HEADER PROTEIN TRANSPORT 23-JUL-07 2QP9
TITLE CRYSTAL STRUCTURE OF S.CEREVISIAE VPS4
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4;
COMPND 3 CHAIN: X;
COMPND 4 FRAGMENT: RESIDUES: 83-437;
COMPND 5 SYNONYM: PROTEIN END13, DOA4-INDEPENDENT DEGRADATION PROTEIN 6,
COMPND 6 VACUOLAR PROTEIN-TARGETING PROTEIN 10;
COMPND 7 ENGINEERED: YES;
COMPND 8 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE;
SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST;
SOURCE 4 ORGANISM_TAXID: 4932;
SOURCE 5 GENE: VPS4, CSC1, DID6, END13, GRD13, VPL4, VPT10;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PSJ3
KEYWDS ATPASE DOMAIN, BETA DOMAIN, C-TERMINAL HELIX, ATP-BINDING, ENDOSOME,
KEYWDS 2 NUCLEOTIDE-BINDING, PROTEIN TRANSPORT, TRANSPORT, VACUOLE
EXPDTA X-RAY DIFFRACTION
AUTHOR J.XIAO,Z.XU
REVDAT 7 21-FEB-24 2QP9 1 REMARK
REVDAT 6 20-OCT-21 2QP9 1 REMARK SEQADV LINK
REVDAT 5 25-OCT-17 2QP9 1 REMARK
REVDAT 4 13-JUL-11 2QP9 1 VERSN
REVDAT 3 24-FEB-09 2QP9 1 VERSN
REVDAT 2 29-JAN-08 2QP9 1 JRNL
REVDAT 1 09-OCT-07 2QP9 0
JRNL AUTH J.XIAO,H.XIA,K.YOSHINO-KOH,J.ZHOU,Z.XU
JRNL TITL STRUCTURAL CHARACTERIZATION OF THE ATPASE REACTION CYCLE OF
JRNL TITL 2 ENDOSOMAL AAA PROTEIN VPS4.
JRNL REF J.MOL.BIOL. V. 374 655 2007
JRNL REFN ISSN 0022-2836
JRNL PMID 17949747
JRNL DOI 10.1016/J.JMB.2007.09.067
REMARK 2
REMARK 2 RESOLUTION. 2.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : REFMAC
REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER,
REMARK 3 : NICHOLLS,WINN,LONG,VAGIN
REMARK 3
REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1
REMARK 3 NUMBER OF REFLECTIONS : 10792
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) : 0.260
REMARK 3 R VALUE (WORKING SET) : 0.258
REMARK 3 FREE R VALUE : 0.288
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100
REMARK 3 FREE R VALUE TEST SET COUNT : 576
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : 20
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.90
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.97
REMARK 3 REFLECTION IN BIN (WORKING SET) : 621
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.64
REMARK 3 BIN R VALUE (WORKING SET) : 0.3180
REMARK 3 BIN FREE R VALUE SET COUNT : 28
REMARK 3 BIN FREE R VALUE : 0.4200
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 2067
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 7
REMARK 3 SOLVENT ATOMS : 0
REMARK 3
REMARK 3 B VALUES.
REMARK 3 B VALUE TYPE : LIKELY RESIDUAL
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 58.58
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 2.69000
REMARK 3 B22 (A**2) : 2.69000
REMARK 3 B33 (A**2) : -4.03000
REMARK 3 B12 (A**2) : 1.34000
REMARK 3 B13 (A**2) : 0.00000
REMARK 3 B23 (A**2) : 0.00000
REMARK 3
REMARK 3 ESTIMATED OVERALL COORDINATE ERROR.
REMARK 3 ESU BASED ON R VALUE (A): 0.707
REMARK 3 ESU BASED ON FREE R VALUE (A): 0.379
REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.333
REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 36.159
REMARK 3
REMARK 3 CORRELATION COEFFICIENTS.
REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.917
REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT
REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2106 ; 0.009 ; 0.022
REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2868 ; 1.137 ; 1.969
REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL
REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 283 ; 5.045 ; 5.000
REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 75 ;36.004 ;24.400
REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 306 ;21.480 ;15.000
REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;20.824 ;15.000
REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 341 ; 0.071 ; 0.200
REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1580 ; 0.003 ; 0.020
REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 954 ; 0.214 ; 0.200
REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL
REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1454 ; 0.303 ; 0.200
REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 53 ; 0.105 ; 0.200
REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL
REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.200 ; 0.200
REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 29 ; 0.372 ; 0.200
REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 3 ; 0.131 ; 0.200
REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL
REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): 1 ; 0.073 ; 0.200
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): 1462 ; 0.515 ; 1.500
REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2244 ; 0.945 ; 2.000
REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 726 ; 1.052 ; 3.000
REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 624 ; 1.645 ; 4.500
REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT
REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL
REMARK 3
REMARK 3 NCS RESTRAINTS STATISTICS
REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
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 : X 129 X 433
REMARK 3 ORIGIN FOR THE GROUP (A): -40.8730 49.5390 17.0750
REMARK 3 T TENSOR
REMARK 3 T11: 0.2791 T22: 0.0063
REMARK 3 T33: 0.2235 T12: -0.1487
REMARK 3 T13: -0.0378 T23: -0.1219
REMARK 3 L TENSOR
REMARK 3 L11: 2.4044 L22: 2.5212
REMARK 3 L33: 4.2527 L12: 1.3263
REMARK 3 L13: -1.2691 L23: -1.3443
REMARK 3 S TENSOR
REMARK 3 S11: -0.1985 S12: 0.1998 S13: 0.0442
REMARK 3 S21: -0.3556 S22: 0.1421 S23: 0.1105
REMARK 3 S31: 0.5084 S32: -0.3062 S33: 0.0564
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : MASK
REMARK 3 PARAMETERS FOR MASK CALCULATION
REMARK 3 VDW PROBE RADIUS : 1.40
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 2QP9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JUL-07.
REMARK 100 THE DEPOSITION ID IS D_1000043883.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL; NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL; NULL
REMARK 200 PH : 6.5
REMARK 200 NUMBER OF CRYSTALS USED : 2
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y; Y
REMARK 200 RADIATION SOURCE : APS; APS
REMARK 200 BEAMLINE : 23-ID-D; 23-ID-D
REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M
REMARK 200 WAVELENGTH OR RANGE (A) : NULL; NULL
REMARK 200 MONOCHROMATOR : NULL; NULL
REMARK 200 OPTICS : NULL; NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD; CCD
REMARK 200 DETECTOR MANUFACTURER : NULL; NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12599
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1
REMARK 200 DATA REDUNDANCY : 13.20
REMARK 200 R MERGE (I) : 0.06300
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 37.5000
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 (%) : 99.2
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : 0.60600
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD
REMARK 200 SOFTWARE USED: SHARP
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 62.63
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.29
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, CDSO4, PH 6.5,
REMARK 280 TEMPERATURE 293K, VAPOR DIFFUSION
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 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 -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 7555 Y,X,-Z+2/3
REMARK 290 8555 X-Y,-Y,-Z
REMARK 290 9555 -X,-X+Y,-Z+1/3
REMARK 290 10555 -Y,-X,-Z+1/6
REMARK 290 11555 -X+Y,Y,-Z+1/2
REMARK 290 12555 X,X-Y,-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 157.37400
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 78.68700
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 118.03050
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 39.34350
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 196.71750
REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 157.37400
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 78.68700
REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 39.34350
REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 118.03050
REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 196.71750
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: MONOMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 APPLY THE FOLLOWING TO CHAINS: X
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 LYS X 83
REMARK 465 LYS X 84
REMARK 465 SER X 85
REMARK 465 PRO X 86
REMARK 465 SER X 87
REMARK 465 ALA X 88
REMARK 465 GLY X 89
REMARK 465 SER X 90
REMARK 465 GLY X 91
REMARK 465 SER X 92
REMARK 465 ASN X 93
REMARK 465 GLY X 94
REMARK 465 GLY X 95
REMARK 465 ASN X 96
REMARK 465 LYS X 97
REMARK 465 LYS X 98
REMARK 465 ILE X 99
REMARK 465 SER X 100
REMARK 465 GLN X 101
REMARK 465 GLU X 102
REMARK 465 GLU X 103
REMARK 465 GLY X 104
REMARK 465 GLU X 105
REMARK 465 ASP X 106
REMARK 465 ASN X 107
REMARK 465 GLY X 108
REMARK 465 GLY X 109
REMARK 465 GLU X 110
REMARK 465 ASP X 111
REMARK 465 ASN X 112
REMARK 465 LYS X 113
REMARK 465 LYS X 114
REMARK 465 LEU X 115
REMARK 465 ARG X 116
REMARK 465 GLY X 117
REMARK 465 ALA X 118
REMARK 465 LEU X 119
REMARK 465 SER X 120
REMARK 465 SER X 121
REMARK 465 ALA X 122
REMARK 465 ILE X 123
REMARK 465 LEU X 124
REMARK 465 SER X 125
REMARK 465 GLU X 126
REMARK 465 LYS X 127
REMARK 465 PRO X 128
REMARK 465 MET X 207
REMARK 465 GLY X 208
REMARK 465 GLU X 209
REMARK 465 THR X 240
REMARK 465 ARG X 241
REMARK 465 GLY X 242
REMARK 465 GLU X 243
REMARK 465 GLY X 244
REMARK 465 GLU X 245
REMARK 465 ASN X 265
REMARK 465 ASP X 266
REMARK 465 SER X 267
REMARK 465 GLU X 366
REMARK 465 ASP X 367
REMARK 465 ASP X 368
REMARK 465 GLU X 369
REMARK 465 THR X 370
REMARK 465 GLN X 434
REMARK 465 GLU X 435
REMARK 465 GLY X 436
REMARK 465 ASN X 437
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 ASN X 129 CG OD1 ND2
REMARK 470 VAL X 130 CG1 CG2
REMARK 470 LYS X 131 CG CD CE NZ
REMARK 470 GLU X 133 CG CD OE1 OE2
REMARK 470 GLU X 139 CG CD OE1 OE2
REMARK 470 LYS X 160 CG CD CE NZ
REMARK 470 ASN X 162 CG OD1 ND2
REMARK 470 LYS X 164 CG CD CE NZ
REMARK 470 THR X 166 OG1 CG2
REMARK 470 ASN X 191 CG OD1 ND2
REMARK 470 VAL X 203 CG1 CG2
REMARK 470 SER X 204 OG
REMARK 470 LYS X 205 CG CD CE NZ
REMARK 470 TRP X 206 CG CD1 CD2 NE1 CE2 CE3 CZ2
REMARK 470 TRP X 206 CZ3 CH2
REMARK 470 SER X 210 OG
REMARK 470 GLU X 211 CG CD OE1 OE2
REMARK 470 LYS X 212 CG CD CE NZ
REMARK 470 SER X 246 OG
REMARK 470 GLU X 247 CG CD OE1 OE2
REMARK 470 SER X 249 OG
REMARK 470 ARG X 250 CG CD NE CZ NH1 NH2
REMARK 470 ARG X 251 CG CD NE CZ NH1 NH2
REMARK 470 VAL X 263 CG1 CG2
REMARK 470 GLN X 268 CG CD OE1 NE2
REMARK 470 SER X 284 OG
REMARK 470 SER X 317 OG
REMARK 470 VAL X 318 CG1 CG2
REMARK 470 THR X 320 OG1 CG2
REMARK 470 LYS X 321 CG CD CE NZ
REMARK 470 GLU X 322 CG CD OE1 OE2
REMARK 470 ASP X 323 CG OD1 OD2
REMARK 470 ARG X 325 CG CD NE CZ NH1 NH2
REMARK 470 LYS X 344 CG CD CE NZ
REMARK 470 ARG X 352 CG CD NE CZ NH1 NH2
REMARK 470 LYS X 353 CG CD CE NZ
REMARK 470 SER X 356 OG
REMARK 470 LYS X 361 CG CD CE NZ
REMARK 470 ASP X 362 CG OD1 OD2
REMARK 470 VAL X 363 CG1 CG2
REMARK 470 SER X 364 OG
REMARK 470 THR X 365 OG1 CG2
REMARK 470 THR X 374 OG1 CG2
REMARK 470 SER X 387 OG
REMARK 470 LYS X 397 CG CD CE NZ
REMARK 470 THR X 402 OG1 CG2
REMARK 470 ILE X 403 CG1 CG2 CD1
REMARK 470 LYS X 404 CG CD CE NZ
REMARK 470 LYS X 408 CG CD CE NZ
REMARK 470 SER X 412 OG
REMARK 470 THR X 413 OG1 CG2
REMARK 470 ARG X 414 CG CD NE CZ NH1 NH2
REMARK 470 THR X 416 OG1 CG2
REMARK 470 VAL X 417 CG1 CG2
REMARK 470 ASN X 418 CG OD1 ND2
REMARK 470 GLU X 419 CG CD OE1 OE2
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 PRO X 378 C - N - CA ANGL. DEV. = 9.3 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: TORSION ANGLES
REMARK 500
REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS:
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2)
REMARK 500
REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI-
REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400
REMARK 500
REMARK 500 M RES CSSEQI PSI PHI
REMARK 500 VAL X 149 -61.80 -103.49
REMARK 500 ASN X 162 0.35 -69.96
REMARK 500 THR X 166 -160.42 -71.63
REMARK 500 SER X 204 46.25 -95.89
REMARK 500 LYS X 205 129.30 -175.36
REMARK 500 GLU X 247 -103.90 62.53
REMARK 500 VAL X 263 -140.88 -84.79
REMARK 500 PRO X 316 104.11 -47.28
REMARK 500 SER X 376 -152.83 -151.34
REMARK 500 PRO X 378 -55.14 -13.08
REMARK 500 ASP X 380 -96.64 -70.22
REMARK 500 LYS X 397 91.51 -67.88
REMARK 500 GLU X 398 98.71 -59.29
REMARK 500 SER X 412 -102.91 -69.26
REMARK 500 THR X 413 113.81 -38.02
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 CD X 603 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU X 189 OE2
REMARK 620 2 ASP X 390 OD2 115.4
REMARK 620 3 ASP X 390 OD1 94.8 48.9
REMARK 620 N 1 2
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 CD X 601 CD
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 GLU X 392 OE1
REMARK 620 2 GLU X 392 OE1 74.8
REMARK 620 3 GLU X 392 OE2 122.0 49.3
REMARK 620 4 ASP X 394 OD1 126.9 142.5 97.1
REMARK 620 5 ASP X 394 OD2 103.5 168.3 134.4 47.4
REMARK 620 N 1 2 3 4
REMARK 800
REMARK 800 SITE
REMARK 800 SITE_IDENTIFIER: AC1
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD X 601
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CD X 603
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 X 701
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2QPA RELATED DB: PDB
REMARK 900 STRUCTURE OF S.CEREVISIAE VPS4 IN THE PRESENCE OF ADP
DBREF 2QP9 X 83 437 UNP P52917 VPS4_YEAST 83 437
SEQADV 2QP9 GLN X 233 UNP P52917 GLU 233 ENGINEERED MUTATION
SEQADV 2QP9 SER X 317 UNP P52917 CYS 317 ENGINEERED MUTATION
SEQADV 2QP9 SER X 376 UNP P52917 CYS 376 ENGINEERED MUTATION
SEQRES 1 X 355 LYS LYS SER PRO SER ALA GLY SER GLY SER ASN GLY GLY
SEQRES 2 X 355 ASN LYS LYS ILE SER GLN GLU GLU GLY GLU ASP ASN GLY
SEQRES 3 X 355 GLY GLU ASP ASN LYS LYS LEU ARG GLY ALA LEU SER SER
SEQRES 4 X 355 ALA ILE LEU SER GLU LYS PRO ASN VAL LYS TRP GLU ASP
SEQRES 5 X 355 VAL ALA GLY LEU GLU GLY ALA LYS GLU ALA LEU LYS GLU
SEQRES 6 X 355 ALA VAL ILE LEU PRO VAL LYS PHE PRO HIS LEU PHE LYS
SEQRES 7 X 355 GLY ASN ARG LYS PRO THR SER GLY ILE LEU LEU TYR GLY
SEQRES 8 X 355 PRO PRO GLY THR GLY LYS SER TYR LEU ALA LYS ALA VAL
SEQRES 9 X 355 ALA THR GLU ALA ASN SER THR PHE PHE SER VAL SER SER
SEQRES 10 X 355 SER ASP LEU VAL SER LYS TRP MET GLY GLU SER GLU LYS
SEQRES 11 X 355 LEU VAL LYS GLN LEU PHE ALA MET ALA ARG GLU ASN LYS
SEQRES 12 X 355 PRO SER ILE ILE PHE ILE ASP GLN VAL ASP ALA LEU THR
SEQRES 13 X 355 GLY THR ARG GLY GLU GLY GLU SER GLU ALA SER ARG ARG
SEQRES 14 X 355 ILE LYS THR GLU LEU LEU VAL GLN MET ASN GLY VAL GLY
SEQRES 15 X 355 ASN ASP SER GLN GLY VAL LEU VAL LEU GLY ALA THR ASN
SEQRES 16 X 355 ILE PRO TRP GLN LEU ASP SER ALA ILE ARG ARG ARG PHE
SEQRES 17 X 355 GLU ARG ARG ILE TYR ILE PRO LEU PRO ASP LEU ALA ALA
SEQRES 18 X 355 ARG THR THR MET PHE GLU ILE ASN VAL GLY ASP THR PRO
SEQRES 19 X 355 SER VAL LEU THR LYS GLU ASP TYR ARG THR LEU GLY ALA
SEQRES 20 X 355 MET THR GLU GLY TYR SER GLY SER ASP ILE ALA VAL VAL
SEQRES 21 X 355 VAL LYS ASP ALA LEU MET GLN PRO ILE ARG LYS ILE GLN
SEQRES 22 X 355 SER ALA THR HIS PHE LYS ASP VAL SER THR GLU ASP ASP
SEQRES 23 X 355 GLU THR ARG LYS LEU THR PRO SER SER PRO GLY ASP ASP
SEQRES 24 X 355 GLY ALA ILE GLU MET SER TRP THR ASP ILE GLU ALA ASP
SEQRES 25 X 355 GLU LEU LYS GLU PRO ASP LEU THR ILE LYS ASP PHE LEU
SEQRES 26 X 355 LYS ALA ILE LYS SER THR ARG PRO THR VAL ASN GLU ASP
SEQRES 27 X 355 ASP LEU LEU LYS GLN GLU GLN PHE THR ARG ASP PHE GLY
SEQRES 28 X 355 GLN GLU GLY ASN
HET CD X 601 1
HET CD X 603 1
HET SO4 X 701 5
HETNAM CD CADMIUM ION
HETNAM SO4 SULFATE ION
FORMUL 2 CD 2(CD 2+)
FORMUL 4 SO4 O4 S 2-
HELIX 1 1 LYS X 131 VAL X 135 5 5
HELIX 2 2 GLY X 137 GLU X 139 5 3
HELIX 3 3 GLY X 140 VAL X 149 1 10
HELIX 4 4 VAL X 149 PHE X 155 1 7
HELIX 5 5 PRO X 156 LYS X 160 5 5
HELIX 6 6 GLY X 178 ASN X 191 1 14
HELIX 7 7 SER X 199 SER X 204 1 6
HELIX 8 8 SER X 210 ASN X 224 1 15
HELIX 9 9 GLN X 233 THR X 238 5 6
HELIX 10 10 GLU X 247 VAL X 263 1 17
HELIX 11 11 ILE X 278 LEU X 282 5 5
HELIX 12 12 ASP X 283 ARG X 289 1 7
HELIX 13 13 ASP X 300 GLY X 313 1 14
HELIX 14 14 THR X 320 THR X 331 1 12
HELIX 15 15 SER X 335 ALA X 357 1 23
HELIX 16 16 SER X 387 ILE X 391 5 5
HELIX 17 17 GLU X 392 LEU X 396 5 5
HELIX 18 18 THR X 402 THR X 413 1 12
HELIX 19 19 ASN X 418 PHE X 432 1 15
SHEET 1 A 5 THR X 193 SER X 198 0
SHEET 2 A 5 SER X 227 ASP X 232 1 O ASP X 232 N VAL X 197
SHEET 3 A 5 VAL X 270 THR X 276 1 O LEU X 273 N ILE X 229
SHEET 4 A 5 ILE X 169 TYR X 172 1 N LEU X 171 O GLY X 274
SHEET 5 A 5 ARG X 292 TYR X 295 1 O ILE X 294 N LEU X 170
SHEET 1 B 3 LEU X 373 SER X 376 0
SHEET 2 B 3 HIS X 359 ASP X 362 -1 N HIS X 359 O SER X 376
SHEET 3 B 3 ALA X 383 GLU X 385 -1 O ILE X 384 N PHE X 360
LINK OE2 GLU X 189 CD CD X 603 1555 1555 2.00
LINK OD2 ASP X 390 CD CD X 603 6664 1555 2.83
LINK OD1 ASP X 390 CD CD X 603 6664 1555 2.41
LINK OE1 GLU X 392 CD CD X 601 1555 1555 2.00
LINK OE1 GLU X 392 CD CD X 601 11455 1555 2.85
LINK OE2 GLU X 392 CD CD X 601 11455 1555 2.12
LINK OD1 ASP X 394 CD CD X 601 1555 1555 2.23
LINK OD2 ASP X 394 CD CD X 601 1555 1555 2.96
CISPEP 1 LYS X 225 PRO X 226 0 -5.12
SITE 1 AC1 2 GLU X 392 ASP X 394
SITE 1 AC2 2 GLU X 189 ASP X 390
SITE 1 AC3 5 GLY X 176 THR X 177 GLY X 178 LYS X 179
SITE 2 AC3 5 ASN X 277
CRYST1 86.553 86.553 236.061 90.00 90.00 120.00 P 65 2 2 12
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 0.011554 0.006670 0.000000 0.00000
SCALE2 0.000000 0.013341 0.000000 0.00000
SCALE3 0.000000 0.000000 0.004236 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
