10 20 30 40 50 60 70 80 1FIO - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER MEMBRANE PROTEIN 04-AUG-00 1FIO
TITLE CRYSTAL STRUCTURE OF YEAST T-SNARE PROTEIN SSO1
COMPND MOL_ID: 1; COMPND 2 MOLECULE: SSO1 PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CYTOPLASMIC DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: YEAST T-SNARE PROTEIN
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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PLM-1
KEYWDS FOUR HELIX BUNDLE, ALPHA HELIX, MEMBRANE PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR M.MUNSON,X.CHEN,A.E.COCINA,S.M.SCHULTZ,F.M.HUGHSON
REVDAT 2 24-FEB-09 1FIO 1 VERSN REVDAT 1 11-OCT-00 1FIO 0
JRNL AUTH M.MUNSON,X.CHEN,A.E.COCINA,S.M.SCHULTZ,F.M.HUGHSON JRNL TITL INTERACTIONS WITHIN THE YEAST T-SNARE SSO1P THAT JRNL TITL 2 CONTROL SNARE COMPLEX ASSEMBLY. JRNL REF NAT.STRUCT.BIOL. V. 7 894 2000 JRNL REFN ISSN 1072-8368 JRNL PMID 11017200 JRNL DOI 10.1038/79659
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.10 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 14025 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) : 0.219 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1398 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.17 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1239 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 126 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1553 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.20 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 8.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 0.90 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.59 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) : 4.830 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.640 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 5.380 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 8.850 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.46 REMARK 3 BSOL : 80.72 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 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MAXIMUM LIKELIHOOD TARGET USING REMARK 3 AMPLITUDES
REMARK 4 REMARK 4 1FIO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-AUG-00. REMARK 100 THE RCSB ID CODE IS RCSB011620.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAR-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X12C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979345 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18088 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : 0.07400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.38000 REMARK 200 R SYM FOR SHELL (I) : 0.38000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIWAVELENGTH REMARK 200 ANOMALOUS DIFFRACTION REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES, PEG 4000, ISOPROPANOL, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 21.25850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.92000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.92750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.92000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.25850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.92750 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: MONOMERIC 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 179 REMARK 465 ALA A 180 REMARK 465 ASN A 181 REMARK 465 ARG A 182 REMARK 465 ARG A 183 REMARK 465 GLY A 184
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 153 -7.95 -54.79 REMARK 500 LEU A 177 27.95 -66.64 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 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 30 N REMARK 620 2 HIS A 31 N 84.9 REMARK 620 3 HIS A 31 ND1 165.7 98.4 REMARK 620 4 HIS A 197 NE2 99.2 118.1 91.6 REMARK 620 5 ASP A 166 OD1 85.1 134.5 82.7 107.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 78 ND1 REMARK 620 2 HIS A 75 ND1 112.4 REMARK 620 3 HIS A 107 NE2 117.7 101.2 REMARK 620 4 GLU A 223 OE1 100.9 139.8 81.6 REMARK 620 5 GLU A 223 OE2 145.9 82.7 86.9 57.3 REMARK 620 N 1 2 3 4
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 501 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 502
DBREF 1FIO A 31 225 UNP P32867 SSO1_YEAST 31 225
SEQADV 1FIO MET A 30 UNP P32867 INITIATING MET
SEQRES 1 A 196 MET HIS ASP PHE VAL GLY PHE MET ASN LYS ILE SER GLN SEQRES 2 A 196 ILE ASN ARG ASP LEU ASP LYS TYR ASP HIS THR ILE ASN SEQRES 3 A 196 GLN VAL ASP SER LEU HIS LYS ARG LEU LEU THR GLU VAL SEQRES 4 A 196 ASN GLU GLU GLN ALA SER HIS LEU ARG HIS SER LEU ASP SEQRES 5 A 196 ASN PHE VAL ALA GLN ALA THR ASP LEU GLN PHE LYS LEU SEQRES 6 A 196 LYS ASN GLU ILE LYS SER ALA GLN ARG ASP GLY ILE HIS SEQRES 7 A 196 ASP THR ASN LYS GLN ALA GLN ALA GLU ASN SER ARG GLN SEQRES 8 A 196 ARG PHE LEU LYS LEU ILE GLN ASP TYR ARG ILE VAL ASP SEQRES 9 A 196 SER ASN TYR LYS GLU GLU ASN LYS GLU GLN ALA LYS ARG SEQRES 10 A 196 GLN TYR MET ILE ILE GLN PRO GLU ALA THR GLU ASP GLU SEQRES 11 A 196 VAL GLU ALA ALA ILE SER ASP VAL GLY GLY GLN GLN ILE SEQRES 12 A 196 PHE SER GLN ALA LEU LEU ASN ALA ASN ARG ARG GLY GLU SEQRES 13 A 196 ALA LYS THR ALA LEU ALA GLU VAL GLN ALA ARG HIS GLN SEQRES 14 A 196 GLU LEU LEU LYS LEU GLU LYS SER MET ALA GLU LEU THR SEQRES 15 A 196 GLN LEU PHE ASN ASP MET GLU GLU LEU VAL ILE GLU GLN SEQRES 16 A 196 GLN
HET ZN A 501 1 HET ZN A 502 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 2(ZN 2+) FORMUL 4 HOH *153(H2 O)
HELIX 1 1 MET A 30 LEU A 65 1 36 HELIX 2 2 ASN A 69 GLY A 105 1 37 HELIX 3 3 ASP A 108 GLN A 152 1 45 HELIX 4 4 THR A 156 ILE A 164 1 9 HELIX 5 5 SER A 165 LEU A 177 1 13 HELIX 6 6 GLU A 185 GLU A 219 1 35
LINK ZN ZN A 501 N MET A 30 1555 1555 2.09 LINK ZN ZN A 501 N HIS A 31 1555 1555 1.96 LINK ZN ZN A 501 ND1 HIS A 31 1555 1555 2.23 LINK ZN ZN A 502 ND1 HIS A 78 1555 1555 2.09 LINK ZN ZN A 502 ND1 HIS A 75 1555 1555 2.14 LINK ZN ZN A 501 NE2 HIS A 197 1555 3646 2.03 LINK ZN ZN A 501 OD1 ASP A 166 1555 3646 1.90 LINK ZN ZN A 502 NE2 HIS A 107 1555 3646 2.02 LINK ZN ZN A 502 OE1 GLU A 223 1555 3646 2.56 LINK ZN ZN A 502 OE2 GLU A 223 1555 3646 1.88
SITE 1 AC1 4 MET A 30 HIS A 31 ASP A 166 HIS A 197 SITE 1 AC2 4 HIS A 75 HIS A 78 HIS A 107 GLU A 223
CRYST1 42.517 49.855 113.840 90.00 90.00 90.00 P 21 21 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 0.023520 0.000000 0.000000 0.00000
SCALE2 0.000000 0.020058 0.000000 0.00000
SCALE3 0.000000 0.000000 0.008784 0.00000