HEADER PROTEIN TRANSPORT 07-SEP-16 5T8L TITLE CRYSTAL STRUCTURE OF SNF7 UNDER 350 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 5T8L 1 REMARK REVDAT 2 25-DEC-19 5T8L 1 REMARK REVDAT 1 16-AUG-17 5T8L 0 JRNL AUTH Q.HUANG,D.SZEBENYI JRNL TITL CRYSTAL STRUCTURE OF SNF7 UNDER 350 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) : 32.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 6472 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 647 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 32.6934 - 3.7594 1.00 1201 133 0.1561 0.2117 REMARK 3 2 3.7594 - 2.9846 1.00 1174 131 0.1840 0.2547 REMARK 3 3 2.9846 - 2.6075 1.00 1178 131 0.2326 0.3301 REMARK 3 4 2.6075 - 2.3692 1.00 1165 130 0.2438 0.3064 REMARK 3 5 2.3692 - 2.1994 0.95 1107 122 0.2420 0.3598 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.340 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 : 0.007 997 REMARK 3 ANGLE : 0.817 1329 REMARK 3 CHIRALITY : 0.040 156 REMARK 3 PLANARITY : 0.006 171 REMARK 3 DIHEDRAL : 16.771 643 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): 21.6292 -0.8140 20.3688 REMARK 3 T TENSOR REMARK 3 T11: 0.2816 T22: 0.2488 REMARK 3 T33: 0.3068 T12: -0.0205 REMARK 3 T13: -0.0100 T23: 0.0314 REMARK 3 L TENSOR REMARK 3 L11: 0.1426 L22: 0.3795 REMARK 3 L33: 0.1193 L12: -0.2634 REMARK 3 L13: -0.0510 L23: 0.1957 REMARK 3 S TENSOR REMARK 3 S11: 0.3331 S12: -0.2831 S13: -0.2874 REMARK 3 S21: -0.1745 S22: -0.0583 S23: -0.0446 REMARK 3 S31: 0.3676 S32: -0.1775 S33: 0.0005 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 60 THROUGH 118 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.2211 9.1945 15.7829 REMARK 3 T TENSOR REMARK 3 T11: 0.2620 T22: 0.3041 REMARK 3 T33: 0.2591 T12: -0.0029 REMARK 3 T13: 0.0089 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 0.1272 L22: 0.0388 REMARK 3 L33: -0.0561 L12: -0.2121 REMARK 3 L13: 0.1112 L23: -0.2601 REMARK 3 S TENSOR REMARK 3 S11: -0.1383 S12: 0.1624 S13: 0.3776 REMARK 3 S21: -0.0080 S22: -0.0082 S23: -0.0086 REMARK 3 S31: -0.0372 S32: -0.0191 S33: -0.0002 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 119 THROUGH 142 ) REMARK 3 ORIGIN FOR THE GROUP (A): -41.3664 28.7229 5.2157 REMARK 3 T TENSOR REMARK 3 T11: 0.4571 T22: 0.4642 REMARK 3 T33: 0.4022 T12: -0.0199 REMARK 3 T13: 0.0205 T23: 0.0503 REMARK 3 L TENSOR REMARK 3 L11: 0.1573 L22: 0.1622 REMARK 3 L33: 0.0655 L12: -0.0948 REMARK 3 L13: 0.0713 L23: 0.0185 REMARK 3 S TENSOR REMARK 3 S11: -0.1357 S12: -0.1154 S13: -0.0069 REMARK 3 S21: -0.2318 S22: -0.2932 S23: 0.0325 REMARK 3 S31: -0.1054 S32: 0.2165 S33: -0.0013 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 5T8L 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_1000223898. 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 : 6489 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 3.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.0000 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 (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 (%): 38.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 6% PEG20000, 110 MM NACL, 70 MM 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 23.73350 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O SER A 119 O HOH A 201 2.16 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 ASP A 124 87.21 80.19 REMARK 500 LYS A 125 92.46 -64.26 REMARK 500 LEU A 139 35.31 -84.32 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5T8B RELATED DB: PDB REMARK 900 RELATED ID: 5T8C RELATED DB: PDB REMARK 900 RELATED ID: 5T8N RELATED DB: PDB REMARK 900 RELATED ID: 5FD9 RELATED DB: PDB REMARK 900 THE SAME PROTEIN UNDER DIFFERENT PRESSURE DBREF 5T8L 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 *47(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 GLU A 138 1 14 CRYST1 30.033 47.467 45.664 90.00 99.13 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 0.033297 0.000000 0.005351 0.00000 SCALE2 0.000000 0.021067 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022180 0.00000