PDB Short entry for 2V6X HEADER PROTEIN TRANSPORT 23-JUL-07 2V6X TITLE STRACTURAL INSIGHT INTO THE INTERACTION BETWEEN ESCRT-III AND VPS4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: MIT DOMAIN RESIUDES 1-82; COMPND 5 SYNONYM: VPS4, PROTEIN END13, DOA4-INDEPENDENT DEGRADATION PROTEIN 6, COMPND 6 VACUOLAR PROTEIN-TARGETING PROTEIN 10; COMPND 7 EC: 3.6.4.6; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: DOA4-INDEPENDENT DEGRADATION PROTEIN 4; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: C-TERMINAL FRAGMENT RESIDUES 102-151; COMPND 13 SYNONYM: VACUOLAR PROTEIN SORTING- ASSOCIATED PROTEIN 2, VPS2, COMPND 14 VACUOLAR PROTEIN-TARGETING PROTEIN 14; COMPND 15 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: POPTG; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 11 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 12 ORGANISM_TAXID: 4932; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 EXPRESSION_SYSTEM_VARIANT: C41; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: POPTG KEYWDS PROTEIN TRANSPORT, VACUOLE, ENDOSOME, TRANSPORT, ESCRT-III, MVB, KEYWDS 2 VPS2, VPS4, SKD1, VPS4B, VPS4A, CHMP2B, CHMP2A, NUCLEOTIDE-BINDING, KEYWDS 3 AAA-ATPASE, ATP-BINDING, MULTIVESICULAR, VACUOLAR PROTEIN SORTING EXPDTA X-RAY DIFFRACTION AUTHOR T.OBITA,O.PERISIC,S.GHAZI-TABATABAI,S.SAKSENA,S.D.EMR,R.L.WILLIAMS REVDAT 6 24-JAN-18 2V6X 1 SOURCE REVDAT 5 28-JUN-17 2V6X 1 REMARK REVDAT 4 13-JUL-11 2V6X 1 VERSN REVDAT 3 24-FEB-09 2V6X 1 VERSN REVDAT 2 20-MAY-08 2V6X 1 REMARK ATOM MASTER REVDAT 1 16-OCT-07 2V6X 0 JRNL AUTH T.OBITA,S.SAKSENA,S.GHAZI-TABATABAI,D.J.GILL,O.PERISIC, JRNL AUTH 2 S.D.EMR,R.L.WILLIAMS JRNL TITL STRUCTURAL BASIS FOR SELECTIVE RECOGNITION OF ESCRT-III BY JRNL TITL 2 THE AAA ATPASE VPS4 JRNL REF NATURE V. 449 735 2007 JRNL REFN ISSN 0028-0836 JRNL PMID 17928861 JRNL DOI 10.1038/NATURE06171 REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.61 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 9483 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) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.228 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 477 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) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 385 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 18 REMARK 3 BIN FREE R VALUE : 0.3580 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 979 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 32 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) : 19.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.95000 REMARK 3 B22 (A**2) : 1.52000 REMARK 3 B33 (A**2) : -0.57000 REMARK 3 B12 (A**2) : 0.00000 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): 0.173 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.150 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.103 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.393 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.935 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.924 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 997 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1343 ; 1.334 ; 1.986 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 120 ; 5.193 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 48 ;34.799 ;26.250 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 187 ;15.331 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 3 ; 8.964 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 151 ; 0.104 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 731 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 391 ; 0.201 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 681 ; 0.291 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 39 ; 0.095 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 54 ; 0.305 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.102 ; 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): 639 ; 0.934 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 980 ; 1.372 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 410 ; 2.731 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 363 ; 3.850 ; 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 : 4 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 -1 A 80 REMARK 3 ORIGIN FOR THE GROUP (A): 32.2842 25.4404 38.2005 REMARK 3 T TENSOR REMARK 3 T11: -.0389 T22: -.0390 REMARK 3 T33: -.0901 T12: .0025 REMARK 3 T13: .0001 T23: .0291 REMARK 3 L TENSOR REMARK 3 L11: 2.5311 L22: 1.5648 REMARK 3 L33: .6999 L12: .6238 REMARK 3 L13: -.3311 L23: .3505 REMARK 3 S TENSOR REMARK 3 S11: -.0750 S12: -.0502 S13: .0999 REMARK 3 S21: -.1098 S22: .1250 S23: -.0049 REMARK 3 S31: .0223 S32: -.0197 S33: -.0499 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 181 B 194 REMARK 3 ORIGIN FOR THE GROUP (A): 52.2448 29.5992 43.9663 REMARK 3 T TENSOR REMARK 3 T11: -.0857 T22: -.0490 REMARK 3 T33: -.0831 T12: -.0120 REMARK 3 T13: -.0028 T23: -.0515 REMARK 3 L TENSOR REMARK 3 L11: 25.8261 L22: 3.3446 REMARK 3 L33: 5.3548 L12: -6.6176 REMARK 3 L13: -10.5281 L23: 3.3369 REMARK 3 S TENSOR REMARK 3 S11: .7420 S12: -.5827 S13: .9180 REMARK 3 S21: -.2828 S22: -.2930 S23: -.2684 REMARK 3 S31: -.4813 S32: .0780 S33: -.4490 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 195 B 206 REMARK 3 ORIGIN FOR THE GROUP (A): 32.0943 16.2354 46.8005 REMARK 3 T TENSOR REMARK 3 T11: -.0869 T22: -.0170 REMARK 3 T33: -.1288 T12: -.0044 REMARK 3 T13: .0179 T23: .0031 REMARK 3 L TENSOR REMARK 3 L11: 25.9606 L22: 8.2359 REMARK 3 L33: 7.5440 L12: 9.5520 REMARK 3 L13: 4.0357 L23: -1.1826 REMARK 3 S TENSOR REMARK 3 S11: -.5471 S12: -.2061 S13: -1.4406 REMARK 3 S21: -.5140 S22: .3731 S23: -.6739 REMARK 3 S31: .0957 S32: -.0546 S33: .1740 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 217 B 231 REMARK 3 ORIGIN FOR THE GROUP (A): 27.9450 35.4968 35.3560 REMARK 3 T TENSOR REMARK 3 T11: .0489 T22: -.0639 REMARK 3 T33: .2208 T12: -.1903 REMARK 3 T13: -.2899 T23: .3115 REMARK 3 L TENSOR REMARK 3 L11: 30.0462 L22: 27.3093 REMARK 3 L33: 3.9751 L12: 8.3824 REMARK 3 L13: 2.3039 L23: -.8659 REMARK 3 S TENSOR REMARK 3 S11: -1.7987 S12: 1.7128 S13: 2.7235 REMARK 3 S21: -1.4646 S22: 1.8775 S23: 2.4026 REMARK 3 S31: -.6202 S32: -.0698 S33: -.0789 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. SEGMENT 207-216 OF VPS2 ARE DISORDERED. REMARK 4 REMARK 4 2V6X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1290031460. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-JAN-07; NULL REMARK 200 TEMPERATURE (KELVIN) : NULL; NULL REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : ESRF; ESRF REMARK 200 BEAMLINE : ID23-1; ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726, 0.9392; 0.9792, 0.9796 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH; ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SCALA REMARK 200 DATA SCALING SOFTWARE : TRUNCATE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9997 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 56.610 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 5.230 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.31 REMARK 200 R MERGE FOR SHELL (I) : 0.44000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.280 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHARP, ARP/WARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES(PH7.0), 2.0M AMMONIUM REMARK 280 SULFATE REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 39.07250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.13500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.07250 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.13500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 TOTAL BURIED SURFACE AREA: 3020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9990 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.2 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A -2 REMARK 465 ALA A 81 REMARK 465 ALA A 82 REMARK 465 GLY B 179 REMARK 465 SER B 180 REMARK 465 ILE B 207 REMARK 465 GLY B 208 REMARK 465 ALA B 209 REMARK 465 GLY B 210 REMARK 465 SER B 211 REMARK 465 GLU B 212 REMARK 465 PHE B 213 REMARK 465 HIS B 214 REMARK 465 GLY B 215 REMARK 465 ASN B 216 REMARK 465 THR B 232 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 CG2 THR A 31 O HOH B 1003 1554 2.06 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 SER A 2 79.28 -101.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B1232 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WR0 RELATED DB: PDB REMARK 900 STRUCTURAL CHARACTERIZATION OF THE MIT DOMAIN FROM HUMANVPS4B REMARK 900 RELATED ID: 1XWI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF VPS4B REMARK 900 RELATED ID: 1YXR RELATED DB: PDB REMARK 900 NMR STRUCTURE OF VPS4A MIT DOMAIN DBREF 2V6X A -2 0 PDB 2V6X 2V6X -2 0 DBREF 2V6X A 1 82 UNP P52917 VPS4_YEAST 1 82 DBREF 2V6X B 179 182 PDB 2V6X 2V6X 179 182 DBREF 2V6X B 183 232 UNP P36108 DID4_YEAST 102 151 SEQRES 1 A 85 GLY SER HIS MSE SER THR GLY ASP PHE LEU THR LYS GLY SEQRES 2 A 85 ILE GLU LEU VAL GLN LYS ALA ILE ASP LEU ASP THR ALA SEQRES 3 A 85 THR GLN TYR GLU GLU ALA TYR THR ALA TYR TYR ASN GLY SEQRES 4 A 85 LEU ASP TYR LEU MSE LEU ALA LEU LYS TYR GLU LYS ASN SEQRES 5 A 85 PRO LYS SER LYS ASP LEU ILE ARG ALA LYS PHE THR GLU SEQRES 6 A 85 TYR LEU ASN ARG ALA GLU GLN LEU LYS LYS HIS LEU GLU SEQRES 7 A 85 SER GLU GLU ALA ASN ALA ALA SEQRES 1 B 54 GLY SER HIS MSE LEU GLN SER THR PRO GLN ASN LEU VAL SEQRES 2 B 54 SER ASN ALA PRO ILE ALA GLU THR ALA MSE GLY ILE ALA SEQRES 3 B 54 GLU PRO ILE GLY ALA GLY SER GLU PHE HIS GLY ASN PRO SEQRES 4 B 54 ASP ASP ASP LEU GLN ALA ARG LEU ASN THR LEU LYS LYS SEQRES 5 B 54 GLN THR MODRES 2V6X MSE A 1 MET SELENOMETHIONINE MODRES 2V6X MSE A 41 MET SELENOMETHIONINE MODRES 2V6X MSE B 182 MET SELENOMETHIONINE MODRES 2V6X MSE B 201 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 41 8 HET MSE B 182 8 HET MSE B 201 8 HET SO4 B1232 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *32(H2 O) HELIX 1 1 ASP A 5 ALA A 23 1 19 HELIX 2 2 GLN A 25 GLU A 47 1 23 HELIX 3 3 ASN A 49 ASN A 80 1 32 HELIX 4 4 PRO B 187 SER B 192 1 6 HELIX 5 5 ILE B 196 MSE B 201 5 6 HELIX 6 6 ASP B 218 LYS B 230 1 13 LINK C HIS A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N SER A 2 1555 1555 1.32 LINK C LEU A 40 N MSE A 41 1555 1555 1.34 LINK C MSE A 41 N LEU A 42 1555 1555 1.33 LINK C HIS B 181 N MSE B 182 1555 1555 1.33 LINK C MSE B 182 N LEU B 183 1555 1555 1.34 LINK C ALA B 200 N MSE B 201 1555 1555 1.33 LINK C MSE B 201 N GLY B 202 1555 1555 1.32 SITE 1 AC1 5 GLN A 15 MSE B 201 GLY B 202 HOH B1008 SITE 2 AC1 5 HOH B1009 CRYST1 78.145 82.270 21.474 90.00 90.00 90.00 P 21 21 2 4 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 0.012797 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012155 0.000000 0.00000 SCALE3 0.000000 0.000000 0.046568 0.00000