HEADER ENDOCYTOSIS,EXOCYTOSIS 02-JUL-15 5CCI TITLE STRUCTURE OF THE MG2+-BOUND SYNAPTOTAGMIN-1 SNARE COMPLEX (SHORT UNIT TITLE 2 CELL FORM) COMPND MOL_ID: 1; COMPND 2 MOLECULE: VESICLE-ASSOCIATED MEMBRANE PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 28-89; COMPND 5 SYNONYM: VAMP-2,SYNAPTOBREVIN-2; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: SYNTAXIN-1A; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 191-256; COMPND 11 SYNONYM: NEURON-SPECIFIC ANTIGEN HPC-1,SYNAPTOTAGMIN-ASSOCIATED 35 COMPND 12 KDA PROTEIN,P35A; COMPND 13 ENGINEERED: YES; COMPND 14 MOL_ID: 3; COMPND 15 MOLECULE: SYNAPTOSOMAL-ASSOCIATED PROTEIN 25; COMPND 16 CHAIN: C; COMPND 17 FRAGMENT: UNP RESIDUES 7-83; COMPND 18 SYNONYM: SNAP-25,SUPER PROTEIN,SUP,SYNAPTOSOMAL-ASSOCIATED 25 KDA COMPND 19 PROTEIN; COMPND 20 ENGINEERED: YES; COMPND 21 MOL_ID: 4; COMPND 22 MOLECULE: SYNAPTOSOMAL-ASSOCIATED PROTEIN 25; COMPND 23 CHAIN: D; COMPND 24 FRAGMENT: UNP RESIDUES 141-204; COMPND 25 SYNONYM: SNAP-25,SUPER PROTEIN,SUP,SYNAPTOSOMAL-ASSOCIATED 25 KDA COMPND 26 PROTEIN; COMPND 27 ENGINEERED: YES; COMPND 28 MOL_ID: 5; COMPND 29 MOLECULE: SYNAPTOTAGMIN-1; COMPND 30 CHAIN: E, F; COMPND 31 FRAGMENT: UNP RESIDUES 141-421; COMPND 32 SYNONYM: SYNAPTOTAGMIN I,SYTI,P65; COMPND 33 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: VAMP2, SYB2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PACYCDUET-1; SOURCE 11 MOL_ID: 2; SOURCE 12 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 13 ORGANISM_COMMON: RAT; SOURCE 14 ORGANISM_TAXID: 10116; SOURCE 15 GENE: STX1A, SAP; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PACYCDUET-1; SOURCE 21 MOL_ID: 3; SOURCE 22 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 23 ORGANISM_COMMON: RAT; SOURCE 24 ORGANISM_TAXID: 10116; SOURCE 25 GENE: SNAP25, SNAP; SOURCE 26 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 27 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 28 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 29 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 30 EXPRESSION_SYSTEM_PLASMID: PETDUET-1; SOURCE 31 MOL_ID: 4; SOURCE 32 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 33 ORGANISM_COMMON: RAT; SOURCE 34 ORGANISM_TAXID: 10116; SOURCE 35 GENE: SNAP25, SNAP; SOURCE 36 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 37 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 38 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 39 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 40 EXPRESSION_SYSTEM_PLASMID: PETDUET-1; SOURCE 41 MOL_ID: 5; SOURCE 42 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 43 ORGANISM_COMMON: RAT; SOURCE 44 ORGANISM_TAXID: 10116; SOURCE 45 GENE: SYT1; SOURCE 46 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 47 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 48 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 49 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 50 EXPRESSION_SYSTEM_PLASMID: PETDUET-1 KEYWDS SYNAPTIC FUSION COMPLEX, SYNAPTOTAGMIN1, NEURONAL SNARE COMPLEX, KEYWDS 2 ENDOCYTOSIS, EXOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR Q.ZHOU,M.ZHAO,A.Y.LYUBIMOV,M.UERVIROJNANGKOORN,W.I.WEIS,A.T.BRUNGER REVDAT 5 27-SEP-23 5CCI 1 JRNL REMARK LINK REVDAT 4 16-SEP-15 5CCI 1 JRNL REVDAT 3 09-SEP-15 5CCI 1 REMARK REVDAT 2 02-SEP-15 5CCI 1 JRNL REVDAT 1 12-AUG-15 5CCI 0 JRNL AUTH Q.ZHOU,Y.LAI,T.BACAJ,M.ZHAO,A.Y.LYUBIMOV, JRNL AUTH 2 M.UERVIROJNANGKOORN,O.B.ZELDIN,A.S.BREWSTER,N.K.SAUTER, JRNL AUTH 3 A.E.COHEN,S.M.SOLTIS,R.ALONSO-MORI,M.CHOLLET,H.T.LEMKE, JRNL AUTH 4 R.A.PFUETZNER,U.B.CHOI,W.I.WEIS,J.DIAO,T.C.SUDHOF, JRNL AUTH 5 A.T.BRUNGER JRNL TITL ARCHITECTURE OF THE SYNAPTOTAGMIN-SNARE MACHINERY FOR JRNL TITL 2 NEURONAL EXOCYTOSIS. JRNL REF NATURE V. 525 62 2015 JRNL REFN ESSN 1476-4687 JRNL PMID 26280336 JRNL DOI 10.1038/NATURE14975 REMARK 2 REMARK 2 RESOLUTION. 4.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 4.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.24 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 25275 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.279 REMARK 3 R VALUE (WORKING SET) : 0.276 REMARK 3 FREE R VALUE : 0.323 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 1283 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 48.2407 - 8.5145 0.92 2565 139 0.1953 0.2355 REMARK 3 2 8.5145 - 6.7641 0.93 2612 133 0.2512 0.3716 REMARK 3 3 6.7641 - 5.9108 0.97 2681 154 0.3079 0.3167 REMARK 3 4 5.9108 - 5.3712 0.96 2665 139 0.3273 0.3375 REMARK 3 5 5.3712 - 4.9866 0.95 2645 140 0.3031 0.3473 REMARK 3 6 4.9866 - 4.6929 0.97 2691 148 0.3088 0.4038 REMARK 3 7 4.6929 - 4.4580 0.98 2755 122 0.3216 0.3288 REMARK 3 8 4.4580 - 4.2641 0.98 2672 172 0.3556 0.3407 REMARK 3 9 4.2641 - 4.1000 0.97 2706 136 0.3980 0.4434 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.610 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.310 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 133.6 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 193.4 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 : 0.003 6613 REMARK 3 ANGLE : 0.714 8905 REMARK 3 CHIRALITY : 0.032 993 REMARK 3 PLANARITY : 0.002 1157 REMARK 3 DIHEDRAL : 10.490 2517 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN E REMARK 3 SELECTION : CHAIN F REMARK 3 ATOM PAIRS NUMBER : 2280 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5CCI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211388. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-AUG-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.21 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15069 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.996 REMARK 200 RESOLUTION RANGE LOW (A) : 146.561 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11900 REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 4.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 4.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 1.05000 REMARK 200 R SYM FOR SHELL (I) : 1.05000 REMARK 200 FOR SHELL : 0.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1N7S,3F04,1UOW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.75% V/V PEG3350, 25 MM HEPES-NA, 75 REMARK 280 MM NACL, 25 MM MGCL2, PH 7.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 34.53200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 85.87950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.53200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 85.87950 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 300 REMARK: AUTHORS STATE THAT THE BIOLOGICAL ASSEMBLY INCLUDES CHAIN A, REMARK 300 B, C, D, CHAIN E 273-421, CHAIN F 273-421, CHAIN F 141-265 FROM REMARK 300 SYMMETRIC NEIGHBOR. 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: HEPTAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 APPLY THE FOLLOWING TO CHAINS: F REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 -34.53200 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 85.87950 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 146.56100 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 GLY A 27 REMARK 465 MET C 7 REMARK 465 ARG C 8 REMARK 465 ASN C 9 REMARK 465 LYS C 83 REMARK 465 GLY D 204 REMARK 465 LYS E 421 REMARK 465 GLU F 268 REMARK 465 GLU F 269 REMARK 465 GLN F 270 REMARK 465 GLU F 271 REMARK 465 LYS F 272 REMARK 465 LEU F 273 REMARK 465 ASP F 303 REMARK 465 VAL F 304 REMARK 465 GLY F 305 REMARK 465 GLY F 306 REMARK 465 LEU F 307 REMARK 465 ILE F 367 REMARK 465 LYS F 421 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET B 190 CG SD CE REMARK 470 MET D 140 CG SD CE REMARK 470 GLU D 183 CB CG CD OE1 OE2 REMARK 470 ASP D 193 CB CG OD1 OD2 REMARK 470 LEU E 186 CG CD1 CD2 REMARK 470 LYS E 189 CB CG CD CE NZ REMARK 470 LYS E 190 CB CG CD CE NZ REMARK 470 LYS E 191 CB CG CD CE NZ REMARK 470 LYS E 192 CB CG CD CE NZ REMARK 470 LYS E 236 CB CG CD CE NZ REMARK 470 LYS E 267 CG CD CE NZ REMARK 470 GLU E 268 CG CD OE1 OE2 REMARK 470 GLU E 269 CG CD OE1 OE2 REMARK 470 GLN E 270 CG CD OE1 NE2 REMARK 470 GLU E 271 CG CD OE1 OE2 REMARK 470 LYS E 272 CG CD CE NZ REMARK 470 LEU E 273 CG CD1 CD2 REMARK 470 ILE E 367 CB CG1 CG2 CD1 REMARK 470 LYS E 369 CB CG CD CE NZ REMARK 470 VAL E 419 CB CG1 CG2 REMARK 470 LYS E 420 CB CG CD CE NZ REMARK 470 LYS F 141 CB CG CD CE NZ REMARK 470 LYS F 192 CB CG CD CE NZ REMARK 470 GLU F 266 CG CD OE1 OE2 REMARK 470 LYS F 267 CG CD CE NZ REMARK 470 LYS F 300 CB CG CD CE NZ REMARK 470 LYS F 301 CB CG CD CE NZ REMARK 470 LYS F 313 CB CG CD CE NZ REMARK 470 LYS F 325 CB CG CD CE NZ REMARK 470 LYS F 326 CG CD CE NZ REMARK 470 LYS F 327 CB CG CD CE NZ REMARK 470 ASN F 333 CB CG OD1 ND2 REMARK 470 LEU F 335 CB CG CD1 CD2 REMARK 470 LYS F 366 CB CG CD CE NZ REMARK 470 LYS F 369 CB CG CD CE NZ REMARK 470 GLU F 410 CB CG CD OE1 OE2 REMARK 470 GLU F 411 CB CG CD OE1 OE2 REMARK 470 GLU F 412 CB CG CD OE1 OE2 REMARK 470 MET F 416 CB CG SD CE REMARK 470 LYS F 420 CB CG CD CE NZ 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 OD2 ASP F 188 CG LYS F 190 1.81 REMARK 500 O LEU E 142 O GLU E 167 1.98 REMARK 500 O LYS E 222 CG MET E 247 2.01 REMARK 500 CD1 LEU E 142 O ILE E 240 2.08 REMARK 500 N LEU E 186 O THR E 223 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 PRO E 284 CD PRO E 284 N -0.108 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 ALA B 191 -165.80 -164.84 REMARK 500 ILE E 163 -72.88 -80.02 REMARK 500 LYS E 191 43.61 71.93 REMARK 500 LYS E 213 83.58 -68.73 REMARK 500 GLU E 257 115.34 -160.71 REMARK 500 LEU E 294 -73.99 -91.48 REMARK 500 ASP E 309 77.99 -117.89 REMARK 500 LEU E 323 -72.51 -80.73 REMARK 500 ILE F 163 -71.00 -79.90 REMARK 500 LYS F 213 83.07 -68.87 REMARK 500 LEU F 294 -72.83 -91.33 REMARK 500 ASP F 309 76.44 -118.57 REMARK 500 LEU F 323 -73.71 -82.08 REMARK 500 ILE F 373 -60.85 -93.38 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 MG E 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP E 172 OD2 REMARK 620 2 ASP E 178 OD2 57.1 REMARK 620 3 PHE E 231 O 96.7 96.6 REMARK 620 4 ASP E 232 OD1 97.6 154.7 86.2 REMARK 620 5 GLU E 346 OE1 101.4 149.7 62.4 23.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG E 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP E 303 OD1 REMARK 620 2 ASP E 303 OD2 54.2 REMARK 620 3 ASP E 309 OD2 94.1 101.5 REMARK 620 4 ASP E 363 OD2 94.9 119.3 134.9 REMARK 620 5 ASP E 365 OD1 141.2 91.6 112.2 86.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG F 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP F 172 OD2 REMARK 620 2 ASP F 178 OD2 85.5 REMARK 620 3 PHE F 231 O 119.2 113.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG F 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET F 302 O REMARK 620 2 ASP F 363 OD1 98.0 REMARK 620 3 ASP F 363 OD2 105.7 49.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG E 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG E 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG F 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG F 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ASP F 188 and LYS F REMARK 800 190 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide ASP F 188 and LYS F REMARK 800 190 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5CCG RELATED DB: PDB REMARK 900 RELATED ID: 5CCH RELATED DB: PDB DBREF 5CCI A 28 89 UNP P63045 VAMP2_RAT 28 89 DBREF 5CCI B 191 256 UNP P32851 STX1A_RAT 191 256 DBREF 5CCI C 7 83 UNP P60881 SNP25_RAT 7 83 DBREF 5CCI D 141 204 UNP P60881 SNP25_RAT 141 204 DBREF 5CCI E 141 421 UNP P21707 SYT1_RAT 141 421 DBREF 5CCI F 141 421 UNP P21707 SYT1_RAT 141 421 SEQADV 5CCI GLY A 27 UNP P63045 EXPRESSION TAG SEQADV 5CCI MET B 190 UNP P32851 INITIATING METHIONINE SEQADV 5CCI MET D 140 UNP P60881 INITIATING METHIONINE SEQRES 1 A 63 GLY SER ASN ARG ARG LEU GLN GLN THR GLN ALA GLN VAL SEQRES 2 A 63 ASP GLU VAL VAL ASP ILE MET ARG VAL ASN VAL ASP LYS SEQRES 3 A 63 VAL LEU GLU ARG ASP GLN LYS LEU SER GLU LEU ASP ASP SEQRES 4 A 63 ARG ALA ASP ALA LEU GLN ALA GLY ALA SER GLN PHE GLU SEQRES 5 A 63 THR SER ALA ALA LYS LEU LYS ARG LYS TYR TRP SEQRES 1 B 67 MET ALA LEU SER GLU ILE GLU THR ARG HIS SER GLU ILE SEQRES 2 B 67 ILE LYS LEU GLU ASN SER ILE ARG GLU LEU HIS ASP MET SEQRES 3 B 67 PHE MET ASP MET ALA MET LEU VAL GLU SER GLN GLY GLU SEQRES 4 B 67 MET ILE ASP ARG ILE GLU TYR ASN VAL GLU HIS ALA VAL SEQRES 5 B 67 ASP TYR VAL GLU ARG ALA VAL SER ASP THR LYS LYS ALA SEQRES 6 B 67 VAL LYS SEQRES 1 C 77 MET ARG ASN GLU LEU GLU GLU MET GLN ARG ARG ALA ASP SEQRES 2 C 77 GLN LEU ALA ASP GLU SER LEU GLU SER THR ARG ARG MET SEQRES 3 C 77 LEU GLN LEU VAL GLU GLU SER LYS ASP ALA GLY ILE ARG SEQRES 4 C 77 THR LEU VAL MET LEU ASP GLU GLN GLY GLU GLN LEU ASP SEQRES 5 C 77 ARG VAL GLU GLU GLY MET ASN HIS ILE ASN GLN ASP MET SEQRES 6 C 77 LYS GLU ALA GLU LYS ASN LEU LYS ASP LEU GLY LYS SEQRES 1 D 65 MET ALA ARG GLU ASN GLU MET ASP GLU ASN LEU GLU GLN SEQRES 2 D 65 VAL SER GLY ILE ILE GLY ASN LEU ARG HIS MET ALA LEU SEQRES 3 D 65 ASP MET GLY ASN GLU ILE ASP THR GLN ASN ARG GLN ILE SEQRES 4 D 65 ASP ARG ILE MET GLU LYS ALA ASP SER ASN LYS THR ARG SEQRES 5 D 65 ILE ASP GLU ALA ASN GLN ARG ALA THR LYS MET LEU GLY SEQRES 1 E 281 LYS LEU GLY LYS LEU GLN TYR SER LEU ASP TYR ASP PHE SEQRES 2 E 281 GLN ASN ASN GLN LEU LEU VAL GLY ILE ILE GLN ALA ALA SEQRES 3 E 281 GLU LEU PRO ALA LEU ASP MET GLY GLY THR SER ASP PRO SEQRES 4 E 281 TYR VAL LYS VAL PHE LEU LEU PRO ASP LYS LYS LYS LYS SEQRES 5 E 281 PHE GLU THR LYS VAL HIS ARG LYS THR LEU ASN PRO VAL SEQRES 6 E 281 PHE ASN GLU GLN PHE THR PHE LYS VAL PRO TYR SER GLU SEQRES 7 E 281 LEU GLY GLY LYS THR LEU VAL MET ALA VAL TYR ASP PHE SEQRES 8 E 281 ASP ARG PHE SER LYS HIS ASP ILE ILE GLY GLU PHE LYS SEQRES 9 E 281 VAL PRO MET ASN THR VAL ASP PHE GLY HIS VAL THR GLU SEQRES 10 E 281 GLU TRP ARG ASP LEU GLN SER ALA GLU LYS GLU GLU GLN SEQRES 11 E 281 GLU LYS LEU GLY ASP ILE CYS PHE SER LEU ARG TYR VAL SEQRES 12 E 281 PRO THR ALA GLY LYS LEU THR VAL VAL ILE LEU GLU ALA SEQRES 13 E 281 LYS ASN LEU LYS LYS MET ASP VAL GLY GLY LEU SER ASP SEQRES 14 E 281 PRO TYR VAL LYS ILE HIS LEU MET GLN ASN GLY LYS ARG SEQRES 15 E 281 LEU LYS LYS LYS LYS THR THR ILE LYS LYS ASN THR LEU SEQRES 16 E 281 ASN PRO TYR TYR ASN GLU SER PHE SER PHE GLU VAL PRO SEQRES 17 E 281 PHE GLU GLN ILE GLN LYS VAL GLN VAL VAL VAL THR VAL SEQRES 18 E 281 LEU ASP TYR ASP LYS ILE GLY LYS ASN ASP ALA ILE GLY SEQRES 19 E 281 LYS VAL PHE VAL GLY TYR ASN SER THR GLY ALA GLU LEU SEQRES 20 E 281 ARG HIS TRP SER ASP MET LEU ALA ASN PRO ARG ARG PRO SEQRES 21 E 281 ILE ALA GLN TRP HIS THR LEU GLN VAL GLU GLU GLU VAL SEQRES 22 E 281 ASP ALA MET LEU ALA VAL LYS LYS SEQRES 1 F 281 LYS LEU GLY LYS LEU GLN TYR SER LEU ASP TYR ASP PHE SEQRES 2 F 281 GLN ASN ASN GLN LEU LEU VAL GLY ILE ILE GLN ALA ALA SEQRES 3 F 281 GLU LEU PRO ALA LEU ASP MET GLY GLY THR SER ASP PRO SEQRES 4 F 281 TYR VAL LYS VAL PHE LEU LEU PRO ASP LYS LYS LYS LYS SEQRES 5 F 281 PHE GLU THR LYS VAL HIS ARG LYS THR LEU ASN PRO VAL SEQRES 6 F 281 PHE ASN GLU GLN PHE THR PHE LYS VAL PRO TYR SER GLU SEQRES 7 F 281 LEU GLY GLY LYS THR LEU VAL MET ALA VAL TYR ASP PHE SEQRES 8 F 281 ASP ARG PHE SER LYS HIS ASP ILE ILE GLY GLU PHE LYS SEQRES 9 F 281 VAL PRO MET ASN THR VAL ASP PHE GLY HIS VAL THR GLU SEQRES 10 F 281 GLU TRP ARG ASP LEU GLN SER ALA GLU LYS GLU GLU GLN SEQRES 11 F 281 GLU LYS LEU GLY ASP ILE CYS PHE SER LEU ARG TYR VAL SEQRES 12 F 281 PRO THR ALA GLY LYS LEU THR VAL VAL ILE LEU GLU ALA SEQRES 13 F 281 LYS ASN LEU LYS LYS MET ASP VAL GLY GLY LEU SER ASP SEQRES 14 F 281 PRO TYR VAL LYS ILE HIS LEU MET GLN ASN GLY LYS ARG SEQRES 15 F 281 LEU LYS LYS LYS LYS THR THR ILE LYS LYS ASN THR LEU SEQRES 16 F 281 ASN PRO TYR TYR ASN GLU SER PHE SER PHE GLU VAL PRO SEQRES 17 F 281 PHE GLU GLN ILE GLN LYS VAL GLN VAL VAL VAL THR VAL SEQRES 18 F 281 LEU ASP TYR ASP LYS ILE GLY LYS ASN ASP ALA ILE GLY SEQRES 19 F 281 LYS VAL PHE VAL GLY TYR ASN SER THR GLY ALA GLU LEU SEQRES 20 F 281 ARG HIS TRP SER ASP MET LEU ALA ASN PRO ARG ARG PRO SEQRES 21 F 281 ILE ALA GLN TRP HIS THR LEU GLN VAL GLU GLU GLU VAL SEQRES 22 F 281 ASP ALA MET LEU ALA VAL LYS LYS HET MG E 501 1 HET MG E 502 1 HET MG F 501 1 HET MG F 502 1 HETNAM MG MAGNESIUM ION FORMUL 7 MG 4(MG 2+) HELIX 1 AA1 SER A 28 TRP A 89 1 62 HELIX 2 AA2 ALA B 191 LYS B 256 1 66 HELIX 3 AA3 LEU C 11 GLY C 82 1 72 HELIX 4 AA4 ALA D 141 MET D 202 1 62 HELIX 5 AA5 PRO E 215 GLY E 220 1 6 HELIX 6 AA6 GLN E 351 LYS E 354 5 4 HELIX 7 AA7 GLY E 384 ASN E 396 1 13 HELIX 8 AA8 VAL E 409 ALA E 418 1 10 HELIX 9 AA9 PRO F 215 GLY F 220 1 6 HELIX 10 AB1 GLN F 351 LYS F 354 5 4 HELIX 11 AB2 GLY F 384 ASN F 396 1 13 HELIX 12 AB3 VAL F 409 ALA F 418 1 10 SHEET 1 AA1 4 VAL E 205 PHE E 212 0 SHEET 2 AA1 4 GLN E 157 ALA E 166 -1 N LEU E 158 O PHE E 212 SHEET 3 AA1 4 LYS E 144 ASP E 152 -1 N SER E 148 O GLY E 161 SHEET 4 AA1 4 THR E 256 ASP E 261 -1 O GLU E 258 N TYR E 147 SHEET 1 AA2 4 PHE E 193 GLU E 194 0 SHEET 2 AA2 4 PRO E 179 LEU E 185 -1 N VAL E 183 O PHE E 193 SHEET 3 AA2 4 THR E 223 ASP E 230 -1 O ALA E 227 N LYS E 182 SHEET 4 AA2 4 ILE E 239 PRO E 246 -1 O ILE E 240 N VAL E 228 SHEET 1 AA3 4 TYR E 338 GLU E 346 0 SHEET 2 AA3 4 LYS E 288 LYS E 297 -1 N LEU E 289 O PHE E 345 SHEET 3 AA3 4 ASP E 275 VAL E 283 -1 N ARG E 281 O THR E 290 SHEET 4 AA3 4 ILE E 401 THR E 406 -1 O GLN E 403 N PHE E 278 SHEET 1 AA4 4 LYS E 321 LYS E 327 0 SHEET 2 AA4 4 PRO E 310 GLN E 318 -1 N LEU E 316 O LEU E 323 SHEET 3 AA4 4 GLN E 356 ASP E 363 -1 O THR E 360 N LYS E 313 SHEET 4 AA4 4 ALA E 372 GLY E 379 -1 O VAL E 378 N VAL E 357 SHEET 1 AA5 4 VAL F 205 PHE F 212 0 SHEET 2 AA5 4 GLN F 157 ALA F 166 -1 N ILE F 163 O ASN F 207 SHEET 3 AA5 4 LYS F 144 ASP F 152 -1 N SER F 148 O GLY F 161 SHEET 4 AA5 4 THR F 256 ASP F 261 -1 O THR F 256 N LEU F 149 SHEET 1 AA6 4 PHE F 193 GLU F 194 0 SHEET 2 AA6 4 PRO F 179 LEU F 185 -1 N VAL F 183 O PHE F 193 SHEET 3 AA6 4 THR F 223 ASP F 230 -1 O ALA F 227 N LYS F 182 SHEET 4 AA6 4 ILE F 239 GLY F 241 -1 O ILE F 240 N VAL F 228 SHEET 1 AA7 4 PHE F 193 GLU F 194 0 SHEET 2 AA7 4 PRO F 179 LEU F 185 -1 N VAL F 183 O PHE F 193 SHEET 3 AA7 4 THR F 223 ASP F 230 -1 O ALA F 227 N LYS F 182 SHEET 4 AA7 4 LYS F 244 PRO F 246 -1 O VAL F 245 N LEU F 224 SHEET 1 AA8 4 TYR F 338 GLU F 346 0 SHEET 2 AA8 4 LYS F 288 LYS F 297 -1 N ILE F 293 O GLU F 341 SHEET 3 AA8 4 ASP F 275 VAL F 283 -1 N ARG F 281 O THR F 290 SHEET 4 AA8 4 ILE F 401 THR F 406 -1 O ILE F 401 N LEU F 280 SHEET 1 AA9 4 LYS F 321 LYS F 327 0 SHEET 2 AA9 4 PRO F 310 GLN F 318 -1 N LEU F 316 O LYS F 324 SHEET 3 AA9 4 GLN F 356 ASP F 363 -1 O THR F 360 N LYS F 313 SHEET 4 AA9 4 GLY F 374 GLY F 379 -1 O GLY F 374 N VAL F 361 LINK OD2 ASP F 188 CD LYS F 190 1555 1555 1.54 LINK OD2 ASP F 188 CE LYS F 190 1555 1555 1.48 LINK OD2 ASP E 172 MG MG E 502 1555 1555 2.86 LINK OD2 ASP E 178 MG MG E 502 1555 1555 2.92 LINK O PHE E 231 MG MG E 502 1555 1555 2.32 LINK OD1 ASP E 232 MG MG E 502 1555 1555 2.97 LINK OD1 ASP E 303 MG MG E 501 1555 1555 2.56 LINK OD2 ASP E 303 MG MG E 501 1555 1555 2.21 LINK OD2 ASP E 309 MG MG E 501 1555 1555 3.00 LINK OE1 GLU E 346 MG MG E 502 1555 4455 2.75 LINK OD2 ASP E 363 MG MG E 501 1555 1555 2.74 LINK OD1 ASP E 365 MG MG E 501 1555 1555 2.30 LINK OD2 ASP F 172 MG MG F 501 1555 1555 2.08 LINK OD2 ASP F 178 MG MG F 501 1555 1555 2.11 LINK O PHE F 231 MG MG F 501 1555 1555 2.32 LINK O MET F 302 MG MG F 502 1555 1555 2.37 LINK OD1 ASP F 363 MG MG F 502 1555 1555 2.80 LINK OD2 ASP F 363 MG MG F 502 1555 1555 2.29 SITE 1 AC1 5 ASP E 303 ASP E 309 ASP E 363 TYR E 364 SITE 2 AC1 5 ASP E 365 SITE 1 AC2 5 ASP E 172 ASP E 178 PHE E 231 ASP E 232 SITE 2 AC2 5 GLU E 346 SITE 1 AC3 4 ASP F 172 ASP F 178 PHE F 231 GLU F 346 SITE 1 AC4 3 MET F 302 ASP F 363 ASP F 365 SITE 1 AC5 7 LEU F 185 LEU F 186 PRO F 187 LYS F 189 SITE 2 AC5 7 LYS F 191 LYS F 192 VAL F 214 SITE 1 AC6 7 LEU F 185 LEU F 186 PRO F 187 LYS F 189 SITE 2 AC6 7 LYS F 191 LYS F 192 VAL F 214 CRYST1 69.064 171.759 146.561 90.00 90.00 90.00 P 21 21 2 8 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 0.014479 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005822 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006823 0.00000