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 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 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