PDB Short entry for 3MHV HEADER PROTEIN TRANSPORT 09-APR-10 3MHV TITLE CRYSTAL STRUCTURE OF VPS4 AND VTA1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN 4; COMPND 3 CHAIN: C; COMPND 4 FRAGMENT: RESIDUES 297-413; COMPND 5 SYNONYM: VPS4, PROTEIN END13, DOA4-INDEPENDENT DEGRADATION PROTEIN 6, COMPND 6 VACUOLAR PROTEIN-TARGETING PROTEIN 10; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: VACUOLAR PROTEIN SORTING-ASSOCIATED PROTEIN VTA1; COMPND 10 CHAIN: A; COMPND 11 FRAGMENT: RESIDUES 289-330; COMPND 12 SYNONYM: VPS20-ASSOCIATED PROTEIN 1; COMPND 13 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 GENE: VPS4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGST2; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 13 ORGANISM_COMMON: YEAST; SOURCE 14 ORGANISM_TAXID: 4932; SOURCE 15 GENE: VTA1; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: ROSSETTA; SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGST2 KEYWDS VPS4, VTA1, AAA, ATPASE, ESCRT, MVB, SORTING, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR D.YANG,J.H.HURLEY REVDAT 2 01-NOV-23 3MHV 1 SEQADV REVDAT 1 06-OCT-10 3MHV 0 JRNL AUTH D.YANG,J.H.HURLEY JRNL TITL STRUCTURAL ROLE OF THE VPS4-VTA1 INTERFACE IN ESCRT-III JRNL TITL 2 RECYCLING JRNL REF STRUCTURE V. 18 976 2010 JRNL REFN ISSN 0969-2126 JRNL PMID 20696398 JRNL DOI 10.1016/J.STR.2010.04.014 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1127778.720 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 80.6 REMARK 3 NUMBER OF REFLECTIONS : 3761 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) : 0.298 REMARK 3 FREE R VALUE : 0.317 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 189 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.025 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.29 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 464 REMARK 3 BIN R VALUE (WORKING SET) : 0.4350 REMARK 3 BIN FREE R VALUE : 0.4100 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 22 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.087 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1099 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 106.3 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -29.41000 REMARK 3 B22 (A**2) : 0.64000 REMARK 3 B33 (A**2) : 28.77000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.54 REMARK 3 ESD FROM SIGMAA (A) : 0.83 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.76 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.74 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.600 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 : FLAT MODEL REMARK 3 KSOL : 0.27 REMARK 3 BSOL : 37.01 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURE WAS REFINED ALSO WITH REMARK 3 REFMAC 5. REMARK 4 REMARK 4 3MHV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000058564. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9719 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3803 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 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 (%) : 80.0 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 62.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.35500 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP, PHASER REMARK 200 STARTING MODEL: PDB ENTRIES: 3EIE AND 2RKL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16%-24% PEG3350, 0.1-0.3M SODIUM REMARK 280 FORMATE, VAPOR DIFFUSION, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-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 44.41950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.41950 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 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, 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 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 THR C 365 REMARK 465 GLU C 366 REMARK 465 ASP C 367 REMARK 465 ASP C 368 REMARK 465 TRP C 388 REMARK 465 THR C 389 REMARK 465 ASP C 390 REMARK 465 ILE C 391 REMARK 465 GLU C 392 REMARK 465 ALA C 393 REMARK 465 ASP C 394 REMARK 465 GLU C 395 REMARK 465 LEU C 396 REMARK 465 LYS C 397 REMARK 465 GLU C 398 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 SER C 377 N - CA - C ANGL. DEV. = -16.4 DEGREES REMARK 500 PRO C 378 C - N - CD ANGL. DEV. = -14.8 DEGREES REMARK 500 ASP C 380 N - CA - C ANGL. DEV. = -21.2 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 C 299 151.26 -48.63 REMARK 500 LEU C 301 -22.52 63.47 REMARK 500 GLU C 309 -82.52 -54.48 REMARK 500 ILE C 310 -52.30 -24.38 REMARK 500 THR C 315 117.02 -37.36 REMARK 500 PRO C 316 105.60 -50.62 REMARK 500 VAL C 318 19.25 -152.23 REMARK 500 ASP C 338 -76.23 -50.96 REMARK 500 LEU C 347 169.80 68.88 REMARK 500 MET C 348 -9.22 61.27 REMARK 500 HIS C 359 110.42 164.78 REMARK 500 THR C 370 97.16 -20.09 REMARK 500 ARG C 371 136.84 75.56 REMARK 500 LYS C 372 80.39 -164.94 REMARK 500 SER C 377 -170.78 -64.30 REMARK 500 ALA C 383 117.54 -25.58 REMARK 500 MET C 386 139.02 -176.83 REMARK 500 ALA C 409 7.12 -66.32 REMARK 500 SER C 412 23.12 -68.91 REMARK 500 ARG A 290 -59.48 88.09 REMARK 500 TYR A 310 16.91 -140.91 REMARK 500 GLU A 311 8.35 57.26 REMARK 500 ASP A 312 82.43 -60.45 REMARK 500 REMARK 500 REMARK: NULL DBREF 3MHV C 299 413 UNP P52917 VPS4_YEAST 299 413 DBREF 3MHV A 289 330 UNP Q06263 VTA1_YEAST 289 330 SEQADV 3MHV GLY C 297 UNP P52917 EXPRESSION TAG SEQADV 3MHV SER C 298 UNP P52917 EXPRESSION TAG SEQRES 1 C 117 GLY SER PRO ASP LEU ALA ALA ARG THR THR MET PHE GLU SEQRES 2 C 117 ILE ASN VAL GLY ASP THR PRO CYS VAL LEU THR LYS GLU SEQRES 3 C 117 ASP TYR ARG THR LEU GLY ALA MET THR GLU GLY TYR SER SEQRES 4 C 117 GLY SER ASP ILE ALA VAL VAL VAL LYS ASP ALA LEU MET SEQRES 5 C 117 GLN PRO ILE ARG LYS ILE GLN SER ALA THR HIS PHE LYS SEQRES 6 C 117 ASP VAL SER THR GLU ASP ASP GLU THR ARG LYS LEU THR SEQRES 7 C 117 PRO CYS SER PRO GLY ASP ASP GLY ALA ILE GLU MET SER SEQRES 8 C 117 TRP THR ASP ILE GLU ALA ASP GLU LEU LYS GLU PRO ASP SEQRES 9 C 117 LEU THR ILE LYS ASP PHE LEU LYS ALA ILE LYS SER THR SEQRES 1 A 42 ASP ARG ALA SER LYS ILE GLU GLN ILE GLN LYS LEU ALA SEQRES 2 A 42 LYS TYR ALA ILE SER ALA LEU ASN TYR GLU ASP LEU PRO SEQRES 3 A 42 THR ALA LYS ASP GLU LEU THR LYS ALA LEU ASP LEU LEU SEQRES 4 A 42 ASN SER ILE HELIX 1 1 ALA C 302 GLY C 313 1 12 HELIX 2 2 THR C 320 THR C 331 1 12 HELIX 3 3 SER C 335 ALA C 346 1 12 HELIX 4 4 MET C 348 ALA C 357 1 10 HELIX 5 5 THR C 402 SER C 412 1 11 HELIX 6 6 SER A 292 ASN A 309 1 18 HELIX 7 7 ASP A 312 ILE A 330 1 19 SHEET 1 A 2 PHE C 360 ASP C 362 0 SHEET 2 A 2 LEU C 373 PRO C 375 -1 O THR C 374 N LYS C 361 CRYST1 37.979 70.322 88.839 90.00 90.00 90.00 P 2 2 21 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 0.026330 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014220 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011256 0.00000