HEADER PROTEIN TRANSPORT 08-OCT-07 2ZAN TITLE CRYSTAL STRUCTURE OF MOUSE SKD1/VPS4B ATP-FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATING PROTEIN 4B; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROTEIN SKD1, SUPPRESSOR OF K+, TRANSPORT GROWTH DEFECT 1; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SKD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPROEXHTB KEYWDS SKD1, VPS4B, AAA ATPASE, ATP-BINDING, MEMBRANE, NUCLEOTIDE-BINDING, KEYWDS 2 PHOSPHORYLATION, PROTEIN TRANSPORT, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR M.INOUE,M.KAWASAKI,H.KAMIKUBO,M.KATAOKA,R.KATO,T.YOSHIMORI, AUTHOR 2 S.WAKATSUKI REVDAT 4 01-NOV-23 2ZAN 1 REMARK REVDAT 3 22-JAN-14 2ZAN 1 JRNL VERSN REVDAT 2 24-FEB-09 2ZAN 1 VERSN REVDAT 1 07-OCT-08 2ZAN 0 JRNL AUTH M.INOUE,H.KAMIKUBO,M.KATAOKA,R.KATO,T.YOSHIMORI,S.WAKATSUKI, JRNL AUTH 2 M.KAWASAKI JRNL TITL NUCLEOTIDE-DEPENDENT CONFORMATIONAL CHANGES AND ASSEMBLY OF JRNL TITL 2 THE AAA ATPASE SKD1/VPS4B JRNL REF TRAFFIC V. 9 2180 2008 JRNL REFN ISSN 1398-9219 JRNL PMID 18796009 JRNL DOI 10.1111/J.1600-0854.2008.00831.X REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 6924 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 SET) : 0.224 REMARK 3 FREE R VALUE : 0.262 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 345 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2429 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 5 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -12.83000 REMARK 3 B22 (A**2) : -12.83000 REMARK 3 B33 (A**2) : 25.65000 REMARK 3 B12 (A**2) : -17.02000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2ZAN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000027731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8611 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%) : 96.5 REMARK 200 DATA REDUNDANCY : 10.40 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.1 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 1XWI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG3350, 0.1 MM MES, ATP SOATING, REMARK 280 PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K 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 87.78533 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 43.89267 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 65.83900 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 21.94633 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 109.73167 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: 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 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 ASN A 5 REMARK 465 THR A 6 REMARK 465 ASN A 7 REMARK 465 LEU A 8 REMARK 465 GLN A 9 REMARK 465 LYS A 10 REMARK 465 ALA A 11 REMARK 465 ILE A 12 REMARK 465 ASP A 13 REMARK 465 LEU A 14 REMARK 465 ALA A 15 REMARK 465 SER A 16 REMARK 465 LYS A 17 REMARK 465 ALA A 18 REMARK 465 ALA A 19 REMARK 465 GLN A 20 REMARK 465 GLU A 21 REMARK 465 ASP A 22 REMARK 465 LYS A 23 REMARK 465 ALA A 24 REMARK 465 GLY A 25 REMARK 465 ASN A 26 REMARK 465 TYR A 27 REMARK 465 GLU A 28 REMARK 465 GLU A 29 REMARK 465 ALA A 30 REMARK 465 LEU A 31 REMARK 465 GLN A 32 REMARK 465 LEU A 33 REMARK 465 TYR A 34 REMARK 465 GLN A 35 REMARK 465 HIS A 36 REMARK 465 ALA A 37 REMARK 465 VAL A 38 REMARK 465 GLN A 39 REMARK 465 TYR A 40 REMARK 465 PHE A 41 REMARK 465 LEU A 42 REMARK 465 HIS A 43 REMARK 465 VAL A 44 REMARK 465 VAL A 45 REMARK 465 LYS A 46 REMARK 465 TYR A 47 REMARK 465 GLU A 48 REMARK 465 ALA A 49 REMARK 465 GLN A 50 REMARK 465 GLY A 51 REMARK 465 ASP A 52 REMARK 465 LYS A 53 REMARK 465 ALA A 54 REMARK 465 LYS A 55 REMARK 465 GLN A 56 REMARK 465 SER A 57 REMARK 465 ILE A 58 REMARK 465 ARG A 59 REMARK 465 ALA A 60 REMARK 465 LYS A 61 REMARK 465 CYS A 62 REMARK 465 THR A 63 REMARK 465 GLU A 64 REMARK 465 TYR A 65 REMARK 465 LEU A 66 REMARK 465 ASP A 67 REMARK 465 ARG A 68 REMARK 465 ALA A 69 REMARK 465 GLU A 70 REMARK 465 LYS A 71 REMARK 465 LEU A 72 REMARK 465 LYS A 73 REMARK 465 GLU A 74 REMARK 465 TYR A 75 REMARK 465 LEU A 76 REMARK 465 LYS A 77 REMARK 465 LYS A 78 REMARK 465 LYS A 79 REMARK 465 GLU A 80 REMARK 465 LYS A 81 REMARK 465 LYS A 82 REMARK 465 PRO A 83 REMARK 465 GLN A 84 REMARK 465 LYS A 85 REMARK 465 PRO A 86 REMARK 465 VAL A 87 REMARK 465 LYS A 88 REMARK 465 GLU A 89 REMARK 465 GLU A 90 REMARK 465 GLN A 91 REMARK 465 SER A 92 REMARK 465 GLY A 93 REMARK 465 PRO A 94 REMARK 465 VAL A 95 REMARK 465 ASP A 96 REMARK 465 GLU A 97 REMARK 465 LYS A 98 REMARK 465 GLY A 99 REMARK 465 ASN A 100 REMARK 465 ASP A 101 REMARK 465 SER A 102 REMARK 465 ASP A 103 REMARK 465 GLY A 104 REMARK 465 GLU A 105 REMARK 465 ALA A 106 REMARK 465 GLU A 107 REMARK 465 SER A 108 REMARK 465 ASP A 109 REMARK 465 ASP A 110 REMARK 465 PRO A 111 REMARK 465 GLU A 112 REMARK 465 LYS A 113 REMARK 465 LYS A 114 REMARK 465 LYS A 115 REMARK 465 LEU A 116 REMARK 465 GLN A 117 REMARK 465 ASN A 118 REMARK 465 GLN A 119 REMARK 465 LEU A 120 REMARK 465 GLN A 121 REMARK 465 GLY A 122 REMARK 465 ALA A 123 REMARK 465 ASP A 203 REMARK 465 LEU A 204 REMARK 465 VAL A 205 REMARK 465 SER A 206 REMARK 465 LYS A 207 REMARK 465 TRP A 208 REMARK 465 LEU A 209 REMARK 465 GLY A 210 REMARK 465 GLU A 211 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 VAL A 377 N - CA - C ANGL. DEV. = 18.2 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 PRO A 129 -144.37 -67.35 REMARK 500 LEU A 139 25.74 49.89 REMARK 500 PHE A 160 48.40 -85.95 REMARK 500 ARG A 164 34.79 -95.04 REMARK 500 PRO A 175 160.81 -36.14 REMARK 500 LYS A 180 -72.26 -46.89 REMARK 500 ASN A 192 -45.60 -28.49 REMARK 500 SER A 200 -129.44 -138.89 REMARK 500 LEU A 215 29.59 -78.53 REMARK 500 LEU A 219 -70.04 -53.34 REMARK 500 GLU A 235 80.77 37.18 REMARK 500 CYS A 240 152.75 175.39 REMARK 500 SER A 244 15.57 106.60 REMARK 500 GLU A 245 111.09 -176.26 REMARK 500 ASN A 246 98.21 157.53 REMARK 500 GLU A 249 -27.99 -39.82 REMARK 500 VAL A 267 108.13 -30.79 REMARK 500 ASN A 269 29.69 -70.66 REMARK 500 THR A 278 147.33 -172.46 REMARK 500 ILE A 280 55.56 -149.59 REMARK 500 SER A 316 -3.11 -46.78 REMARK 500 THR A 333 33.17 -99.99 REMARK 500 ALA A 359 156.52 -48.78 REMARK 500 ASN A 374 48.59 -94.19 REMARK 500 ASN A 378 16.19 53.10 REMARK 500 MET A 394 167.67 172.36 REMARK 500 SER A 420 30.00 -86.03 REMARK 500 ASP A 439 -7.21 54.86 REMARK 500 GLU A 443 -21.00 67.21 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 MG A 445 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 181 OG REMARK 620 2 ATP A 446 O3G 128.4 REMARK 620 3 ATP A 446 O2B 64.6 69.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 445 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 446 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XWI RELATED DB: PDB REMARK 900 MODEL IN MOLECULAR REPLACEMENT REMARK 900 RELATED ID: 2ZAM RELATED DB: PDB REMARK 900 RELATED ID: 2ZAO RELATED DB: PDB DBREF 2ZAN A 1 444 UNP P46467 VPS4B_MOUSE 1 444 SEQRES 1 A 444 MET ALA SER THR ASN THR ASN LEU GLN LYS ALA ILE ASP SEQRES 2 A 444 LEU ALA SER LYS ALA ALA GLN GLU ASP LYS ALA GLY ASN SEQRES 3 A 444 TYR GLU GLU ALA LEU GLN LEU TYR GLN HIS ALA VAL GLN SEQRES 4 A 444 TYR PHE LEU HIS VAL VAL LYS TYR GLU ALA GLN GLY ASP SEQRES 5 A 444 LYS ALA LYS GLN SER ILE ARG ALA LYS CYS THR GLU TYR SEQRES 6 A 444 LEU ASP ARG ALA GLU LYS LEU LYS GLU TYR LEU LYS LYS SEQRES 7 A 444 LYS GLU LYS LYS PRO GLN LYS PRO VAL LYS GLU GLU GLN SEQRES 8 A 444 SER GLY PRO VAL ASP GLU LYS GLY ASN ASP SER ASP GLY SEQRES 9 A 444 GLU ALA GLU SER ASP ASP PRO GLU LYS LYS LYS LEU GLN SEQRES 10 A 444 ASN GLN LEU GLN GLY ALA ILE VAL ILE GLU ARG PRO ASN SEQRES 11 A 444 VAL LYS TRP SER ASP VAL ALA GLY LEU GLU GLY ALA LYS SEQRES 12 A 444 GLU ALA LEU LYS GLU ALA VAL ILE LEU PRO ILE LYS PHE SEQRES 13 A 444 PRO HIS LEU PHE THR GLY LYS ARG THR PRO TRP ARG GLY SEQRES 14 A 444 ILE LEU LEU PHE GLY PRO PRO GLY THR GLY LYS SER TYR SEQRES 15 A 444 LEU ALA LYS ALA VAL ALA THR GLU ALA ASN ASN SER THR SEQRES 16 A 444 PHE PHE SER ILE SER SER SER ASP LEU VAL SER LYS TRP SEQRES 17 A 444 LEU GLY GLU SER GLU LYS LEU VAL LYS ASN LEU PHE GLN SEQRES 18 A 444 LEU ALA ARG GLU ASN LYS PRO SER ILE ILE PHE ILE ASP SEQRES 19 A 444 GLU ILE ASP SER LEU CYS GLY SER ARG SER GLU ASN GLU SEQRES 20 A 444 SER GLU ALA ALA ARG ARG ILE LYS THR GLU PHE LEU VAL SEQRES 21 A 444 GLN MET GLN GLY VAL GLY VAL ASP ASN ASP GLY ILE LEU SEQRES 22 A 444 VAL LEU GLY ALA THR ASN ILE PRO TRP VAL LEU ASP SER SEQRES 23 A 444 ALA ILE ARG ARG ARG PHE GLU LYS ARG ILE TYR ILE PRO SEQRES 24 A 444 LEU PRO GLU ALA HIS ALA ARG ALA ALA MET PHE ARG LEU SEQRES 25 A 444 HIS LEU GLY SER THR GLN ASN SER LEU THR GLU ALA ASP SEQRES 26 A 444 PHE GLN GLU LEU GLY ARG LYS THR ASP GLY TYR SER GLY SEQRES 27 A 444 ALA ASP ILE SER ILE ILE VAL ARG ASP ALA LEU MET GLN SEQRES 28 A 444 PRO VAL ARG LYS VAL GLN SER ALA THR HIS PHE LYS LYS SEQRES 29 A 444 VAL ARG GLY PRO SER ARG ALA ASP PRO ASN CYS ILE VAL SEQRES 30 A 444 ASN ASP LEU LEU THR PRO CYS SER PRO GLY ASP PRO GLY SEQRES 31 A 444 ALA ILE GLU MET THR TRP MET ASP VAL PRO GLY ASP LYS SEQRES 32 A 444 LEU LEU GLU PRO VAL VAL SER MET TRP ASP MET LEU ARG SEQRES 33 A 444 SER LEU SER SER THR LYS PRO THR VAL ASN GLU GLN ASP SEQRES 34 A 444 LEU LEU LYS LEU LYS LYS PHE THR GLU ASP PHE GLY GLN SEQRES 35 A 444 GLU GLY HET MG A 445 1 HET ATP A 446 31 HETNAM MG MAGNESIUM ION HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE FORMUL 2 MG MG 2+ FORMUL 3 ATP C10 H16 N5 O13 P3 FORMUL 4 HOH *5(H2 O) HELIX 1 1 LYS A 132 VAL A 136 5 5 HELIX 2 2 LEU A 139 ILE A 151 1 13 HELIX 3 3 ILE A 151 PHE A 156 1 6 HELIX 4 4 THR A 161 THR A 165 5 5 HELIX 5 5 GLY A 179 ALA A 191 1 13 HELIX 6 6 LEU A 215 ASN A 226 1 12 HELIX 7 7 SER A 248 ALA A 250 5 3 HELIX 8 8 ALA A 251 VAL A 260 1 10 HELIX 9 9 ILE A 280 LEU A 284 5 5 HELIX 10 10 ASP A 285 ARG A 290 1 6 HELIX 11 11 GLU A 302 GLY A 315 1 14 HELIX 12 12 THR A 322 THR A 333 1 12 HELIX 13 13 SER A 337 MET A 350 1 14 HELIX 14 14 MET A 350 ALA A 359 1 10 HELIX 15 15 MET A 411 SER A 420 1 10 HELIX 16 16 ASN A 426 THR A 437 1 12 SHEET 1 A 5 THR A 195 ILE A 199 0 SHEET 2 A 5 SER A 229 ILE A 233 1 O PHE A 232 N PHE A 197 SHEET 3 A 5 LEU A 273 THR A 278 1 O LEU A 275 N ILE A 231 SHEET 4 A 5 GLY A 169 PHE A 173 1 N LEU A 172 O GLY A 276 SHEET 5 A 5 LYS A 294 TYR A 297 1 O ILE A 296 N LEU A 171 SHEET 1 B 2 ASN A 319 SER A 320 0 SHEET 2 B 2 VAL A 409 SER A 410 1 O VAL A 409 N SER A 320 SHEET 1 C 3 LEU A 380 CYS A 384 0 SHEET 2 C 3 HIS A 361 VAL A 365 -1 N VAL A 365 O LEU A 380 SHEET 3 C 3 ALA A 391 GLU A 393 -1 O ILE A 392 N PHE A 362 LINK OG SER A 181 MG MG A 445 1555 1555 2.27 LINK MG MG A 445 O3G ATP A 446 1555 1555 2.45 LINK MG MG A 445 O2B ATP A 446 1555 1555 2.36 CISPEP 1 LYS A 227 PRO A 228 0 -0.52 SITE 1 AC1 3 SER A 181 ASP A 234 ATP A 446 SITE 1 AC2 18 ASP A 135 VAL A 136 ALA A 137 PRO A 176 SITE 2 AC2 18 GLY A 177 THR A 178 GLY A 179 LYS A 180 SITE 3 AC2 18 SER A 181 TYR A 182 ASN A 279 MET A 309 SITE 4 AC2 18 HIS A 313 GLY A 338 ALA A 339 SER A 342 SITE 5 AC2 18 MG A 445 HOH A 449 CRYST1 75.607 75.607 131.678 90.00 90.00 120.00 P 65 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.013226 0.007636 0.000000 0.00000 SCALE2 0.000000 0.015272 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007594 0.00000