HEADER PROTEIN TRANSPORT 04-JUN-99 1QQE TITLE CRYSTAL STRUCTURE OF THE VESICULAR TRANSPORT PROTEIN SEC17 COMPND MOL_ID: 1; COMPND 2 MOLECULE: VESICULAR TRANSPORT PROTEIN SEC17; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: 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; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEX-4T-1 KEYWDS HELIX-TURN-HELIX TPR-LIKE REPEAT, PROTEIN TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR L.M.RICE,A.T.BRUNGER REVDAT 5 14-FEB-24 1QQE 1 REMARK REVDAT 4 03-NOV-21 1QQE 1 SEQADV REVDAT 3 24-FEB-09 1QQE 1 VERSN REVDAT 2 01-APR-03 1QQE 1 JRNL REVDAT 1 08-SEP-99 1QQE 0 JRNL AUTH L.M.RICE,A.T.BRUNGER JRNL TITL CRYSTAL STRUCTURE OF THE VESICULAR TRANSPORT PROTEIN SEC17: JRNL TITL 2 IMPLICATIONS FOR SNAP FUNCTION IN SNARE COMPLEX DISASSEMBLY. JRNL REF MOL.CELL V. 4 85 1999 JRNL REFN ISSN 1097-2765 JRNL PMID 10445030 JRNL DOI 10.1016/S1097-2765(00)80190-2 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.5 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1407425.600 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 11625 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) : 0.260 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.500 REMARK 3 FREE R VALUE TEST SET COUNT : 1098 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3144 REMARK 3 BIN R VALUE (WORKING SET) : 0.4410 REMARK 3 BIN FREE R VALUE : 0.4750 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 378 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2216 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 4 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 90.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 67.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.25000 REMARK 3 B22 (A**2) : -7.25000 REMARK 3 B33 (A**2) : 14.51000 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) : 0.48 REMARK 3 ESD FROM SIGMAA (A) : 0.73 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) : 0.51 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.81 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 : 0.35 REMARK 3 BSOL : 30.45 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.PA REMARK 3 PARAMETER FILE 2 : WATER_REP.PARA REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1QQE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY NDB. REMARK 100 THE DEPOSITION ID IS D_1000009144. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-FEB-99 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11997 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.47200 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: NULL REMARK 200 SOFTWARE USED: CNS 0.5 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POLYETHYLENEIMINE, SODIUM CITRATE, REMARK 280 SODIUM CHLORIDE, GLYCEROL, DTT, PH 5.9, MICROBATCH, TEMPERATURE REMARK 280 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 23.05000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.52500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 34.57500 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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 GLU A 228 REMARK 465 ASP A 229 REMARK 465 PRO A 230 REMARK 465 ASN A 231 REMARK 465 PHE A 232 REMARK 465 ALA A 233 REMARK 465 ASP A 234 REMARK 465 SER A 235 REMARK 465 ARG A 236 REMARK 465 LEU A 291 REMARK 465 LEU A 292 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 28 156.91 -26.10 REMARK 500 LEU A 53 -66.69 18.42 REMARK 500 ALA A 76 -82.94 -63.13 REMARK 500 SER A 89 -17.77 -45.80 REMARK 500 ASP A 130 -86.52 -108.88 REMARK 500 ASP A 133 70.79 -104.97 REMARK 500 TYR A 141 -17.80 -48.06 REMARK 500 ASP A 151 -1.65 -59.81 REMARK 500 GLN A 152 16.67 56.90 REMARK 500 ALA A 155 -63.65 -22.48 REMARK 500 ASP A 171 -2.14 -57.38 REMARK 500 SER A 178 -19.60 -49.89 REMARK 500 SER A 187 48.76 -87.89 REMARK 500 SER A 188 -9.21 -152.00 REMARK 500 ARG A 192 6.40 -64.64 REMARK 500 GLN A 195 -58.38 -16.18 REMARK 500 ASP A 214 78.80 -105.63 REMARK 500 SER A 238 -17.36 -47.59 REMARK 500 ASP A 246 -68.53 -91.45 REMARK 500 ALA A 247 -28.76 -34.82 REMARK 500 ASN A 249 -4.03 -47.77 REMARK 500 SER A 253 42.76 -70.69 REMARK 500 GLU A 254 -30.96 -142.10 REMARK 500 SER A 257 -11.07 -46.56 REMARK 500 PHE A 263 -16.93 -48.52 REMARK 500 MET A 267 67.34 160.29 REMARK 500 ARG A 268 131.07 -28.62 REMARK 500 LYS A 271 -52.71 -23.35 REMARK 500 SER A 283 -18.07 -47.61 REMARK 500 REMARK 500 REMARK: NULL DBREF 1QQE A 1 292 UNP P32602 SEC17_YEAST 1 292 SEQADV 1QQE ILE A 1 UNP P32602 MET 1 ENGINEERED MUTATION SEQRES 1 A 292 ILE SER ASP PRO VAL GLU LEU LEU LYS ARG ALA GLU LYS SEQRES 2 A 292 LYS GLY VAL PRO SER SER GLY PHE MET LYS LEU PHE SER SEQRES 3 A 292 GLY SER ASP SER TYR LYS PHE GLU GLU ALA ALA ASP LEU SEQRES 4 A 292 CYS VAL GLN ALA ALA THR ILE TYR ARG LEU ARG LYS GLU SEQRES 5 A 292 LEU ASN LEU ALA GLY ASP SER PHE LEU LYS ALA ALA ASP SEQRES 6 A 292 TYR GLN LYS LYS ALA GLY ASN GLU ASP GLU ALA GLY ASN SEQRES 7 A 292 THR TYR VAL GLU ALA TYR LYS CYS PHE LYS SER GLY GLY SEQRES 8 A 292 ASN SER VAL ASN ALA VAL ASP SER LEU GLU ASN ALA ILE SEQRES 9 A 292 GLN ILE PHE THR HIS ARG GLY GLN PHE ARG ARG GLY ALA SEQRES 10 A 292 ASN PHE LYS PHE GLU LEU GLY GLU ILE LEU GLU ASN ASP SEQRES 11 A 292 LEU HIS ASP TYR ALA LYS ALA ILE ASP CYS TYR GLU LEU SEQRES 12 A 292 ALA GLY GLU TRP TYR ALA GLN ASP GLN SER VAL ALA LEU SEQRES 13 A 292 SER ASN LYS CYS PHE ILE LYS CYS ALA ASP LEU LYS ALA SEQRES 14 A 292 LEU ASP GLY GLN TYR ILE GLU ALA SER ASP ILE TYR SER SEQRES 15 A 292 LYS LEU ILE LYS SER SER MET GLY ASN ARG LEU SER GLN SEQRES 16 A 292 TRP SER LEU LYS ASP TYR PHE LEU LYS LYS GLY LEU CYS SEQRES 17 A 292 GLN LEU ALA ALA THR ASP ALA VAL ALA ALA ALA ARG THR SEQRES 18 A 292 LEU GLN GLU GLY GLN SER GLU ASP PRO ASN PHE ALA ASP SEQRES 19 A 292 SER ARG GLU SER ASN PHE LEU LYS SER LEU ILE ASP ALA SEQRES 20 A 292 VAL ASN GLU GLY ASP SER GLU GLN LEU SER GLU HIS CYS SEQRES 21 A 292 LYS GLU PHE ASP ASN PHE MET ARG LEU ASP LYS TRP LYS SEQRES 22 A 292 ILE THR ILE LEU ASN LYS ILE LYS GLU SER ILE GLN GLN SEQRES 23 A 292 GLN GLU ASP ASP LEU LEU FORMUL 2 HOH *4(H2 O) HELIX 1 1 ASP A 3 GLY A 15 1 13 HELIX 2 2 GLY A 20 SER A 26 1 7 HELIX 3 3 ASP A 29 ARG A 50 1 22 HELIX 4 4 LEU A 53 ALA A 70 1 18 HELIX 5 5 ASN A 72 GLY A 90 1 19 HELIX 6 6 ASN A 92 ARG A 110 1 19 HELIX 7 7 GLN A 112 ASP A 130 1 19 HELIX 8 8 ASP A 133 ASP A 151 1 19 HELIX 9 9 SER A 153 ASP A 171 1 19 HELIX 10 10 GLN A 173 SER A 187 1 15 HELIX 11 11 SER A 194 TRP A 196 5 3 HELIX 12 12 SER A 197 ALA A 212 1 16 HELIX 13 13 ASP A 214 GLU A 224 1 11 HELIX 14 14 GLY A 225 SER A 227 5 3 HELIX 15 15 GLU A 237 GLU A 250 1 14 HELIX 16 16 GLN A 255 ASP A 264 1 10 HELIX 17 17 ASP A 270 ASP A 289 1 20 CRYST1 107.900 107.900 46.100 90.00 90.00 90.00 P 41 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 0.009268 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009268 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021692 0.00000