HEADER DNA BINDING PROTEIN 26-FEB-21 7NPD TITLE VIBIRO CHOLERAE PARA2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: WALKER A-TYPE ATPASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CHROMOSOME (PLASMID) PARTITIONING PROTEIN PARA,CHROMOSOME COMPND 5 PARTITIONING PROTEIN PARA,PARA FAMILY PROTEIN,PLASMID PARTITION COMPND 6 PROTEIN A,PARA2VC,PARA2,AAA FAMILY ATPASE; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO CHOLERAE; SOURCE 3 ORGANISM_TAXID: 666; SOURCE 4 GENE: PARA, BC353_10845, C9J66_03480, ERS013138_01197, SOURCE 5 ERS013166_00021, ERS013186_00500, ERS013193_00027, ERS013197_04093, SOURCE 6 ERS013198_00323, ERS013199_01186, ERS013200_00295, ERS013202_00851, SOURCE 7 ERS013206_01885, F0315_18570, FLM02_03395, FXF03_20770, HPY05_13545; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ATPASE, CHROMOSOME SEGREGATION, BACTERIAL CELL DIVISION, HYDROLASE, KEYWDS 2 DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.V.PARKER,J.R.C.BERGERON REVDAT 3 31-JAN-24 7NPD 1 REMARK REVDAT 2 13-OCT-21 7NPD 1 JRNL REMARK REVDAT 1 19-MAY-21 7NPD 0 JRNL AUTH A.V.PARKER,D.MANN,S.B.TZOKOV,L.C.HWANG,J.R.C.BERGERON JRNL TITL THE STRUCTURE OF THE BACTERIAL DNA SEGREGATION ATPASE JRNL TITL 2 FILAMENT REVEALS THE CONFORMATIONAL PLASTICITY OF PARA UPON JRNL TITL 3 DNA BINDING. JRNL REF NAT COMMUN V. 12 5166 2021 JRNL REFN ESSN 2041-1723 JRNL PMID 34453062 JRNL DOI 10.1038/S41467-021-25429-2 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.31 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.2 REMARK 3 NUMBER OF REFLECTIONS : 14628 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.280 REMARK 3 R VALUE (WORKING SET) : 0.274 REMARK 3 FREE R VALUE : 0.337 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1469 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.3100 - 5.1800 1.00 1837 205 0.2452 0.2891 REMARK 3 2 5.1800 - 4.1200 1.00 1778 201 0.2121 0.2882 REMARK 3 3 4.1200 - 3.6000 1.00 1760 194 0.2459 0.3309 REMARK 3 4 3.5900 - 3.2700 1.00 1752 195 0.3119 0.4059 REMARK 3 5 3.2700 - 3.0300 1.00 1725 190 0.3678 0.4044 REMARK 3 6 3.0300 - 2.8500 1.00 1758 198 0.4202 0.4881 REMARK 3 7 2.8500 - 2.7100 0.78 1336 151 0.4427 0.4910 REMARK 3 8 2.7100 - 2.6000 0.45 788 88 0.4386 0.4397 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.480 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 48.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 81.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 4 THROUGH 33 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.3458 -11.8084 23.8788 REMARK 3 T TENSOR REMARK 3 T11: 0.6431 T22: 0.4893 REMARK 3 T33: 0.5180 T12: 0.0000 REMARK 3 T13: 0.0600 T23: -0.2328 REMARK 3 L TENSOR REMARK 3 L11: -0.0084 L22: -0.0005 REMARK 3 L33: 0.0035 L12: -0.0031 REMARK 3 L13: -0.0038 L23: 0.0019 REMARK 3 S TENSOR REMARK 3 S11: -0.0447 S12: -0.0624 S13: -0.1336 REMARK 3 S21: 0.0702 S22: -0.0048 S23: -0.0613 REMARK 3 S31: 0.1442 S32: 0.0537 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 34 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.8545 25.3187 14.4061 REMARK 3 T TENSOR REMARK 3 T11: 0.3047 T22: -0.8315 REMARK 3 T33: 0.0997 T12: -0.4398 REMARK 3 T13: 0.0274 T23: 0.6350 REMARK 3 L TENSOR REMARK 3 L11: 0.0127 L22: 0.0190 REMARK 3 L33: 0.0122 L12: -0.0175 REMARK 3 L13: -0.0034 L23: -0.0076 REMARK 3 S TENSOR REMARK 3 S11: 0.0116 S12: 0.2811 S13: -0.1508 REMARK 3 S21: -0.0463 S22: -0.4473 S23: 0.1268 REMARK 3 S31: -0.3380 S32: -0.2503 S33: 0.0000 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 180 THROUGH 203 ) REMARK 3 ORIGIN FOR THE GROUP (A): -1.4999 8.1847 10.6868 REMARK 3 T TENSOR REMARK 3 T11: 0.5101 T22: 0.5223 REMARK 3 T33: 0.3888 T12: 0.0873 REMARK 3 T13: 0.0412 T23: 0.1129 REMARK 3 L TENSOR REMARK 3 L11: -0.0042 L22: -0.0029 REMARK 3 L33: -0.0004 L12: -0.0088 REMARK 3 L13: 0.0020 L23: 0.0033 REMARK 3 S TENSOR REMARK 3 S11: -0.0660 S12: -0.0065 S13: -0.0005 REMARK 3 S21: -0.0510 S22: -0.0215 S23: 0.0040 REMARK 3 S31: 0.0001 S32: 0.0113 S33: -0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 204 THROUGH 406 ) REMARK 3 ORIGIN FOR THE GROUP (A): -0.7991 17.3988 30.9706 REMARK 3 T TENSOR REMARK 3 T11: 0.2986 T22: -0.6985 REMARK 3 T33: 0.1152 T12: -0.8307 REMARK 3 T13: 0.0952 T23: 0.7952 REMARK 3 L TENSOR REMARK 3 L11: -0.0055 L22: -0.0049 REMARK 3 L33: 0.0028 L12: -0.0164 REMARK 3 L13: -0.0157 L23: -0.0201 REMARK 3 S TENSOR REMARK 3 S11: -0.0506 S12: -0.1429 S13: -0.2841 REMARK 3 S21: 0.3669 S22: -0.2059 S23: -0.2574 REMARK 3 S31: -0.3103 S32: 0.1910 S33: 0.0000 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7NPD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1292114397. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14628 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 38.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.01654 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 36.8100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37520 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 3EZ7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRI-SODIUM CITRATE PH 5.5 20% REMARK 280 W/V PEG 3000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -Y,-X,-Z+1/3 REMARK 290 5555 -X+Y,Y,-Z+2/3 REMARK 290 6555 X,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 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 142.91533 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 71.45767 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 71.45767 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 142.91533 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 BIOMT1 2 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 71.45767 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 ALA A 2 REMARK 465 MET A 3 REMARK 465 GLY A 120 REMARK 465 GLY A 121 REMARK 465 THR A 122 REMARK 465 GLY A 123 REMARK 465 VAL A 183 REMARK 465 PRO A 184 REMARK 465 ASP A 185 REMARK 465 GLY A 186 REMARK 465 VAL A 187 REMARK 465 VAL A 369 REMARK 465 ASN A 370 REMARK 465 ASP A 371 REMARK 465 PHE A 372 REMARK 465 GLU A 373 REMARK 465 GLY A 374 REMARK 465 GLY A 375 REMARK 465 GLY A 407 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 4 CG CD CE NZ REMARK 470 GLU A 6 CG CD OE1 OE2 REMARK 470 GLN A 7 CG CD OE1 NE2 REMARK 470 LEU A 12 CG CD1 CD2 REMARK 470 GLN A 14 CG CD OE1 NE2 REMARK 470 GLN A 17 CG CD OE1 NE2 REMARK 470 LEU A 18 CG CD1 CD2 REMARK 470 GLN A 20 CG CD OE1 NE2 REMARK 470 GLN A 21 CG CD OE1 NE2 REMARK 470 VAL A 22 CG1 CG2 REMARK 470 GLN A 23 CG CD OE1 NE2 REMARK 470 ASP A 25 CG OD1 OD2 REMARK 470 GLU A 28 CG CD OE1 OE2 REMARK 470 GLU A 32 CG CD OE1 OE2 REMARK 470 ARG A 34 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 37 CG CD OE1 OE2 REMARK 470 LYS A 44 CG CD CE NZ REMARK 470 ARG A 56 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 57 CG CD CE NZ REMARK 470 GLU A 60 CG CD OE1 OE2 REMARK 470 LYS A 103 CG CD CE NZ REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 GLU A 107 CG CD OE1 OE2 REMARK 470 LYS A 109 CG CD CE NZ REMARK 470 LYS A 119 CG CD CE NZ REMARK 470 LYS A 124 CG CD CE NZ REMARK 470 LEU A 166 CG CD1 CD2 REMARK 470 GLN A 188 CG CD OE1 NE2 REMARK 470 GLU A 192 CG CD OE1 OE2 REMARK 470 LYS A 196 CG CD CE NZ REMARK 470 TYR A 226 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 227 CG CD1 CD2 REMARK 470 GLN A 229 CG CD OE1 NE2 REMARK 470 ASN A 230 CG OD1 ND2 REMARK 470 GLN A 231 CG CD OE1 NE2 REMARK 470 ARG A 237 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 240 CG CD CE NZ REMARK 470 LYS A 242 CG CD CE NZ REMARK 470 LYS A 283 CG CD CE NZ REMARK 470 LEU A 285 CG CD1 CD2 REMARK 470 GLN A 295 CG CD OE1 NE2 REMARK 470 LYS A 309 CG CD CE NZ REMARK 470 THR A 319 OG1 CG2 REMARK 470 MET A 320 CG SD CE REMARK 470 ASP A 324 CG OD1 OD2 REMARK 470 ASN A 325 CG OD1 ND2 REMARK 470 LYS A 326 CG CD CE NZ REMARK 470 LYS A 327 CG CD CE NZ REMARK 470 GLN A 328 CG CD OE1 NE2 REMARK 470 GLU A 334 CG CD OE1 OE2 REMARK 470 MET A 335 CG SD CE REMARK 470 TYR A 337 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LEU A 338 CG CD1 CD2 REMARK 470 LEU A 339 CG CD1 CD2 REMARK 470 ARG A 350 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 352 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 376 CG CD CE NZ REMARK 470 LYS A 377 CG CD 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 OE1 GLU A 222 O HOH A 501 1.39 REMARK 500 OE1 GLN A 163 O HOH A 502 1.96 REMARK 500 O LEU A 15 OG1 THR A 19 1.97 REMARK 500 NE2 GLN A 163 O HOH A 503 1.98 REMARK 500 O ALA A 136 O HOH A 504 2.00 REMARK 500 ND2 ASN A 11 O HOH A 505 2.03 REMARK 500 O LEU A 135 O HOH A 506 2.03 REMARK 500 O VAL A 331 O HOH A 507 2.06 REMARK 500 O ILE A 27 CD1 LEU A 31 2.08 REMARK 500 O THR A 202 N TYR A 204 2.14 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 OE2 GLU A 67 NZ LYS A 98 6565 2.11 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 SER A 165 CB SER A 165 OG 0.114 REMARK 500 VAL A 300 CB VAL A 300 CG1 -0.284 REMARK 500 VAL A 300 CB VAL A 300 CG2 -0.182 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 LEU A 15 CA - CB - CG ANGL. DEV. = -15.6 DEGREES REMARK 500 LEU A 31 CA - CB - CG ANGL. DEV. = -22.3 DEGREES REMARK 500 LEU A 31 CB - CG - CD1 ANGL. DEV. = 11.1 DEGREES REMARK 500 SER A 165 C - N - CA ANGL. DEV. = 15.3 DEGREES REMARK 500 GLU A 168 CA - CB - CG ANGL. DEV. = -20.9 DEGREES REMARK 500 LEU A 180 CA - CB - CG ANGL. DEV. = -14.7 DEGREES REMARK 500 LEU A 233 CB - CG - CD1 ANGL. DEV. = -17.1 DEGREES REMARK 500 LEU A 233 CB - CG - CD2 ANGL. DEV. = 10.8 DEGREES REMARK 500 LEU A 297 CA - CB - CG ANGL. DEV. = 24.8 DEGREES REMARK 500 PRO A 298 C - N - CD ANGL. DEV. = -15.3 DEGREES REMARK 500 LEU A 397 CA - CB - CG ANGL. DEV. = 22.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 GLN A 20 32.16 -79.75 REMARK 500 GLN A 23 -149.68 -160.27 REMARK 500 ALA A 24 63.77 84.09 REMARK 500 ARG A 35 33.17 -97.26 REMARK 500 ASP A 36 86.97 -65.60 REMARK 500 LYS A 44 -16.58 85.50 REMARK 500 ARG A 102 36.01 -80.51 REMARK 500 LYS A 103 -25.96 44.53 REMARK 500 ARG A 142 72.97 50.36 REMARK 500 GLN A 153 34.61 -91.82 REMARK 500 SER A 165 -12.69 72.02 REMARK 500 LEU A 166 -170.42 165.77 REMARK 500 GLU A 168 12.98 -68.54 REMARK 500 THR A 170 -70.87 -44.32 REMARK 500 ASP A 181 114.88 71.37 REMARK 500 GLN A 203 -17.45 55.71 REMARK 500 PRO A 214 -25.64 -39.01 REMARK 500 ASP A 216 -9.31 -57.44 REMARK 500 ASN A 230 125.81 -172.73 REMARK 500 SER A 232 -71.35 -88.24 REMARK 500 LEU A 233 44.44 88.63 REMARK 500 LEU A 243 -58.99 -126.17 REMARK 500 LEU A 297 57.07 -99.36 REMARK 500 GLU A 306 -27.53 -35.46 REMARK 500 ASP A 307 -0.39 -55.29 REMARK 500 LYS A 309 22.05 -74.38 REMARK 500 GLU A 312 -77.62 -96.49 REMARK 500 MET A 320 76.91 56.54 REMARK 500 ASP A 323 39.59 -94.72 REMARK 500 SER A 330 10.38 -66.83 REMARK 500 GLN A 342 15.73 85.69 REMARK 500 PRO A 349 -172.65 -66.26 REMARK 500 SER A 351 97.20 65.75 REMARK 500 ARG A 352 -43.72 -29.80 REMARK 500 THR A 378 -51.33 -157.05 REMARK 500 ALA A 380 -53.48 79.34 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 ARG A 102 LYS A 103 149.55 REMARK 500 SER A 165 LEU A 166 129.09 REMARK 500 GLN A 188 VAL A 189 -147.07 REMARK 500 LEU A 297 PRO A 298 135.43 REMARK 500 LYS A 377 THR A 378 144.17 REMARK 500 LEU A 379 ALA A 380 -141.41 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 ASP A 181 11.28 REMARK 500 ALA A 380 -10.45 REMARK 500 REMARK 500 REMARK: NULL DBREF1 7NPD A 3 407 UNP A0A085S0Z4_VIBCL DBREF2 7NPD A A0A085S0Z4 1 405 SEQADV 7NPD MET A 1 UNP A0A085S0Z INITIATING METHIONINE SEQADV 7NPD ALA A 2 UNP A0A085S0Z EXPRESSION TAG SEQRES 1 A 407 MET ALA MET LYS ARG GLU GLN THR ILE GLU ASN LEU TYR SEQRES 2 A 407 GLN LEU ALA GLN LEU THR GLN GLN VAL GLN ALA ASP ARG SEQRES 3 A 407 ILE GLU ILE VAL LEU GLU GLU ARG ARG ASP GLU HIS PHE SEQRES 4 A 407 PRO PRO MET SER LYS ALA LEU MET GLU THR ARG SER GLY SEQRES 5 A 407 LEU THR ARG ARG LYS LEU ASP GLU ALA ILE ALA LYS MET SEQRES 6 A 407 GLU GLU ALA GLY HIS GLN PHE THR LYS ASN ASN ALA ASN SEQRES 7 A 407 HIS TYR SER ILE SER LEU SER GLU ALA HIS MET LEU MET SEQRES 8 A 407 ASP ALA ALA GLY VAL PRO LYS PHE HIS GLU ARG LYS LYS SEQRES 9 A 407 ASN ASN GLU ASN LYS PRO TRP ILE ILE ASN VAL GLN ASN SEQRES 10 A 407 GLN LYS GLY GLY THR GLY LYS SER MET THR ALA VAL HIS SEQRES 11 A 407 LEU ALA ALA CYS LEU ALA LEU ASN LEU ASP LYS ARG TYR SEQRES 12 A 407 ARG ILE CYS LEU ILE ASP LEU ASP PRO GLN GLY SER LEU SEQRES 13 A 407 ARG LEU PHE LEU ASN PRO GLN ILE SER LEU ALA GLU HIS SEQRES 14 A 407 THR ASN ILE TYR SER ALA VAL ASP ILE MET LEU ASP ASN SEQRES 15 A 407 VAL PRO ASP GLY VAL GLN VAL ASP THR GLU PHE LEU ARG SEQRES 16 A 407 LYS ASN VAL MET LEU PRO THR GLN TYR PRO ASN LEU LYS SEQRES 17 A 407 THR ILE SER ALA PHE PRO GLU ASP ALA MET PHE ASN ALA SEQRES 18 A 407 GLU ALA TRP GLN TYR LEU SER GLN ASN GLN SER LEU ASP SEQRES 19 A 407 ILE VAL ARG LEU LEU LYS GLU LYS LEU ILE ASP LYS ILE SEQRES 20 A 407 ALA SER ASP PHE ASP ILE ILE MET ILE ASP THR GLY PRO SEQRES 21 A 407 HIS VAL ASP PRO LEU VAL TRP ASN ALA MET TYR ALA SER SEQRES 22 A 407 ASN ALA LEU LEU ILE PRO CYS ALA ALA LYS ARG LEU ASP SEQRES 23 A 407 TRP ALA SER THR VAL ASN PHE PHE GLN HIS LEU PRO THR SEQRES 24 A 407 VAL TYR GLU MET PHE PRO GLU ASP TRP LYS GLY LEU GLU SEQRES 25 A 407 PHE VAL ARG LEU MET PRO THR MET PHE GLU ASP ASP ASN SEQRES 26 A 407 LYS LYS GLN VAL SER VAL LEU THR GLU MET ASN TYR LEU SEQRES 27 A 407 LEU GLY ASP GLN VAL MET MET ALA THR ILE PRO ARG SER SEQRES 28 A 407 ARG ALA PHE GLU THR CYS ALA ASP THR TYR SER THR VAL SEQRES 29 A 407 PHE ASP LEU THR VAL ASN ASP PHE GLU GLY GLY LYS LYS SEQRES 30 A 407 THR LEU ALA THR ALA GLN ASP ALA VAL GLN LYS SER ALA SEQRES 31 A 407 LEU GLU LEU GLU ARG VAL LEU HIS SER HIS TRP SER SER SEQRES 32 A 407 LEU ASN GLN GLY FORMUL 2 HOH *47(H2 O) HELIX 1 AA1 LYS A 4 GLN A 20 1 17 HELIX 2 AA2 ASP A 25 GLU A 32 1 8 HELIX 3 AA3 LYS A 44 GLY A 52 1 9 HELIX 4 AA4 THR A 54 ALA A 68 1 15 HELIX 5 AA5 SER A 83 GLY A 95 1 13 HELIX 6 AA6 PHE A 99 LYS A 103 5 5 HELIX 7 AA7 MET A 126 LEU A 137 1 12 HELIX 8 AA8 SER A 174 LEU A 180 1 7 HELIX 9 AA9 ASP A 190 VAL A 198 1 9 HELIX 10 AB1 PHE A 213 ASP A 216 5 4 HELIX 11 AB2 ALA A 217 TYR A 226 1 10 HELIX 12 AB3 ARG A 237 LEU A 243 1 7 HELIX 13 AB4 ILE A 244 ALA A 248 5 5 HELIX 14 AB5 ASP A 263 TYR A 271 1 9 HELIX 15 AB6 LYS A 283 LEU A 297 1 15 HELIX 16 AB7 PRO A 298 MET A 303 1 6 HELIX 17 AB8 ASN A 325 GLY A 340 1 16 HELIX 18 AB9 SER A 351 TYR A 361 1 11 HELIX 19 AC1 THR A 363 LEU A 367 5 5 HELIX 20 AC2 ALA A 380 GLN A 406 1 27 SHEET 1 AA1 7 LEU A 200 TYR A 204 0 SHEET 2 AA1 7 LEU A 207 ILE A 210 -1 O LEU A 207 N TYR A 204 SHEET 3 AA1 7 ILE A 145 ASP A 149 1 N ASP A 149 O ILE A 210 SHEET 4 AA1 7 ILE A 253 ASP A 257 1 O MET A 255 N ILE A 148 SHEET 5 AA1 7 TRP A 111 VAL A 115 1 N ILE A 113 O ILE A 256 SHEET 6 AA1 7 ALA A 275 ALA A 281 1 O ALA A 275 N ASN A 114 SHEET 7 AA1 7 VAL A 314 THR A 319 1 O THR A 319 N CYS A 280 CRYST1 63.247 63.247 214.373 90.00 90.00 120.00 P 32 1 2 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 0.015811 0.009129 0.000000 0.00000 SCALE2 0.000000 0.018257 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004665 0.00000