HEADER PROTEIN TRANSPORT 17-OCT-07 2RKO TITLE CRYSTAL STRUCTURE OF THE VPS4P-DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: AAA-ATPASE DOMAIN, UNP RESIDUES 124-437; COMPND 5 SYNONYM: VPS4P, PROTEIN END13, DOA4-INDEPENDENT DEGRADATION PROTEIN COMPND 6 6, VACUOLAR PROTEIN-TARGETING PROTEIN 10; COMPND 7 ENGINEERED: 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: VPS4P; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET20B(+) DERIVATIVE KEYWDS AAA-ATPASE DOMAIN, ATP-BINDING, ENDOSOME, MEMBRANE, NUCLEOTIDE- KEYWDS 2 BINDING, PHOSPHORYLATION, PROTEIN TRANSPORT, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.HARTMANN,M.G.GRUETTER REVDAT 5 25-OCT-23 2RKO 1 SEQADV REVDAT 4 13-JUL-11 2RKO 1 VERSN REVDAT 3 24-FEB-09 2RKO 1 VERSN REVDAT 2 25-MAR-08 2RKO 1 JRNL REMARK REVDAT 1 26-FEB-08 2RKO 0 JRNL AUTH C.HARTMANN,M.CHAMI,U.ZACHARIAE,B.L.DE GROOT,A.ENGEL, JRNL AUTH 2 M.G.GRUETTER JRNL TITL VACUOLAR PROTEIN SORTING: TWO DIFFERENT FUNCTIONAL STATES OF JRNL TITL 2 THE AAA-ATPASE VPS4P JRNL REF J.MOL.BIOL. V. 377 352 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18272179 JRNL DOI 10.1016/J.JMB.2008.01.010 REMARK 2 REMARK 2 RESOLUTION. 3.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 3.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 9386 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) : 0.270 REMARK 3 R VALUE (WORKING SET) : 0.268 REMARK 3 FREE R VALUE : 0.298 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 471 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) : 3.35 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 630 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3240 REMARK 3 BIN FREE R VALUE SET COUNT : 34 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2173 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 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) : 88.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.29000 REMARK 3 B22 (A**2) : 2.29000 REMARK 3 B33 (A**2) : -3.44000 REMARK 3 B12 (A**2) : 1.15000 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): 0.993 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.463 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.388 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 53.402 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.913 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1869 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1173 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2539 ; 1.107 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 2805 ; 0.830 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 273 ; 5.129 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 51 ;34.438 ;25.294 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 227 ;18.419 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ; 9.295 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 288 ; 0.050 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2207 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 356 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 611 ; 0.260 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1302 ; 0.208 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1045 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 949 ; 0.090 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 77 ; 0.164 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 2 ; 0.097 ; 0.200 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): 6 ; 0.176 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 12 ; 0.240 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.112 ; 0.200 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): 1675 ; 2.767 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 560 ; 0.502 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2067 ; 3.813 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 612 ; 5.690 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 472 ; 7.976 ; 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 : A 129 A 433 REMARK 3 ORIGIN FOR THE GROUP (A): 29.5343 20.0701 9.4270 REMARK 3 T TENSOR REMARK 3 T11: -0.2001 T22: -0.3411 REMARK 3 T33: -0.4068 T12: -0.1310 REMARK 3 T13: -0.1284 T23: -0.0423 REMARK 3 L TENSOR REMARK 3 L11: 1.4178 L22: 9.3412 REMARK 3 L33: 0.5794 L12: -0.3439 REMARK 3 L13: -0.2649 L23: -0.0197 REMARK 3 S TENSOR REMARK 3 S11: -0.1375 S12: -0.3605 S13: 0.3196 REMARK 3 S21: 0.6917 S22: -0.1432 S23: 0.2121 REMARK 3 S31: 0.1474 S32: -0.1838 S33: 0.2807 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 2RKO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000044975. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9446 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.350 REMARK 200 RESOLUTION RANGE LOW (A) : 94.498 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 0.05700 REMARK 200 FOR THE DATA SET : 22.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : 0.44000 REMARK 200 FOR SHELL : 4.900 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 1XWI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M MES, 0.8M-1.9M MGSO4, PH 5.9-6.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 292K 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 117.75467 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 58.87733 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 88.31600 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 29.43867 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 147.19333 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 117.75467 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 58.87733 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 29.43867 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 88.31600 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 147.19333 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 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 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 107 REMARK 465 GLY A 108 REMARK 465 HIS A 109 REMARK 465 HIS A 110 REMARK 465 HIS A 111 REMARK 465 HIS A 112 REMARK 465 HIS A 113 REMARK 465 HIS A 114 REMARK 465 SER A 115 REMARK 465 ARG A 116 REMARK 465 GLY A 117 REMARK 465 LEU A 118 REMARK 465 VAL A 119 REMARK 465 PRO A 120 REMARK 465 ARG A 121 REMARK 465 GLY A 122 REMARK 465 SER A 123 REMARK 465 LEU A 124 REMARK 465 SER A 125 REMARK 465 GLU A 126 REMARK 465 LYS A 127 REMARK 465 PRO A 128 REMARK 465 LYS A 205 REMARK 465 TRP A 206 REMARK 465 MET A 207 REMARK 465 GLY A 239 REMARK 465 THR A 240 REMARK 465 ARG A 241 REMARK 465 GLY A 242 REMARK 465 GLU A 243 REMARK 465 GLY A 244 REMARK 465 GLU A 245 REMARK 465 SER A 246 REMARK 465 GLU A 247 REMARK 465 GLY A 264 REMARK 465 ASN A 265 REMARK 465 ASP A 266 REMARK 465 SER A 267 REMARK 465 SER A 364 REMARK 465 THR A 365 REMARK 465 GLU A 366 REMARK 465 ASP A 367 REMARK 465 ASP A 368 REMARK 465 GLU A 369 REMARK 465 THR A 370 REMARK 465 ARG A 371 REMARK 465 LYS A 372 REMARK 465 GLN A 434 REMARK 465 GLU A 435 REMARK 465 GLY A 436 REMARK 465 ASN A 437 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 ALA A 383 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 131 CG CD CE NZ REMARK 480 GLU A 133 CG CD OE1 OE2 REMARK 480 ASP A 134 CB CG OD1 OD2 REMARK 480 LYS A 142 CD CE NZ REMARK 480 LYS A 146 CG CD CE NZ REMARK 480 GLU A 147 CG CD OE1 OE2 REMARK 480 LYS A 154 CB CG CD CE NZ REMARK 480 LYS A 160 CB CG CD CE NZ REMARK 480 ASN A 162 CB CG OD1 ND2 REMARK 480 LYS A 164 CB CG CD CE NZ REMARK 480 THR A 166 CB OG1 CG2 REMARK 480 SER A 167 CB OG REMARK 480 TYR A 181 CB CG CD1 CD2 CE1 CE2 CZ REMARK 480 TYR A 181 OH REMARK 480 LYS A 184 CD CE NZ REMARK 480 SER A 200 CB OG REMARK 480 VAL A 203 CB CG1 CG2 REMARK 480 SER A 204 CB OG REMARK 480 GLU A 209 CB CG CD OE1 OE2 REMARK 480 GLU A 211 CB CG CD OE1 OE2 REMARK 480 LYS A 212 CG CD CE NZ REMARK 480 LYS A 215 CG CD CE NZ REMARK 480 ARG A 222 CB CG CD NE CZ NH1 NH2 REMARK 480 GLU A 223 CG CD OE1 OE2 REMARK 480 LYS A 225 CB CG CD CE NZ REMARK 480 GLU A 233 CG CD OE1 OE2 REMARK 480 LEU A 237 CB CG CD1 CD2 REMARK 480 THR A 238 CB OG1 CG2 REMARK 480 ALA A 248 CB REMARK 480 SER A 249 CB OG REMARK 480 ARG A 250 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 251 CB CG CD NE CZ NH1 NH2 REMARK 480 LYS A 253 CG CD CE NZ REMARK 480 THR A 254 OG1 CG2 REMARK 480 ASN A 261 CB CG OD1 ND2 REMARK 480 GLN A 268 CB CG CD OE1 NE2 REMARK 480 GLN A 281 CG CD OE1 NE2 REMARK 480 LEU A 282 CG CD1 CD2 REMARK 480 SER A 284 CB OG REMARK 480 ARG A 287 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 288 CB CG CD NE CZ NH1 NH2 REMARK 480 ARG A 289 CB CG CD NE CZ NH1 NH2 REMARK 480 GLU A 291 CB CG CD OE1 OE2 REMARK 480 ARG A 292 CG CD NE CZ NH1 NH2 REMARK 480 ARG A 293 CB CG CD NE CZ NH1 NH2 REMARK 480 ASP A 300 CB CG OD1 OD2 REMARK 480 ALA A 302 CB REMARK 480 ARG A 304 CB CG CD NE CZ NH1 NH2 REMARK 480 GLU A 309 CG CD OE1 OE2 REMARK 480 ASP A 314 CB CG OD1 OD2 REMARK 480 LYS A 321 CG CD CE NZ REMARK 480 ARG A 325 CG CD NE CZ NH1 NH2 REMARK 480 GLU A 332 CG CD OE1 OE2 REMARK 480 LYS A 353 CG CD CE NZ REMARK 480 PHE A 360 CG CD1 CD2 CE1 CE2 CZ REMARK 480 LYS A 361 CG CD CE NZ REMARK 480 VAL A 363 CG1 CG2 REMARK 480 ASP A 380 CB CG OD1 OD2 REMARK 480 ILE A 391 CB CG1 CG2 CD1 REMARK 480 GLU A 392 CG CD OE1 OE2 REMARK 480 ALA A 393 CB REMARK 480 ASP A 394 CB CG OD1 OD2 REMARK 480 GLU A 395 CB CG CD OE1 OE2 REMARK 480 LYS A 397 CB CG CD CE NZ REMARK 480 LYS A 404 CB CG CD CE NZ REMARK 480 LYS A 408 CG CD CE NZ REMARK 480 LYS A 411 CB CG CD CE NZ REMARK 480 ARG A 414 CB CG CD NE CZ NH1 NH2 REMARK 480 ASN A 418 CB CG OD1 ND2 REMARK 480 ASP A 420 CB CG OD1 OD2 REMARK 480 ASP A 421 CB CG OD1 OD2 REMARK 480 LEU A 423 CB CG CD1 CD2 REMARK 480 LYS A 424 CG CD CE NZ REMARK 480 GLN A 425 CB CG CD OE1 NE2 REMARK 480 GLU A 426 CB CG CD OE1 OE2 REMARK 480 GLN A 427 CB CG CD OE1 NE2 REMARK 480 ARG A 430 CB CG CD NE CZ NH1 NH2 REMARK 480 ASP A 431 CB CG OD1 OD2 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 GLU A 133 CB GLU A 133 CG -0.167 REMARK 500 ASP A 134 CA ASP A 134 CB -0.267 REMARK 500 LYS A 146 CB LYS A 146 CG -0.348 REMARK 500 GLU A 147 CB GLU A 147 CG 0.126 REMARK 500 LYS A 164 CA LYS A 164 CB -0.195 REMARK 500 SER A 167 CA SER A 167 CB -0.191 REMARK 500 TYR A 181 CA TYR A 181 CB -0.163 REMARK 500 SER A 204 CA SER A 204 CB -0.162 REMARK 500 GLU A 223 CB GLU A 223 CG -0.424 REMARK 500 GLU A 233 CB GLU A 233 CG -0.139 REMARK 500 LEU A 237 CA LEU A 237 CB -0.178 REMARK 500 ALA A 248 CA ALA A 248 CB 0.155 REMARK 500 THR A 254 CB THR A 254 OG1 0.129 REMARK 500 ARG A 287 CB ARG A 287 CG -0.359 REMARK 500 ARG A 288 CA ARG A 288 CB -0.216 REMARK 500 ARG A 292 CB ARG A 292 CG 0.190 REMARK 500 ARG A 293 CA ARG A 293 CB -0.236 REMARK 500 ASP A 300 CA ASP A 300 CB -0.178 REMARK 500 ARG A 304 CA ARG A 304 CB -0.256 REMARK 500 PHE A 360 CB PHE A 360 CG -0.151 REMARK 500 VAL A 363 CB VAL A 363 CG1 0.408 REMARK 500 VAL A 363 CB VAL A 363 CG2 -0.348 REMARK 500 ASP A 380 CA ASP A 380 CB -0.165 REMARK 500 ALA A 393 CA ALA A 393 CB -0.164 REMARK 500 ASP A 394 CA ASP A 394 CB -0.179 REMARK 500 LYS A 397 CA LYS A 397 CB -0.165 REMARK 500 LYS A 404 CA LYS A 404 CB -0.162 REMARK 500 ASN A 418 CA ASN A 418 CB -0.199 REMARK 500 LEU A 423 CA LEU A 423 CB -0.171 REMARK 500 GLU A 426 CA GLU A 426 CB -0.141 REMARK 500 ARG A 430 CA ARG A 430 CB -0.223 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 A 142 CB - CG - CD ANGL. DEV. = 25.2 DEGREES REMARK 500 LYS A 146 CA - CB - CG ANGL. DEV. = 20.8 DEGREES REMARK 500 GLU A 147 CA - CB - CG ANGL. DEV. = -19.7 DEGREES REMARK 500 GLU A 223 CA - CB - CG ANGL. DEV. = 18.1 DEGREES REMARK 500 ALA A 248 N - CA - CB ANGL. DEV. = -10.1 DEGREES REMARK 500 LEU A 282 CA - CB - CG ANGL. DEV. = 14.1 DEGREES REMARK 500 LEU A 282 CB - CG - CD1 ANGL. DEV. = -11.5 DEGREES REMARK 500 ALA A 302 CB - CA - C ANGL. DEV. = 10.4 DEGREES REMARK 500 VAL A 363 CA - CB - CG1 ANGL. DEV. = -12.6 DEGREES REMARK 500 VAL A 363 CA - CB - CG2 ANGL. DEV. = 14.4 DEGREES REMARK 500 GLU A 395 N - CA - CB ANGL. DEV. = 11.5 DEGREES REMARK 500 LYS A 404 N - CA - CB ANGL. DEV. = 12.3 DEGREES REMARK 500 ARG A 414 CB - CA - C ANGL. DEV. = -14.1 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 ALA A 136 -64.35 -26.58 REMARK 500 ALA A 141 -50.08 -152.75 REMARK 500 LYS A 154 96.23 -58.55 REMARK 500 PHE A 155 94.80 46.98 REMARK 500 ASN A 162 -5.18 -56.82 REMARK 500 PRO A 165 -171.28 -63.42 REMARK 500 LYS A 179 -48.46 -12.74 REMARK 500 GLU A 209 28.81 -149.08 REMARK 500 ARG A 222 -71.32 -48.35 REMARK 500 GLU A 223 28.64 -67.04 REMARK 500 LYS A 225 -145.24 46.24 REMARK 500 SER A 249 -42.11 -148.09 REMARK 500 ASN A 261 120.95 -27.76 REMARK 500 GLU A 291 -72.60 -71.03 REMARK 500 LEU A 301 -16.04 -29.98 REMARK 500 ILE A 310 -73.24 -67.18 REMARK 500 ASN A 311 27.72 -66.00 REMARK 500 CYS A 317 -155.58 -168.17 REMARK 500 GLN A 355 -76.20 -64.98 REMARK 500 ALA A 383 91.66 -68.98 REMARK 500 MET A 386 -164.96 -167.83 REMARK 500 THR A 413 59.08 -142.22 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 GLY A 382 11.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XWI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VPS4B REMARK 999 REMARK 999 SEQUENCE REMARK 999 THIS IS A N-TERMINAL DELETION MUTANT (1-123) OF UNIPROT, REMARK 999 P52917. DBREF 2RKO A 124 437 UNP P52917 VPS4_YEAST 124 437 SEQADV 2RKO MET A 107 UNP P52917 EXPRESSION TAG SEQADV 2RKO GLY A 108 UNP P52917 EXPRESSION TAG SEQADV 2RKO HIS A 109 UNP P52917 EXPRESSION TAG SEQADV 2RKO HIS A 110 UNP P52917 EXPRESSION TAG SEQADV 2RKO HIS A 111 UNP P52917 EXPRESSION TAG SEQADV 2RKO HIS A 112 UNP P52917 EXPRESSION TAG SEQADV 2RKO HIS A 113 UNP P52917 EXPRESSION TAG SEQADV 2RKO HIS A 114 UNP P52917 EXPRESSION TAG SEQADV 2RKO SER A 115 UNP P52917 EXPRESSION TAG SEQADV 2RKO ARG A 116 UNP P52917 EXPRESSION TAG SEQADV 2RKO GLY A 117 UNP P52917 EXPRESSION TAG SEQADV 2RKO LEU A 118 UNP P52917 EXPRESSION TAG SEQADV 2RKO VAL A 119 UNP P52917 EXPRESSION TAG SEQADV 2RKO PRO A 120 UNP P52917 EXPRESSION TAG SEQADV 2RKO ARG A 121 UNP P52917 EXPRESSION TAG SEQADV 2RKO GLY A 122 UNP P52917 EXPRESSION TAG SEQADV 2RKO SER A 123 UNP P52917 EXPRESSION TAG SEQRES 1 A 331 MET GLY HIS HIS HIS HIS HIS HIS SER ARG GLY LEU VAL SEQRES 2 A 331 PRO ARG GLY SER LEU SER GLU LYS PRO ASN VAL LYS TRP SEQRES 3 A 331 GLU ASP VAL ALA GLY LEU GLU GLY ALA LYS GLU ALA LEU SEQRES 4 A 331 LYS GLU ALA VAL ILE LEU PRO VAL LYS PHE PRO HIS LEU SEQRES 5 A 331 PHE LYS GLY ASN ARG LYS PRO THR SER GLY ILE LEU LEU SEQRES 6 A 331 TYR GLY PRO PRO GLY THR GLY LYS SER TYR LEU ALA LYS SEQRES 7 A 331 ALA VAL ALA THR GLU ALA ASN SER THR PHE PHE SER VAL SEQRES 8 A 331 SER SER SER ASP LEU VAL SER LYS TRP MET GLY GLU SER SEQRES 9 A 331 GLU LYS LEU VAL LYS GLN LEU PHE ALA MET ALA ARG GLU SEQRES 10 A 331 ASN LYS PRO SER ILE ILE PHE ILE ASP GLU VAL ASP ALA SEQRES 11 A 331 LEU THR GLY THR ARG GLY GLU GLY GLU SER GLU ALA SER SEQRES 12 A 331 ARG ARG ILE LYS THR GLU LEU LEU VAL GLN MET ASN GLY SEQRES 13 A 331 VAL GLY ASN ASP SER GLN GLY VAL LEU VAL LEU GLY ALA SEQRES 14 A 331 THR ASN ILE PRO TRP GLN LEU ASP SER ALA ILE ARG ARG SEQRES 15 A 331 ARG PHE GLU ARG ARG ILE TYR ILE PRO LEU PRO ASP LEU SEQRES 16 A 331 ALA ALA ARG THR THR MET PHE GLU ILE ASN VAL GLY ASP SEQRES 17 A 331 THR PRO CYS VAL LEU THR LYS GLU ASP TYR ARG THR LEU SEQRES 18 A 331 GLY ALA MET THR GLU GLY TYR SER GLY SER ASP ILE ALA SEQRES 19 A 331 VAL VAL VAL LYS ASP ALA LEU MET GLN PRO ILE ARG LYS SEQRES 20 A 331 ILE GLN SER ALA THR HIS PHE LYS ASP VAL SER THR GLU SEQRES 21 A 331 ASP ASP GLU THR ARG LYS LEU THR PRO CYS SER PRO GLY SEQRES 22 A 331 ASP ASP GLY ALA ILE GLU MET SER TRP THR ASP ILE GLU SEQRES 23 A 331 ALA ASP GLU LEU LYS GLU PRO ASP LEU THR ILE LYS ASP SEQRES 24 A 331 PHE LEU LYS ALA ILE LYS SER THR ARG PRO THR VAL ASN SEQRES 25 A 331 GLU ASP ASP LEU LEU LYS GLN GLU GLN PHE THR ARG ASP SEQRES 26 A 331 PHE GLY GLN GLU GLY ASN HELIX 1 1 LYS A 131 ALA A 136 1 6 HELIX 2 2 ALA A 141 VAL A 149 1 9 HELIX 3 3 VAL A 149 LYS A 154 1 6 HELIX 4 4 PHE A 155 PHE A 159 5 5 HELIX 5 5 GLY A 178 ALA A 190 1 13 HELIX 6 6 SER A 199 SER A 204 1 6 HELIX 7 7 SER A 210 GLU A 223 1 14 HELIX 8 8 GLU A 233 THR A 238 5 6 HELIX 9 9 SER A 249 ASN A 261 1 13 HELIX 10 10 ILE A 278 LEU A 282 5 5 HELIX 11 11 ASP A 283 PHE A 290 1 8 HELIX 12 12 ALA A 302 ASN A 311 1 10 HELIX 13 13 THR A 320 MET A 330 1 11 HELIX 14 14 SER A 335 SER A 356 1 22 HELIX 15 15 THR A 402 SER A 412 1 11 HELIX 16 16 ASN A 418 GLY A 433 1 16 SHEET 1 A 5 THR A 193 SER A 198 0 SHEET 2 A 5 SER A 227 ASP A 232 1 O PHE A 230 N PHE A 195 SHEET 3 A 5 VAL A 270 THR A 276 1 O LEU A 273 N ILE A 231 SHEET 4 A 5 GLY A 168 TYR A 172 1 N LEU A 171 O GLY A 274 SHEET 5 A 5 ARG A 292 TYR A 295 1 O ILE A 294 N LEU A 170 SHEET 1 B 3 THR A 374 CYS A 376 0 SHEET 2 B 3 HIS A 359 LYS A 361 -1 N LYS A 361 O THR A 374 SHEET 3 B 3 ILE A 384 GLU A 385 -1 O ILE A 384 N PHE A 360 CRYST1 109.116 109.116 176.632 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 0.009165 0.005291 0.000000 0.00000 SCALE2 0.000000 0.010582 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005661 0.00000