HEADER PROTEIN TRANSPORT 07-SEP-16 5T8N TITLE CRYSTAL STRUCTURE OF SNF7 UNDER 200 MPA COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLAR-SORTING PROTEIN SNF7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 12-150; COMPND 5 SYNONYM: DOA4-INDEPENDENT DEGRADATION PROTEIN 1,SUCROSE NONFERMENTING COMPND 6 PROTEIN 7,VACUOLAR PROTEIN-SORTING-ASSOCIATED PROTEIN 32; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE (STRAIN ATCC 204508 / SOURCE 3 S288C); SOURCE 4 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 5 ORGANISM_TAXID: 559292; SOURCE 6 STRAIN: ATCC 204508 / S288C; SOURCE 7 GENE: SNF7, DID1, VPS32, YLR025W; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SNF7, HIGH-PRESSURE CRYOCOOLING, RESOLUTION, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Q.HUANG,D.SZEBENYI REVDAT 3 04-OCT-23 5T8N 1 REMARK REVDAT 2 25-DEC-19 5T8N 1 REMARK REVDAT 1 16-AUG-17 5T8N 0 JRNL AUTH Q.HUANG,D.SZEBENYI JRNL TITL CRYSTAL STRUCTURE OF SNF7 UNDER 200 MPA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.TANG,W.M.HENNE,P.P.BORBAT,N.J.BUCHKOVICH,J.H.FREED,Y.MAO, REMARK 1 AUTH 2 J.C.FROMME,S.D.EMR REMARK 1 TITL STRUCTURAL BASIS FOR ACTIVATION, ASSEMBLY AND MEMBRANE REMARK 1 TITL 2 BINDING OF ESCRT-III SNF7 FILAMENTS. REMARK 1 REF ELIFE V. 4 2015 REMARK 1 REFN ESSN 2050-084X REMARK 1 PMID 26670543 REMARK 1 DOI 10.7554/ELIFE.12548 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 3 NUMBER OF REFLECTIONS : 6151 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.345 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.010 REMARK 3 FREE R VALUE TEST SET COUNT : 616 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 44.6533 - 3.4987 0.90 1333 149 0.2214 0.3136 REMARK 3 2 3.4987 - 2.7771 0.97 1396 156 0.2643 0.3915 REMARK 3 3 2.7771 - 2.4261 1.00 1453 160 0.2716 0.3986 REMARK 3 4 2.4261 - 2.2043 0.94 1353 151 0.2531 0.3167 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 37.210 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 997 REMARK 3 ANGLE : 1.018 1329 REMARK 3 CHIRALITY : 0.048 156 REMARK 3 PLANARITY : 0.004 171 REMARK 3 DIHEDRAL : 19.941 643 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 18 THROUGH 59 ) REMARK 3 ORIGIN FOR THE GROUP (A): 21.6932 -0.8213 20.2742 REMARK 3 T TENSOR REMARK 3 T11: 0.3919 T22: 0.4021 REMARK 3 T33: 0.3971 T12: -0.0158 REMARK 3 T13: 0.0121 T23: -0.0048 REMARK 3 L TENSOR REMARK 3 L11: 6.3529 L22: 1.0400 REMARK 3 L33: 3.6183 L12: -1.1101 REMARK 3 L13: 3.9252 L23: -0.2184 REMARK 3 S TENSOR REMARK 3 S11: 0.3592 S12: 0.1983 S13: -0.6501 REMARK 3 S21: -0.0458 S22: -0.0104 S23: 0.0265 REMARK 3 S31: 0.4351 S32: 0.1557 S33: -0.3808 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 60 THROUGH 118 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2575 9.1634 15.7106 REMARK 3 T TENSOR REMARK 3 T11: 0.3467 T22: 0.4184 REMARK 3 T33: 0.3589 T12: -0.0617 REMARK 3 T13: 0.0686 T23: -0.0034 REMARK 3 L TENSOR REMARK 3 L11: 8.2458 L22: 0.6377 REMARK 3 L33: 1.3526 L12: -1.3177 REMARK 3 L13: 2.9302 L23: -0.4415 REMARK 3 S TENSOR REMARK 3 S11: -0.2838 S12: -0.4084 S13: 1.1081 REMARK 3 S21: 0.0852 S22: -0.0183 S23: -0.1177 REMARK 3 S31: -0.0132 S32: -0.2447 S33: 0.0640 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 119 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.1100 28.9342 5.3353 REMARK 3 T TENSOR REMARK 3 T11: 0.8659 T22: 0.8524 REMARK 3 T33: 0.5451 T12: 0.0866 REMARK 3 T13: 0.0666 T23: 0.1450 REMARK 3 L TENSOR REMARK 3 L11: 4.4932 L22: 2.4832 REMARK 3 L33: 3.0780 L12: -2.0040 REMARK 3 L13: -0.9612 L23: -1.6689 REMARK 3 S TENSOR REMARK 3 S11: 0.1169 S12: 0.7122 S13: 0.4998 REMARK 3 S21: -0.4859 S22: -0.2934 S23: -0.2052 REMARK 3 S31: 0.4929 S32: 0.4071 S33: 0.1285 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5T8N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000223899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CHESS REMARK 200 BEAMLINE : F1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.978 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6164 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 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 (%) : 95.7 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5FD9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% PEG20000, 110MM NACL, 70MM MES REMARK 280 PH5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 23.92200 REMARK 290 SMTRY3 2 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: 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 ASN A 12 REMARK 465 ALA A 13 REMARK 465 LYS A 14 REMARK 465 ASN A 15 REMARK 465 LYS A 16 REMARK 465 GLU A 17 REMARK 465 ILE A 143 REMARK 465 SER A 144 REMARK 465 ASP A 145 REMARK 465 ALA A 146 REMARK 465 ILE A 147 REMARK 465 SER A 148 REMARK 465 ARG A 149 REMARK 465 PRO A 150 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 ARG A 25 NE ARG A 25 CZ -0.084 REMARK 500 ARG A 25 CZ ARG A 25 NH1 -0.087 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 ARG A 25 NE - CZ - NH1 ANGL. DEV. = -3.6 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 LYS A 125 -9.37 64.15 REMARK 500 ASP A 141 -55.88 -123.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FD9 RELATED DB: PDB REMARK 900 THE SAME PROTEIN UNDER DIFFERENT PRESSURE REMARK 900 RELATED ID: 5T8B RELATED DB: PDB REMARK 900 RELATED ID: 5T8C RELATED DB: PDB REMARK 900 RELATED ID: 5T8L RELATED DB: PDB DBREF 5T8N A 12 150 UNP P39929 SNF7_YEAST 12 150 SEQRES 1 A 139 ASN ALA LYS ASN LYS GLU SER PRO THR LYS ALA ILE VAL SEQRES 2 A 139 ARG LEU ARG GLU HIS ILE ASN LEU LEU SER LYS LYS GLN SEQRES 3 A 139 SER HIS LEU ARG THR GLN ILE THR ASN GLN GLU ASN GLU SEQRES 4 A 139 ALA ARG ILE PHE LEU THR LYS GLY ASN LYS VAL MET ALA SEQRES 5 A 139 LYS ASN ALA LEU LYS LYS LYS LYS THR ILE GLU GLN LEU SEQRES 6 A 139 LEU SER LYS VAL GLU GLY THR MET GLU SER MET GLU GLN SEQRES 7 A 139 GLN LEU PHE SER ILE GLU SER ALA ASN LEU ASN LEU GLU SEQRES 8 A 139 THR MET ARG ALA MET GLN GLU GLY ALA LYS ALA MET LYS SEQRES 9 A 139 THR ILE HIS SER GLY LEU ASP ILE ASP LYS VAL ASP GLU SEQRES 10 A 139 THR MET ASP GLU ILE ARG GLU GLN VAL GLU LEU GLY ASP SEQRES 11 A 139 GLU ILE SER ASP ALA ILE SER ARG PRO FORMUL 2 HOH *13(H2 O) HELIX 1 AA1 SER A 18 LYS A 57 1 40 HELIX 2 AA2 ASN A 59 SER A 119 1 61 HELIX 3 AA3 LYS A 125 LEU A 139 1 15 CISPEP 1 ILE A 123 ASP A 124 0 -6.77 CRYST1 29.826 47.844 45.185 90.00 98.87 90.00 P 1 21 1 2 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 0.033528 0.000000 0.005235 0.00000 SCALE2 0.000000 0.020901 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022399 0.00000