 4014 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 12881435 JRNL DOI 10.1093/EMBOJ/CDG377 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.78 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 20729 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 SET) : 0.191 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1616 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3025 REMARK 3 BIN R VALUE (WORKING SET) : 0.2010 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.00 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 264 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3450 REMARK 3 NUCLEIC ACID ATOMS : 645 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 328 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.45000 REMARK 3 B22 (A**2) : -0.99000 REMARK 3 B33 (A**2) : -5.47000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 3.92000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.17 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.140 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.450 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.290 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.090 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.040 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 41.72 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA-VVN.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OUP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 26-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018682. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-NOV-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL12B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9065 REMARK 200 MONOCHROMATOR : NULL 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 : 21165 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.28200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: SEMET-VVN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, CALCIUM ACETATE, PH 7.3, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 25.05500 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: TWO PROTEIN/DNA COMPLEXES PER ASYMMETRY UINT. CHAINS A,E,F REMARK 300 ARE ENZYME/PRODUCT COMPLEX. CHAINS B,C,D ARE ENZYME/SUBSTRATE REMARK 300 COMPLEX 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, G, F, 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 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 GLN B 229 REMARK 465 THR B 230 REMARK 465 GLN B 231 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 DG G 7 P DG G 7 OP3 -0.086 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 B 172 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 68 5.30 -168.12 REMARK 500 ASN A 105 -89.63 -110.39 REMARK 500 ASP A 106 114.21 -31.70 REMARK 500 SER A 131 -138.31 42.59 REMARK 500 ASP A 142 61.75 -153.24 REMARK 500 SER A 145 -169.73 -127.61 REMARK 500 TRP B 50 82.57 -69.12 REMARK 500 LEU B 59 -19.08 -48.81 REMARK 500 LYS B 68 -47.31 -147.65 REMARK 500 LYS B 104 -38.40 -175.98 REMARK 500 SER B 131 -129.59 51.36 REMARK 500 TRP B 138 -177.21 -175.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA E 4 0.06 SIDE CHAIN REMARK 500 DT E 5 0.07 SIDE CHAIN REMARK 500 DG G 7 0.05 SIDE CHAIN REMARK 500 DG F 11 0.05 SIDE CHAIN REMARK 500 DT F 13 0.06 SIDE CHAIN 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 CA B 300 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH C 461 O REMARK 620 2 GLU B 79 OE1 93.5 REMARK 620 3 ASN B 127 OD1 87.9 75.2 REMARK 620 4 HOH B 443 O 159.9 102.3 84.1 REMARK 620 5 HOH B 718 O 84.0 88.9 161.7 108.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 300 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG G 7 OP3 REMARK 620 2 HOH G 720 O 75.2 REMARK 620 3 GLU A 79 OE1 158.3 84.0 REMARK 620 4 ASN A 127 OD1 92.9 90.8 93.6 REMARK 620 5 HOH A 420 O 85.5 160.4 115.5 87.1 REMARK 620 6 HOH A 719 O 92.1 84.4 79.5 172.0 99.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 300 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OUO RELATED DB: PDB REMARK 900 1OUO CONTAINS THE SAME PROTEIN COMPLEXED WITH MG DBREF 1OUP A 19 231 UNP Q8DCA6 Q8DCA6_VIBVU 19 231 DBREF 1OUP B 19 231 UNP Q8DCA6 Q8DCA6_VIBVU 19 231 DBREF 1OUP C 1 8 PDB 1OUP 1OUP 1 8 DBREF 1OUP D 9 16 PDB 1OUP 1OUP 9 16 DBREF 1OUP E 1 6 PDB 1OUP 1OUP 1 6 DBREF 1OUP G 7 8 PDB 1OUP 1OUP 7 8 DBREF 1OUP F 9 16 PDB 1OUP 1OUP 9 16 SEQADV 1OUP ALA A 80 UNP Q8DCA6 HIS 80 ENGINEERED MUTATION SEQADV 1OUP PRO A 163 UNP Q8DCA6 GLN 163 SEE REMARK 999 SEQADV 1OUP ASP A 164 UNP Q8DCA6 THR 164 SEE REMARK 999 SEQADV 1OUP ARG A 165 UNP Q8DCA6 GLU 165 SEE REMARK 999 SEQADV 1OUP ALA A 166 UNP Q8DCA6 LEU 166 SEE REMARK 999 SEQADV 1OUP ALA B 80 UNP Q8DCA6 HIS 80 ENGINEERED MUTATION SEQADV 1OUP PRO B 163 UNP Q8DCA6 GLN 163 SEE REMARK 999 SEQADV 1OUP ASP B 164 UNP Q8DCA6 THR 164 SEE REMARK 999 SEQADV 1OUP ARG B 165 UNP Q8DCA6 GLU 165 SEE REMARK 999 SEQADV 1OUP ALA B 166 UNP Q8DCA6 LEU 166 SEE REMARK 999 SEQRES 1 C 8 DG DC DG DA DT DC DG DC SEQRES 1 D 8 DG DC DG DA DT DC DG DC SEQRES 1 E 6 DG DC DG DA DT DC SEQRES 1 G 2 DG DC SEQRES 1 F 8 DG DC DG DA DT DC DG DC SEQRES 1 A 213 ALA PRO PRO SER SER PHE SER ALA ALA LYS GLN GLN ALA SEQRES 2 A 213 VAL LYS ILE TYR GLN ASP HIS PRO ILE SER PHE TYR CYS SEQRES 3 A 213 GLY CYS ASP ILE GLU TRP GLN GLY LYS LYS GLY ILE PRO SEQRES 4 A 213 ASN LEU GLU THR CYS GLY TYR GLN VAL ARG LYS GLN GLN SEQRES 5 A 213 THR ARG ALA SER ARG ILE GLU TRP GLU ALA VAL VAL PRO SEQRES 6 A 213 ALA TRP GLN PHE GLY HIS HIS ARG GLN CYS TRP GLN LYS SEQRES 7 A 213 GLY GLY ARG LYS ASN CYS SER LYS ASN ASP GLN GLN PHE SEQRES 8 A 213 ARG LEU MET GLU ALA ASP LEU HIS ASN LEU THR PRO ALA SEQRES 9 A 213 ILE GLY GLU VAL ASN GLY ASP ARG SER ASN PHE ASN PHE SEQRES 10 A 213 SER GLN TRP ASN GLY VAL ASP GLY VAL SER TYR GLY ARG SEQRES 11 A 213 CYS GLU MET GLN VAL ASN PHE LYS GLN ARG LYS VAL MET SEQRES 12 A 213 PRO PRO ASP ARG ALA ARG GLY SER ILE ALA ARG THR TYR SEQRES 13 A 213 LEU TYR MET SER GLN GLU TYR GLY PHE GLN LEU SER LYS SEQRES 14 A 213 GLN GLN GLN GLN LEU MET GLN ALA TRP ASN LYS SER TYR SEQRES 15 A 213 PRO VAL ASP GLU TRP GLU CYS THR ARG ASP ASP ARG ILE SEQRES 16 A 213 ALA LYS ILE GLN GLY ASN HIS ASN PRO PHE VAL GLN GLN SEQRES 17 A 213 SER CYS GLN THR GLN SEQRES 1 B 213 ALA PRO PRO SER SER PHE SER ALA ALA LYS GLN GLN ALA SEQRES 2 B 213 VAL LYS ILE TYR GLN ASP HIS PRO ILE SER PHE TYR CYS SEQRES 3 B 213 GLY CYS ASP ILE GLU TRP GLN GLY LYS LYS GLY ILE PRO SEQRES 4 B 213 ASN LEU GLU THR CYS GLY TYR GLN VAL ARG LYS GLN GLN SEQRES 5 B 213 THR ARG ALA SER ARG ILE GLU TRP GLU ALA VAL VAL PRO SEQRES 6 B 213 ALA TRP GLN PHE GLY HIS HIS ARG GLN CYS TRP GLN LYS SEQRES 7 B 213 GLY GLY ARG LYS ASN CYS SER LYS ASN ASP GLN GLN PHE SEQRES 8 B 213 ARG LEU MET GLU ALA ASP LEU HIS ASN LEU THR PRO ALA SEQRES 9 B 213 ILE GLY GLU VAL ASN GLY ASP ARG SER ASN PHE ASN PHE SEQRES 10 B 213 SER GLN TRP ASN GLY VAL ASP GLY VAL SER TYR GLY ARG SEQRES 11 B 213 CYS GLU MET GLN VAL ASN PHE LYS GLN ARG LYS VAL MET SEQRES 12 B 213 PRO PRO ASP ARG ALA ARG GLY SER ILE ALA ARG THR TYR SEQRES 13 B 213 LEU TYR MET SER GLN GLU TYR GLY PHE GLN LEU SER LYS SEQRES 14 B 213 GLN GLN GLN GLN LEU MET GLN ALA TRP ASN LYS SER TYR SEQRES 15 B 213 PRO VAL ASP GLU TRP GLU CYS THR ARG ASP ASP ARG ILE SEQRES 16 B 213 ALA LYS ILE GLN GLY ASN HIS ASN PRO PHE VAL GLN GLN SEQRES 17 B 213 SER CYS GLN THR GLN HET CA A 300 1 HET CA B 300 1 HETNAM CA CALCIUM ION FORMUL 8 CA 2(CA 2+) FORMUL 10 HOH *328(H2 O) HELIX 1 1 SER A 23 TYR A 35 1 13 HELIX 2 2 GLN A 69 SER A 74 1 6 HELIX 3 3 PRO A 83 HIS A 89 1 7 HELIX 4 4 ARG A 91 ASN A 105 1 15 HELIX 5 5 ASP A 106 GLU A 113 1 8 HELIX 6 6 ALA A 114 HIS A 117 5 4 HELIX 7 7 GLY A 124 SER A 131 1 8 HELIX 8 8 PRO A 163 GLY A 182 1 20 HELIX 9 9 SER A 186 TYR A 200 1 15 HELIX 10 10 ASP A 203 GLY A 218 1 16 HELIX 11 11 ASN A 221 GLN A 229 1 9 HELIX 12 12 SER B 23 TYR B 35 1 13 HELIX 13 13 GLN B 69 SER B 74 1 6 HELIX 14 14 PRO B 83 HIS B 89 1 7 HELIX 15 15 ARG B 91 ASP B 106 1 16 HELIX 16 16 ASP B 106 ASP B 115 1 10 HELIX 17 17 GLY B 124 SER B 131 1 8 HELIX 18 18 PRO B 163 GLY B 182 1 20 HELIX 19 19 SER B 186 TYR B 200 1 15 HELIX 20 20 ASP B 203 GLY B 218 1 16 HELIX 21 21 ASN B 221 GLN B 226 1 6 SHEET 1 A 2 ILE A 48 GLN A 51 0 SHEET 2 A 2 LYS A 54 PRO A 57 -1 O LYS A 54 N GLN A 51 SHEET 1 B 2 ILE A 76 ALA A 80 0 SHEET 2 B 2 LEU A 119 ILE A 123 -1 O THR A 120 N GLU A 79 SHEET 1 C 4 ASN A 134 PHE A 135 0 SHEET 2 C 4 LYS A 159 MET A 161 1 O VAL A 160 N ASN A 134 SHEET 3 C 4 CYS A 149 ASN A 154 -1 N ASN A 154 O LYS A 159 SHEET 4 C 4 VAL A 144 TYR A 146 -1 N VAL A 144 O VAL A 153 SHEET 1 D 2 ILE B 48 GLU B 49 0 SHEET 2 D 2 ILE B 56 PRO B 57 -1 O ILE B 56 N GLU B 49 SHEET 1 E 2 ILE B 76 ALA B 80 0 SHEET 2 E 2 LEU B 119 ILE B 123 -1 O THR B 120 N GLU B 79 SHEET 1 F 4 ASN B 134 PHE B 135 0 SHEET 2 F 4 LYS B 159 MET B 161 1 O VAL B 160 N ASN B 134 SHEET 3 F 4 CYS B 149 ASN B 154 -1 N GLN B 152 O MET B 161 SHEET 4 F 4 VAL B 144 TYR B 146 -1 N VAL B 144 O VAL B 153 SSBOND 1 CYS A 44 CYS A 149 1555 1555 2.04 SSBOND 2 CYS A 46 CYS A 62 1555 1555 2.04 SSBOND 3 CYS A 93 CYS A 102 1555 1555 2.04 SSBOND 4 CYS A 207 CYS A 228 1555 1555 2.02 SSBOND 5 CYS B 44 CYS B 149 1555 1555 2.04 SSBOND 6 CYS B 46 CYS B 62 1555 1555 2.03 SSBOND 7 CYS B 93 CYS B 102 1555 1555 2.04 SSBOND 8 CYS B 207 CYS B 228 1555 1555 2.03 LINK O HOH C 461 CA CA B 300 1555 1555 2.53 LINK OP3 DG G 7 CA CA A 300 1555 1555 2.21 LINK O HOH G 720 CA CA A 300 1555 1555 2.07 LINK OE1 GLU A 79 CA CA A 300 1555 1555 2.07 LINK OD1 ASN A 127 CA CA A 300 1555 1555 2.33 LINK CA CA A 300 O HOH A 420 1555 1555 2.57 LINK CA CA A 300 O HOH A 719 1555 1555 2.34 LINK OE1 GLU B 79 CA CA B 300 1555 1555 2.25 LINK OD1 ASN B 127 CA CA B 300 1555 1555 2.36 LINK CA CA B 300 O HOH B 443 1555 1555 2.42 LINK CA CA B 300 O HOH B 718 1555 1555 2.53 SITE 1 AC1 6 GLU A 79 ASN A 127 HOH A 420 HOH A 719 SITE 2 AC1 6 DG G 7 HOH G 720 SITE 1 AC2 6 GLU B 79 ASN B 127 HOH B 443 HOH B 718 SITE 2 AC2 6 DG C 7 HOH C 461 CRYST1 53.740 50.110 89.610 90.00 97.53 90.00 P 1 21 1 6 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 0.018609 0.000000 0.002459 0.00000 SCALE2 0.000000 0.019955 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011257 0.00000