HEADER HYDROLASE 02-DEC-14 4D82 TITLE METALLOSPHERA SEDULA VPS4 CRYSTAL STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AAA ATPASE, CENTRAL DOMAIN PROTEIN; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: AAA, UNP RESIDUES 75-369; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: TRUNCATION OF THE RESIDUES 1-74 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: METALLOSPHAERA SEDULA; SOURCE 3 ORGANISM_TAXID: 43687; SOURCE 4 GENE: HA72_1672; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLAMSID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PDEST-17 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.CAILLAT,P.MACHEBOEUF,Y.WU,A.A.MCCARTHY,E.BOERI-ERBA,G.EFFANTIN, AUTHOR 2 H.G.GOTTLINGER,W.WEISSENHORN,P.RENESTO REVDAT 3 20-DEC-23 4D82 1 COMPND SOURCE REMARK DBREF REVDAT 3 2 1 SEQADV ATOM REVDAT 2 16-DEC-15 4D82 1 JRNL REVDAT 1 25-NOV-15 4D82 0 JRNL AUTH C.CAILLAT,P.MACHEBOEUF,Y.WU,A.A.MCCARTHY,E.BOERI-ERBA, JRNL AUTH 2 G.EFFANTIN,H.G.GOTTLINGER,W.WEISSENHORN,P.RENESTO JRNL TITL ASYMMETRIC RING STRUCTURE OF VPS4 REQUIRED FOR ESCRT-III JRNL TITL 2 DISASSEMBLY. JRNL REF NAT.COMMUN. V. 6 8781 2015 JRNL REFN ESSN 2041-1723 JRNL PMID 26632262 JRNL DOI 10.1038/NCOMMS9781 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 130.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 20131 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) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.228 REMARK 3 FREE R VALUE : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1081 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) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.28 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1502 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.2910 REMARK 3 BIN FREE R VALUE SET COUNT : 93 REMARK 3 BIN FREE R VALUE : 0.3260 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6519 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 81 REMARK 3 SOLVENT ATOMS : 12 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 54.46 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.73000 REMARK 3 B22 (A**2) : 1.73000 REMARK 3 B33 (A**2) : -5.63000 REMARK 3 B12 (A**2) : 0.87000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.502 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.419 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 52.939 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.899 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.844 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6742 ; 0.011 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6662 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9107 ; 1.549 ; 1.994 REMARK 3 BOND ANGLES OTHERS (DEGREES): 15376 ; 1.094 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 809 ; 6.504 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 301 ;37.403 ;24.319 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1271 ;16.852 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;20.852 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1006 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7368 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1441 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 3248 ; 1.929 ; 3.116 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3247 ; 1.930 ; 3.116 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4050 ; 3.344 ; 4.666 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3494 ; 1.635 ; 3.288 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 5056 ; 2.866 ; 4.853 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 3 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 97 365 C 97 365 16462 0.10 0.05 REMARK 3 2 A 97 365 B 97 365 16767 0.09 0.05 REMARK 3 3 C 90 365 B 90 365 16697 0.11 0.05 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 97 A 366 REMARK 3 ORIGIN FOR THE GROUP (A): 25.3160 190.8430 0.4850 REMARK 3 T TENSOR REMARK 3 T11: 0.1089 T22: 0.0184 REMARK 3 T33: 0.2463 T12: 0.0027 REMARK 3 T13: 0.0215 T23: -0.0218 REMARK 3 L TENSOR REMARK 3 L11: 0.5155 L22: 3.4887 REMARK 3 L33: 1.2136 L12: -0.5760 REMARK 3 L13: 0.3011 L23: -0.6460 REMARK 3 S TENSOR REMARK 3 S11: 0.0686 S12: -0.0159 S13: 0.0147 REMARK 3 S21: 0.2069 S22: -0.0776 S23: 0.1371 REMARK 3 S31: -0.1467 S32: 0.0522 S33: 0.0090 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 : C 90 C 366 REMARK 3 ORIGIN FOR THE GROUP (A): -27.0100 248.0870 -37.1300 REMARK 3 T TENSOR REMARK 3 T11: 0.0361 T22: 0.1728 REMARK 3 T33: 0.3822 T12: -0.0103 REMARK 3 T13: -0.0000 T23: 0.0780 REMARK 3 L TENSOR REMARK 3 L11: 2.5141 L22: 1.8416 REMARK 3 L33: 1.5763 L12: -1.5137 REMARK 3 L13: -0.7397 L23: 0.8171 REMARK 3 S TENSOR REMARK 3 S11: 0.1499 S12: 0.2563 S13: 0.0789 REMARK 3 S21: 0.0137 S22: -0.0596 S23: -0.0087 REMARK 3 S31: -0.0114 S32: -0.2650 S33: -0.0904 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 88 B 366 REMARK 3 ORIGIN FOR THE GROUP (A): -1.0470 204.5940 -16.5720 REMARK 3 T TENSOR REMARK 3 T11: 0.1355 T22: 0.0101 REMARK 3 T33: 0.2497 T12: 0.0320 REMARK 3 T13: 0.0287 T23: 0.0171 REMARK 3 L TENSOR REMARK 3 L11: 3.5742 L22: 1.1833 REMARK 3 L33: 0.5747 L12: -1.2282 REMARK 3 L13: 0.5006 L23: -0.0242 REMARK 3 S TENSOR REMARK 3 S11: 0.0078 S12: 0.0447 S13: -0.2043 REMARK 3 S21: 0.0205 S22: 0.0201 S23: 0.0354 REMARK 3 S31: -0.0190 S32: 0.0082 S33: -0.0279 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 4D82 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1290062470. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JAN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.872600 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21217 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 130.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.51000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4D81 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1,4 M SODIUM/POTASSIUM PHOSPHATE PH REMARK 280 5.6 (1.26 M SODIUM DIHYDROGEN PHOSPHATE MONOHYDRATE AND 0.14 M REMARK 280 DI-POTASSIUM HYDROGEN PHOSPHATE) AND 7.5% (V/V) GLYCEROL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 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 65.72667 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 32.86333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 49.29500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 16.43167 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 82.15833 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 GLY A 74 REMARK 465 VAL A 75 REMARK 465 PRO A 76 REMARK 465 GLU A 77 REMARK 465 GLY A 78 REMARK 465 GLY A 79 REMARK 465 GLU A 80 REMARK 465 GLU A 81 REMARK 465 THR A 82 REMARK 465 GLU A 83 REMARK 465 LYS A 84 REMARK 465 ALA A 85 REMARK 465 GLU A 86 REMARK 465 GLU A 87 REMARK 465 ASP A 88 REMARK 465 ILE A 89 REMARK 465 VAL A 90 REMARK 465 MET A 91 REMARK 465 LYS A 92 REMARK 465 GLU A 93 REMARK 465 LYS A 94 REMARK 465 PRO A 95 REMARK 465 LYS A 96 REMARK 465 SER A 213 REMARK 465 GLU A 214 REMARK 465 VAL A 215 REMARK 465 LYS A 367 REMARK 465 ALA A 368 REMARK 465 LEU A 369 REMARK 465 GLY B 74 REMARK 465 VAL B 75 REMARK 465 PRO B 76 REMARK 465 GLU B 77 REMARK 465 GLY B 78 REMARK 465 GLY B 79 REMARK 465 GLU B 80 REMARK 465 GLU B 81 REMARK 465 THR B 82 REMARK 465 GLU B 83 REMARK 465 LYS B 84 REMARK 465 ALA B 85 REMARK 465 GLU B 86 REMARK 465 GLU B 87 REMARK 465 TYR B 211 REMARK 465 THR B 212 REMARK 465 SER B 213 REMARK 465 GLU B 214 REMARK 465 VAL B 215 REMARK 465 LYS B 367 REMARK 465 ALA B 368 REMARK 465 LEU B 369 REMARK 465 GLY C 74 REMARK 465 VAL C 75 REMARK 465 PRO C 76 REMARK 465 GLU C 77 REMARK 465 GLY C 78 REMARK 465 GLY C 79 REMARK 465 GLU C 80 REMARK 465 GLU C 81 REMARK 465 THR C 82 REMARK 465 GLU C 83 REMARK 465 LYS C 84 REMARK 465 ALA C 85 REMARK 465 GLU C 86 REMARK 465 GLU C 87 REMARK 465 ASP C 88 REMARK 465 ILE C 89 REMARK 465 THR C 212 REMARK 465 SER C 213 REMARK 465 GLU C 214 REMARK 465 VAL C 215 REMARK 465 GLY C 216 REMARK 465 LYS C 367 REMARK 465 ALA C 368 REMARK 465 LEU C 369 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 SER C 210 OG REMARK 470 TYR C 211 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLU C 218 CG CD OE1 OE2 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 O TRP B 362 O LYS B 365 1.69 REMARK 500 O TRP A 362 O LYS A 365 1.76 REMARK 500 OH TYR A 304 O ARG A 347 2.06 REMARK 500 OH TYR C 304 O ARG C 347 2.08 REMARK 500 NH1 ARG A 319 OD1 ASP A 339 2.13 REMARK 500 NH1 ARG B 319 OD1 ASP B 339 2.15 REMARK 500 O HIS A 363 O LYS A 365 2.16 REMARK 500 C HIS A 363 O LYS A 365 2.19 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 LYS B 365 N - CA - C ANGL. DEV. = -19.9 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 211 -60.21 -132.06 REMARK 500 ARG A 333 152.49 -49.06 REMARK 500 ILE B 89 11.52 55.70 REMARK 500 ARG B 122 58.49 -140.04 REMARK 500 ARG B 333 154.32 -49.06 REMARK 500 SER B 350 -5.03 82.94 REMARK 500 ARG C 122 59.60 -141.11 REMARK 500 ASP C 234 129.66 -39.33 REMARK 500 ARG C 333 153.86 -48.76 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 LYS B 365 PHE B 366 34.13 REMARK 500 ARG C 252 LEU C 253 147.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP C 1367 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP B 1367 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ADP A 1367 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4D81 RELATED DB: PDB REMARK 900 METALLOSPHERA SEDULA VPS4 CRYSTAL STRUCTURE DBREF1 4D82 A 75 369 UNP A0A088E656_9CREN DBREF2 4D82 A A0A088E656 75 369 DBREF1 4D82 B 75 369 UNP A0A088E656_9CREN DBREF2 4D82 B A0A088E656 75 369 DBREF1 4D82 C 75 369 UNP A0A088E656_9CREN DBREF2 4D82 C A0A088E656 75 369 SEQADV 4D82 GLY A 74 UNP A0A088E65 EXPRESSION TAG SEQADV 4D82 GLY B 74 UNP A0A088E65 EXPRESSION TAG SEQADV 4D82 GLY C 74 UNP A0A088E65 EXPRESSION TAG SEQRES 1 A 296 GLY VAL PRO GLU GLY GLY GLU GLU THR GLU LYS ALA GLU SEQRES 2 A 296 GLU ASP ILE VAL MET LYS GLU LYS PRO LYS VAL THR LEU SEQRES 3 A 296 ASN GLU ILE VAL GLY LEU GLU ASP VAL LYS GLU ALA LEU SEQRES 4 A 296 LYS GLU ALA VAL VAL TYR PRO SER LYS ARG PRO ASP LEU SEQRES 5 A 296 PHE PRO LEU GLY TRP PRO ARG GLY ILE LEU LEU TYR GLY SEQRES 6 A 296 PRO PRO GLY CYS GLY LYS THR MET ILE ALA ALA ALA VAL SEQRES 7 A 296 ALA ASN GLU LEU ASP SER GLU PHE ILE HIS VAL ASP ALA SEQRES 8 A 296 ALA SER ILE MET SER LYS TRP LEU GLY GLU ALA GLU LYS SEQRES 9 A 296 ASN VAL ALA LYS ILE PHE LYS THR ALA ARG GLU LEU SER SEQRES 10 A 296 LYS LYS GLU ASN LYS PRO ALA ILE ILE PHE ILE ASP GLU SEQRES 11 A 296 LEU ASP ALA LEU LEU ALA SER TYR THR SER GLU VAL GLY SEQRES 12 A 296 GLY GLU ALA ARG VAL ARG ASN GLN PHE LEU LYS GLU MET SEQRES 13 A 296 ASP GLY LEU ALA ASP LYS ASN GLU ILE SER LYS VAL TYR SEQRES 14 A 296 VAL ILE GLY ALA THR ASN LYS PRO TRP ARG LEU ASP GLU SEQRES 15 A 296 PRO PHE LEU ARG ARG PHE GLN LYS ARG ILE TYR ILE THR SEQRES 16 A 296 LEU PRO ASP LYS ALA HIS ARG LEU GLU LEU LEU LYS HIS SEQRES 17 A 296 TYR SER SER LYS VAL LYS LEU ASP PRO ASN VAL ASN LEU SEQRES 18 A 296 GLU GLU LEU ALA GLU LEU THR ASP GLY TYR THR ALA SER SEQRES 19 A 296 ASP ILE ARG ASP ILE VAL GLN SER ALA HIS MET ARG VAL SEQRES 20 A 296 VAL LYS GLU MET PHE GLU LYS ASN LEU GLN GLU PRO ARG SEQRES 21 A 296 ALA ILE ASN MET ASP ASP PHE ARG GLU VAL LEU LYS VAL SEQRES 22 A 296 ARG LYS PRO SER VAL ASN GLN ASP MET LEU LYS ALA TYR SEQRES 23 A 296 ALA ALA TRP HIS GLU LYS PHE LYS ALA LEU SEQRES 1 B 296 GLY VAL PRO GLU GLY GLY GLU GLU THR GLU LYS ALA GLU SEQRES 2 B 296 GLU ASP ILE VAL MET LYS GLU LYS PRO LYS VAL THR LEU SEQRES 3 B 296 ASN GLU ILE VAL GLY LEU GLU ASP VAL LYS GLU ALA LEU SEQRES 4 B 296 LYS GLU ALA VAL VAL TYR PRO SER LYS ARG PRO ASP LEU SEQRES 5 B 296 PHE PRO LEU GLY TRP PRO ARG GLY ILE LEU LEU TYR GLY SEQRES 6 B 296 PRO PRO GLY CYS GLY LYS THR MET ILE ALA ALA ALA VAL SEQRES 7 B 296 ALA ASN GLU LEU ASP SER GLU PHE ILE HIS VAL ASP ALA SEQRES 8 B 296 ALA SER ILE MET SER LYS TRP LEU GLY GLU ALA GLU LYS SEQRES 9 B 296 ASN VAL ALA LYS ILE PHE LYS THR ALA ARG GLU LEU SER SEQRES 10 B 296 LYS LYS GLU ASN LYS PRO ALA ILE ILE PHE ILE ASP GLU SEQRES 11 B 296 LEU ASP ALA LEU LEU ALA SER TYR THR SER GLU VAL GLY SEQRES 12 B 296 GLY GLU ALA ARG VAL ARG ASN GLN PHE LEU LYS GLU MET SEQRES 13 B 296 ASP GLY LEU ALA ASP LYS ASN GLU ILE SER LYS VAL TYR SEQRES 14 B 296 VAL ILE GLY ALA THR ASN LYS PRO TRP ARG LEU ASP GLU SEQRES 15 B 296 PRO PHE LEU ARG ARG PHE GLN LYS ARG ILE TYR ILE THR SEQRES 16 B 296 LEU PRO ASP LYS ALA HIS ARG LEU GLU LEU LEU LYS HIS SEQRES 17 B 296 TYR SER SER LYS VAL LYS LEU ASP PRO ASN VAL ASN LEU SEQRES 18 B 296 GLU GLU LEU ALA GLU LEU THR ASP GLY TYR THR ALA SER SEQRES 19 B 296 ASP ILE ARG ASP ILE VAL GLN SER ALA HIS MET ARG VAL SEQRES 20 B 296 VAL LYS GLU MET PHE GLU LYS ASN LEU GLN GLU PRO ARG SEQRES 21 B 296 ALA ILE ASN MET ASP ASP PHE ARG GLU VAL LEU LYS VAL SEQRES 22 B 296 ARG LYS PRO SER VAL ASN GLN ASP MET LEU LYS ALA TYR SEQRES 23 B 296 ALA ALA TRP HIS GLU LYS PHE LYS ALA LEU SEQRES 1 C 296 GLY VAL PRO GLU GLY GLY GLU GLU THR GLU LYS ALA GLU SEQRES 2 C 296 GLU ASP ILE VAL MET LYS GLU LYS PRO LYS VAL THR LEU SEQRES 3 C 296 ASN GLU ILE VAL GLY LEU GLU ASP VAL LYS GLU ALA LEU SEQRES 4 C 296 LYS GLU ALA VAL VAL TYR PRO SER LYS ARG PRO ASP LEU SEQRES 5 C 296 PHE PRO LEU GLY TRP PRO ARG GLY ILE LEU LEU TYR GLY SEQRES 6 C 296 PRO PRO GLY CYS GLY LYS THR MET ILE ALA ALA ALA VAL SEQRES 7 C 296 ALA ASN GLU LEU ASP SER GLU PHE ILE HIS VAL ASP ALA SEQRES 8 C 296 ALA SER ILE MET SER LYS TRP LEU GLY GLU ALA GLU LYS SEQRES 9 C 296 ASN VAL ALA LYS ILE PHE LYS THR ALA ARG GLU LEU SER SEQRES 10 C 296 LYS LYS GLU ASN LYS PRO ALA ILE ILE PHE ILE ASP GLU SEQRES 11 C 296 LEU ASP ALA LEU LEU ALA SER TYR THR SER GLU VAL GLY SEQRES 12 C 296 GLY GLU ALA ARG VAL ARG ASN GLN PHE LEU LYS GLU MET SEQRES 13 C 296 ASP GLY LEU ALA ASP LYS ASN GLU ILE SER LYS VAL TYR SEQRES 14 C 296 VAL ILE GLY ALA THR ASN LYS PRO TRP ARG LEU ASP GLU SEQRES 15 C 296 PRO PHE LEU ARG ARG PHE GLN LYS ARG ILE TYR ILE THR SEQRES 16 C 296 LEU PRO ASP LYS ALA HIS ARG LEU GLU LEU LEU LYS HIS SEQRES 17 C 296 TYR SER SER LYS VAL LYS LEU ASP PRO ASN VAL ASN LEU SEQRES 18 C 296 GLU GLU LEU ALA GLU LEU THR ASP GLY TYR THR ALA SER SEQRES 19 C 296 ASP ILE ARG ASP ILE VAL GLN SER ALA HIS MET ARG VAL SEQRES 20 C 296 VAL LYS GLU MET PHE GLU LYS ASN LEU GLN GLU PRO ARG SEQRES 21 C 296 ALA ILE ASN MET ASP ASP PHE ARG GLU VAL LEU LYS VAL SEQRES 22 C 296 ARG LYS PRO SER VAL ASN GLN ASP MET LEU LYS ALA TYR SEQRES 23 C 296 ALA ALA TRP HIS GLU LYS PHE LYS ALA LEU HET ADP A1367 27 HET ADP B1367 27 HET ADP C1367 27 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 4 ADP 3(C10 H15 N5 O10 P2) FORMUL 7 HOH *12(H2 O) HELIX 1 1 THR A 98 ILE A 102 5 5 HELIX 2 2 LEU A 105 VAL A 116 1 12 HELIX 3 3 VAL A 116 ARG A 122 1 7 HELIX 4 4 PRO A 123 PHE A 126 5 4 HELIX 5 5 GLY A 143 ASP A 156 1 14 HELIX 6 6 ALA A 164 MET A 168 1 5 HELIX 7 7 GLY A 173 ASN A 194 1 22 HELIX 8 8 GLU A 203 ALA A 209 5 7 HELIX 9 9 GLY A 217 GLY A 231 1 15 HELIX 10 10 LYS A 249 LEU A 253 5 5 HELIX 11 11 ASP A 254 ARG A 260 1 7 HELIX 12 12 ASP A 271 SER A 284 1 14 HELIX 13 13 ASN A 293 THR A 301 1 9 HELIX 14 14 THR A 305 LYS A 327 1 23 HELIX 15 15 ASN A 336 ARG A 347 1 12 HELIX 16 16 ASN A 352 LYS A 365 1 14 HELIX 17 17 THR B 98 ILE B 102 5 5 HELIX 18 18 LEU B 105 VAL B 116 1 12 HELIX 19 19 VAL B 116 ARG B 122 1 7 HELIX 20 20 PRO B 123 PHE B 126 5 4 HELIX 21 21 GLY B 143 ASP B 156 1 14 HELIX 22 22 ALA B 164 MET B 168 1 5 HELIX 23 23 GLY B 173 ASN B 194 1 22 HELIX 24 24 GLU B 203 ALA B 209 5 7 HELIX 25 25 GLY B 216 GLY B 231 1 16 HELIX 26 26 LYS B 249 LEU B 253 5 5 HELIX 27 27 ASP B 254 ARG B 260 1 7 HELIX 28 28 ASP B 271 SER B 284 1 14 HELIX 29 29 ASN B 293 THR B 301 1 9 HELIX 30 30 THR B 305 LYS B 327 1 23 HELIX 31 31 ASN B 336 ARG B 347 1 12 HELIX 32 32 ASN B 352 LYS B 365 1 14 HELIX 33 33 THR C 98 ILE C 102 5 5 HELIX 34 34 LEU C 105 VAL C 116 1 12 HELIX 35 35 VAL C 116 ARG C 122 1 7 HELIX 36 36 PRO C 123 PHE C 126 5 4 HELIX 37 37 GLY C 143 ASP C 156 1 14 HELIX 38 38 ALA C 164 MET C 168 1 5 HELIX 39 39 TRP C 171 ASN C 194 1 24 HELIX 40 40 GLU C 203 ALA C 209 5 7 HELIX 41 41 GLY C 217 GLY C 231 1 15 HELIX 42 42 ASP C 254 ARG C 260 1 7 HELIX 43 43 ASP C 271 SER C 284 1 14 HELIX 44 44 ASN C 293 THR C 301 1 9 HELIX 45 45 THR C 305 LYS C 327 1 23 HELIX 46 46 ASN C 336 ARG C 347 1 12 HELIX 47 47 ASN C 352 PHE C 366 1 15 SHEET 1 AA 5 GLU A 158 ASP A 163 0 SHEET 2 AA 5 ALA A 197 ASP A 202 1 O ILE A 198 N ILE A 160 SHEET 3 AA 5 VAL A 241 THR A 247 1 O TYR A 242 N ILE A 199 SHEET 4 AA 5 GLY A 133 TYR A 137 1 O ILE A 134 N GLY A 245 SHEET 5 AA 5 LYS A 263 TYR A 266 1 O LYS A 263 N LEU A 135 SHEET 1 BA 6 LYS B 92 GLU B 93 0 SHEET 2 BA 6 GLU B 158 ASP B 163 -1 O PHE B 159 N GLU B 93 SHEET 3 BA 6 ALA B 197 ASP B 202 1 O ILE B 198 N ILE B 160 SHEET 4 BA 6 VAL B 241 THR B 247 1 O TYR B 242 N ILE B 199 SHEET 5 BA 6 GLY B 133 TYR B 137 1 O ILE B 134 N GLY B 245 SHEET 6 BA 6 LYS B 263 TYR B 266 1 O LYS B 263 N LEU B 135 SHEET 1 CA 5 GLU C 158 ASP C 163 0 SHEET 2 CA 5 ALA C 197 ASP C 202 1 O ILE C 198 N ILE C 160 SHEET 3 CA 5 VAL C 241 THR C 247 1 O TYR C 242 N ILE C 199 SHEET 4 CA 5 GLY C 133 TYR C 137 1 O ILE C 134 N GLY C 245 SHEET 5 CA 5 LYS C 263 TYR C 266 1 O LYS C 263 N LEU C 135 CISPEP 1 GLY A 216 GLY A 217 0 4.30 CISPEP 2 LYS A 365 PHE A 366 0 3.89 CISPEP 3 VAL C 90 MET C 91 0 -7.32 SITE 1 AC1 15 GLU C 101 ILE C 102 VAL C 103 PRO C 139 SITE 2 AC1 15 PRO C 140 GLY C 141 CYS C 142 GLY C 143 SITE 3 AC1 15 LYS C 144 THR C 145 MET C 146 TYR C 282 SITE 4 AC1 15 ALA C 306 SER C 307 ARG C 310 SITE 1 AC2 13 ILE B 102 VAL B 103 LEU B 105 GLY B 141 SITE 2 AC2 13 CYS B 142 GLY B 143 LYS B 144 THR B 145 SITE 3 AC2 13 MET B 146 TYR B 282 ALA B 306 SER B 307 SITE 4 AC2 13 ARG B 310 SITE 1 AC3 14 ILE A 102 VAL A 103 LEU A 105 GLY A 141 SITE 2 AC3 14 CYS A 142 GLY A 143 LYS A 144 THR A 145 SITE 3 AC3 14 MET A 146 TYR A 282 ALA A 306 SER A 307 SITE 4 AC3 14 ARG A 310 HOH A2005 CRYST1 151.187 151.187 98.590 90.00 90.00 120.00 P 65 18 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 0.006614 0.003819 0.000000 0.00000 SCALE2 0.000000 0.007638 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010143 0.00000