HEADER HYDROLASE 14-JUN-06 2IVK TITLE CRYSTAL STRUCTURE OF THE PERIPLASMIC ENDONUCLEASE VVN COMPLEXED WITH A TITLE 2 16-BP DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDONUCLEASE I; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: VVN NUCLEASE; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*T)-3'; COMPND 10 CHAIN: E, G; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*AP*AP*TP*TP*CP*GP*AP*TP*CP*GP *AP*AP*TP*TP*C)-3'; COMPND 14 CHAIN: F, H; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 4; COMPND 17 MOLECULE: 5'-D(*GP*AP*AP*TP*TP*CP*GP*AP*TP*CP *GP*AP*AP*TP*TP*C)-3'; COMPND 18 CHAIN: I, J; COMPND 19 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 3 ORGANISM_TAXID: 672; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PTYB2; SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 12 ORGANISM_TAXID: 32630; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 16 ORGANISM_TAXID: 32630; SOURCE 17 MOL_ID: 4; SOURCE 18 SYNTHETIC: YES; SOURCE 19 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 20 ORGANISM_TAXID: 32630 KEYWDS DNASE, ENDONUCLEASE, DNA HYDROLYSIS, PROTEIN NUCLEIC ACID KEYWDS 2 INTERACTIONS, DNA CLEAVAGE PREFERENCE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.T.WANG,W.J.YANG,C.L.LI,L.G.DOUDEVA,H.S.YUAN REVDAT 6 13-NOV-24 2IVK 1 REMARK REVDAT 5 13-DEC-23 2IVK 1 REMARK REVDAT 4 29-MAR-17 2IVK 1 SOURCE REVDAT 3 24-FEB-09 2IVK 1 VERSN REVDAT 2 13-FEB-07 2IVK 1 JRNL REVDAT 1 02-JAN-07 2IVK 0 JRNL AUTH Y.T.WANG,W.J.YANG,C.L.LI,L.G.DOUDEVA,H.S.YUAN JRNL TITL STRUCTURAL BASIS FOR SEQUENCE-DEPENDENT DNA CLEAVAGE BY JRNL TITL 2 NONSPECIFIC ENDONUCLEASES. JRNL REF NUCLEIC ACIDS RES. V. 35 584 2007 JRNL REFN ISSN 0305-1048 JRNL PMID 17175542 JRNL DOI 10.1093/NAR/GKL621 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 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 : MLF REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 186489.800 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 24597 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) : 0.237 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1922 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3520 REMARK 3 BIN R VALUE (WORKING SET) : 0.3810 REMARK 3 BIN FREE R VALUE : 0.4350 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 292 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.025 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6902 REMARK 3 NUCLEIC ACID ATOMS : 1868 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 111 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 83.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.52000 REMARK 3 B22 (A**2) : -4.06000 REMARK 3 B33 (A**2) : 9.58000 REMARK 3 B12 (A**2) : -14.52000 REMARK 3 B13 (A**2) : -10.35000 REMARK 3 B23 (A**2) : -17.18000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.53 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) : 0.51 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.69 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.270 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) : 4.190 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.240 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.670 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.630 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.27 REMARK 3 BSOL : 30.90 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 2IVK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUN-06. REMARK 100 THE DEPOSITION ID IS D_1290029073. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-05 REMARK 200 TEMPERATURE (KELVIN) : 113.0 REMARK 200 PH : 7.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24597 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 37.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.40 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.300 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 1OUP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350, 0.2 M DI-SODIUM TARTRATE REMARK 280 DEHYDRATE, PH 7.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: DECAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DECAMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H, I, J 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, HIS 80 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN B, HIS 80 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN C, HIS 80 TO ALA REMARK 400 ENGINEERED RESIDUE IN CHAIN D, HIS 80 TO ALA 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 THR A 230 REMARK 465 GLN A 231 REMARK 465 THR D 230 REMARK 465 GLN D 231 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 GLN A 229 CA C O CB CG CD OE1 REMARK 470 GLN A 229 NE2 REMARK 470 GLN D 229 CA C O CB CG CD OE1 REMARK 470 GLN D 229 NE2 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 NH2 ARG B 72 O HOH B 2005 2.02 REMARK 500 OP1 DA I 2 O HOH I 2001 2.08 REMARK 500 N GLY C 218 O HOH C 2017 2.11 REMARK 500 O3' DC I 6 O HOH I 2002 2.13 REMARK 500 N HIS D 117 O HOH D 2014 2.14 REMARK 500 OE1 GLU B 79 O HOH B 2006 2.14 REMARK 500 OE1 GLU C 79 O HOH C 2004 2.14 REMARK 500 N GLN C 217 O HOH C 2017 2.18 REMARK 500 N CYS D 46 O HOH D 2005 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLN C 191 OP1 DT J 21 1565 2.17 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 DC F 32 C4' - C3' - O3' ANGL. DEV. = 14.6 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 SER A 22 -63.12 -14.55 REMARK 500 PHE A 24 -70.25 -63.64 REMARK 500 HIS A 38 72.60 -165.31 REMARK 500 VAL A 66 99.35 -48.77 REMARK 500 LYS A 68 -32.96 -161.44 REMARK 500 THR A 71 -76.10 -53.80 REMARK 500 HIS A 89 -15.33 -47.11 REMARK 500 ARG A 110 -28.15 -39.73 REMARK 500 ASP A 115 105.31 -58.81 REMARK 500 ASN A 118 -16.36 -49.62 REMARK 500 ASN A 127 -70.14 -64.77 REMARK 500 SER A 131 -80.42 59.44 REMARK 500 ASN A 132 14.06 -161.91 REMARK 500 CYS A 149 97.35 -40.26 REMARK 500 ARG A 158 73.88 32.25 REMARK 500 ARG A 167 -29.48 -30.10 REMARK 500 ILE A 170 -75.64 -68.22 REMARK 500 GLN A 184 153.47 -40.84 REMARK 500 LYS A 198 -79.65 -64.96 REMARK 500 SER A 199 3.00 -47.28 REMARK 500 ASP A 203 -160.78 -123.43 REMARK 500 GLU A 204 -74.28 -65.13 REMARK 500 ARG A 212 27.30 -72.98 REMARK 500 ILE A 213 -47.90 -143.25 REMARK 500 VAL A 224 11.40 -140.59 REMARK 500 GLN A 225 -57.09 -128.87 REMARK 500 GLN A 226 8.49 -61.15 REMARK 500 ASP B 37 30.35 -92.79 REMARK 500 HIS B 38 56.35 -149.15 REMARK 500 PRO B 39 68.64 -64.92 REMARK 500 VAL B 66 144.20 -38.35 REMARK 500 LYS B 68 -36.21 -147.93 REMARK 500 SER B 131 -119.39 52.14 REMARK 500 SER B 136 -147.86 -144.72 REMARK 500 GLN B 137 144.35 -173.23 REMARK 500 SER B 145 -166.71 -108.52 REMARK 500 GLU B 150 31.48 -73.36 REMARK 500 ARG B 158 63.03 28.62 REMARK 500 SER B 186 177.99 -55.65 REMARK 500 CYS B 228 48.36 -71.24 REMARK 500 THR B 230 46.45 -94.28 REMARK 500 HIS C 38 56.13 -147.04 REMARK 500 PRO C 39 68.90 -64.45 REMARK 500 VAL C 66 143.84 -38.07 REMARK 500 LYS C 68 -35.70 -149.49 REMARK 500 SER C 131 -119.79 50.69 REMARK 500 SER C 136 -149.30 -146.15 REMARK 500 GLN C 137 142.83 -171.95 REMARK 500 SER C 145 -167.09 -109.67 REMARK 500 TYR C 146 59.94 -142.49 REMARK 500 REMARK 500 THIS ENTRY HAS 81 RAMACHANDRAN OUTLIERS. 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 TYR C 43 0.07 SIDE CHAIN REMARK 500 DG E 1 0.05 SIDE CHAIN REMARK 500 DT E 4 0.08 SIDE CHAIN REMARK 500 DG F 23 0.06 SIDE CHAIN REMARK 500 DA F 29 0.08 SIDE CHAIN REMARK 500 DG G 1 0.06 SIDE CHAIN REMARK 500 DA G 2 0.06 SIDE CHAIN REMARK 500 DT G 4 0.09 SIDE CHAIN REMARK 500 DA H 29 0.09 SIDE CHAIN REMARK 500 DT H 31 0.08 SIDE CHAIN REMARK 500 DA I 3 0.06 SIDE CHAIN REMARK 500 DG J 17 0.06 SIDE CHAIN REMARK 500 DA J 19 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2IVK A 19 231 UNP Q7MHK3 Q7MHK3_VIBVY 19 231 DBREF 2IVK B 19 231 UNP Q7MHK3 Q7MHK3_VIBVY 19 231 DBREF 2IVK C 19 231 UNP Q7MHK3 Q7MHK3_VIBVY 19 231 DBREF 2IVK D 19 231 UNP Q7MHK3 Q7MHK3_VIBVY 19 231 DBREF 2IVK E 1 15 PDB 2IVK 2IVK 1 15 DBREF 2IVK F 18 32 PDB 2IVK 2IVK 18 32 DBREF 2IVK G 1 15 PDB 2IVK 2IVK 1 15 DBREF 2IVK H 18 32 PDB 2IVK 2IVK 18 32 DBREF 2IVK I 1 16 PDB 2IVK 2IVK 1 16 DBREF 2IVK J 17 32 PDB 2IVK 2IVK 17 32 SEQADV 2IVK ALA A 80 UNP Q7MHK3 HIS 80 ENGINEERED MUTATION SEQADV 2IVK ALA B 80 UNP Q7MHK3 HIS 80 ENGINEERED MUTATION SEQADV 2IVK ALA C 80 UNP Q7MHK3 HIS 80 ENGINEERED MUTATION SEQADV 2IVK ALA D 80 UNP Q7MHK3 HIS 80 ENGINEERED MUTATION 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 SEQRES 1 C 213 ALA PRO PRO SER SER PHE SER ALA ALA LYS GLN GLN ALA SEQRES 2 C 213 VAL LYS ILE TYR GLN ASP HIS PRO ILE SER PHE TYR CYS SEQRES 3 C 213 GLY CYS ASP ILE GLU TRP GLN GLY LYS LYS GLY ILE PRO SEQRES 4 C 213 ASN LEU GLU THR CYS GLY TYR GLN VAL ARG LYS GLN GLN SEQRES 5 C 213 THR ARG ALA SER ARG ILE GLU TRP GLU ALA VAL VAL PRO SEQRES 6 C 213 ALA TRP GLN PHE GLY HIS HIS ARG GLN CYS TRP GLN LYS SEQRES 7 C 213 GLY GLY ARG LYS ASN CYS SER LYS ASN ASP GLN GLN PHE SEQRES 8 C 213 ARG LEU MET GLU ALA ASP LEU HIS ASN LEU THR PRO ALA SEQRES 9 C 213 ILE GLY GLU VAL ASN GLY ASP ARG SER ASN PHE ASN PHE SEQRES 10 C 213 SER GLN TRP ASN GLY VAL ASP GLY VAL SER TYR GLY ARG SEQRES 11 C 213 CYS GLU MET GLN VAL ASN PHE LYS GLN ARG LYS VAL MET SEQRES 12 C 213 PRO PRO ASP ARG ALA ARG GLY SER ILE ALA ARG THR TYR SEQRES 13 C 213 LEU TYR MET SER GLN GLU TYR GLY PHE GLN LEU SER LYS SEQRES 14 C 213 GLN GLN GLN GLN LEU MET GLN ALA TRP ASN LYS SER TYR SEQRES 15 C 213 PRO VAL ASP GLU TRP GLU CYS THR ARG ASP ASP ARG ILE SEQRES 16 C 213 ALA LYS ILE GLN GLY ASN HIS ASN PRO PHE VAL GLN GLN SEQRES 17 C 213 SER CYS GLN THR GLN SEQRES 1 D 213 ALA PRO PRO SER SER PHE SER ALA ALA LYS GLN GLN ALA SEQRES 2 D 213 VAL LYS ILE TYR GLN ASP HIS PRO ILE SER PHE TYR CYS SEQRES 3 D 213 GLY CYS ASP ILE GLU TRP GLN GLY LYS LYS GLY ILE PRO SEQRES 4 D 213 ASN LEU GLU THR CYS GLY TYR GLN VAL ARG LYS GLN GLN SEQRES 5 D 213 THR ARG ALA SER ARG ILE GLU TRP GLU ALA VAL VAL PRO SEQRES 6 D 213 ALA TRP GLN PHE GLY HIS HIS ARG GLN CYS TRP GLN LYS SEQRES 7 D 213 GLY GLY ARG LYS ASN CYS SER LYS ASN ASP GLN GLN PHE SEQRES 8 D 213 ARG LEU MET GLU ALA ASP LEU HIS ASN LEU THR PRO ALA SEQRES 9 D 213 ILE GLY GLU VAL ASN GLY ASP ARG SER ASN PHE ASN PHE SEQRES 10 D 213 SER GLN TRP ASN GLY VAL ASP GLY VAL SER TYR GLY ARG SEQRES 11 D 213 CYS GLU MET GLN VAL ASN PHE LYS GLN ARG LYS VAL MET SEQRES 12 D 213 PRO PRO ASP ARG ALA ARG GLY SER ILE ALA ARG THR TYR SEQRES 13 D 213 LEU TYR MET SER GLN GLU TYR GLY PHE GLN LEU SER LYS SEQRES 14 D 213 GLN GLN GLN GLN LEU MET GLN ALA TRP ASN LYS SER TYR SEQRES 15 D 213 PRO VAL ASP GLU TRP GLU CYS THR ARG ASP ASP ARG ILE SEQRES 16 D 213 ALA LYS ILE GLN GLY ASN HIS ASN PRO PHE VAL GLN GLN SEQRES 17 D 213 SER CYS GLN THR GLN SEQRES 1 E 15 DG DA DA DT DT DC DG DA DT DC DG DA DA SEQRES 2 E 15 DT DT SEQRES 1 F 15 DA DA DT DT DC DG DA DT DC DG DA DA DT SEQRES 2 F 15 DT DC SEQRES 1 G 15 DG DA DA DT DT DC DG DA DT DC DG DA DA SEQRES 2 G 15 DT DT SEQRES 1 H 15 DA DA DT DT DC DG DA DT DC DG DA DA DT SEQRES 2 H 15 DT DC SEQRES 1 I 16 DG DA DA DT DT DC DG DA DT DC DG DA DA SEQRES 2 I 16 DT DT DC SEQRES 1 J 16 DG DA DA DT DT DC DG DA DT DC DG DA DA SEQRES 2 J 16 DT DT DC FORMUL 11 HOH *111(H2 O) HELIX 1 1 SER A 23 TYR A 35 1 13 HELIX 2 2 ASN A 58 GLY A 63 1 6 HELIX 3 3 GLN A 69 ARG A 75 1 7 HELIX 4 4 ARG A 91 GLU A 113 1 23 HELIX 5 5 ALA A 114 HIS A 117 5 4 HELIX 6 6 GLY A 124 SER A 131 1 8 HELIX 7 7 PRO A 163 TYR A 181 1 19 HELIX 8 8 SER A 186 SER A 199 1 14 HELIX 9 9 ASP A 203 ASP A 210 1 8 HELIX 10 10 ASP A 210 LYS A 215 1 6 HELIX 11 11 ASN A 221 GLN A 225 5 5 HELIX 12 12 SER B 23 TYR B 35 1 13 HELIX 13 13 GLN B 36 HIS B 38 5 3 HELIX 14 14 LEU B 59 GLY B 63 5 5 HELIX 15 15 THR B 71 SER B 74 5 4 HELIX 16 16 PRO B 83 HIS B 89 1 7 HELIX 17 17 ARG B 91 ALA B 114 1 24 HELIX 18 18 GLY B 124 ARG B 130 1 7 HELIX 19 19 PRO B 163 TYR B 181 1 19 HELIX 20 20 SER B 186 TYR B 200 1 15 HELIX 21 21 ASP B 203 ALA B 214 1 12 HELIX 22 22 ASN B 221 CYS B 228 1 8 HELIX 23 23 SER C 23 TYR C 35 1 13 HELIX 24 24 GLN C 36 HIS C 38 5 3 HELIX 25 25 LEU C 59 GLY C 63 5 5 HELIX 26 26 GLN C 69 SER C 74 1 6 HELIX 27 27 PRO C 83 HIS C 89 1 7 HELIX 28 28 ARG C 91 ALA C 114 1 24 HELIX 29 29 GLY C 124 ARG C 130 1 7 HELIX 30 30 PRO C 163 TYR C 181 1 19 HELIX 31 31 SER C 186 TYR C 200 1 15 HELIX 32 32 ASP C 203 ALA C 214 1 12 HELIX 33 33 ASN C 221 CYS C 228 1 8 HELIX 34 34 SER D 23 TYR D 35 1 13 HELIX 35 35 ASN D 58 GLY D 63 1 6 HELIX 36 36 GLN D 69 ARG D 75 1 7 HELIX 37 37 ARG D 91 GLU D 113 1 23 HELIX 38 38 ALA D 114 HIS D 117 5 4 HELIX 39 39 GLY D 124 SER D 131 1 8 HELIX 40 40 PRO D 163 TYR D 181 1 19 HELIX 41 41 SER D 186 SER D 199 1 14 HELIX 42 42 ASP D 203 ASP D 210 1 8 HELIX 43 43 ASP D 210 LYS D 215 1 6 HELIX 44 44 ASN D 221 GLN D 225 5 5 SHEET 1 AA 2 ILE A 48 GLN A 51 0 SHEET 2 AA 2 LYS A 54 PRO A 57 -1 O LYS A 54 N GLN A 51 SHEET 1 AB 2 ILE A 76 ALA A 80 0 SHEET 2 AB 2 LEU A 119 ILE A 123 -1 O THR A 120 N GLU A 79 SHEET 1 AC 4 ASN A 134 PHE A 135 0 SHEET 2 AC 4 LYS A 159 MET A 161 1 N VAL A 160 O ASN A 134 SHEET 3 AC 4 GLN A 152 ASN A 154 -1 O GLN A 152 N MET A 161 SHEET 4 AC 4 VAL A 144 SER A 145 -1 O VAL A 144 N VAL A 153 SHEET 1 BA 2 ILE B 48 GLN B 51 0 SHEET 2 BA 2 LYS B 54 PRO B 57 -1 O LYS B 54 N GLN B 51 SHEET 1 BB 2 ILE B 76 ALA B 80 0 SHEET 2 BB 2 LEU B 119 ILE B 123 -1 O THR B 120 N GLU B 79 SHEET 1 BC 2 ASN B 134 PHE B 135 0 SHEET 2 BC 2 LYS B 159 VAL B 160 1 N VAL B 160 O ASN B 134 SHEET 1 BD 2 VAL B 144 TYR B 146 0 SHEET 2 BD 2 CYS B 149 VAL B 153 -1 O CYS B 149 N TYR B 146 SHEET 1 CA 2 ILE C 48 GLN C 51 0 SHEET 2 CA 2 LYS C 54 PRO C 57 -1 O LYS C 54 N GLN C 51 SHEET 1 CB 2 ILE C 76 ALA C 80 0 SHEET 2 CB 2 LEU C 119 ILE C 123 -1 O THR C 120 N GLU C 79 SHEET 1 CC 2 ASN C 134 PHE C 135 0 SHEET 2 CC 2 LYS C 159 VAL C 160 1 N VAL C 160 O ASN C 134 SHEET 1 CD 2 VAL C 144 TYR C 146 0 SHEET 2 CD 2 CYS C 149 VAL C 153 -1 O CYS C 149 N TYR C 146 SHEET 1 DA 2 ILE D 48 GLN D 51 0 SHEET 2 DA 2 LYS D 54 PRO D 57 -1 O LYS D 54 N GLN D 51 SHEET 1 DB 2 ILE D 76 ALA D 80 0 SHEET 2 DB 2 LEU D 119 ILE D 123 -1 O THR D 120 N GLU D 79 SHEET 1 DC 4 ASN D 134 PHE D 135 0 SHEET 2 DC 4 LYS D 159 MET D 161 1 N VAL D 160 O ASN D 134 SHEET 3 DC 4 GLN D 152 ASN D 154 -1 O GLN D 152 N MET D 161 SHEET 4 DC 4 VAL D 144 SER D 145 -1 O VAL D 144 N VAL D 153 SSBOND 1 CYS A 44 CYS A 149 1555 1555 2.04 SSBOND 2 CYS A 46 CYS A 62 1555 1555 2.03 SSBOND 3 CYS A 93 CYS A 102 1555 1555 2.04 SSBOND 4 CYS A 207 CYS A 228 1555 1555 2.03 SSBOND 5 CYS B 44 CYS B 149 1555 1555 2.03 SSBOND 6 CYS B 46 CYS B 62 1555 1555 2.01 SSBOND 7 CYS B 93 CYS B 102 1555 1555 2.03 SSBOND 8 CYS B 207 CYS B 228 1555 1555 2.05 SSBOND 9 CYS C 44 CYS C 149 1555 1555 2.03 SSBOND 10 CYS C 46 CYS C 62 1555 1555 2.02 SSBOND 11 CYS C 93 CYS C 102 1555 1555 2.03 SSBOND 12 CYS C 207 CYS C 228 1555 1555 2.04 SSBOND 13 CYS D 44 CYS D 149 1555 1555 2.04 SSBOND 14 CYS D 46 CYS D 62 1555 1555 2.03 SSBOND 15 CYS D 93 CYS D 102 1555 1555 2.03 SSBOND 16 CYS D 207 CYS D 228 1555 1555 2.03 CRYST1 64.636 64.705 79.157 74.45 73.56 75.56 P 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 0.015471 -0.003984 -0.003805 0.00000 SCALE2 0.000000 0.015959 -0.003473 0.00000 SCALE3 0.000000 0.000000 0.013480 0.00000