HEADER METAL BINDING PROTEIN 16-JUN-04 1W15 TITLE RAT SYNAPTOTAGMIN 4 C2B DOMAIN IN THE PRESENCE OF CALCIUM COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN IV; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C2B DOMAIN, RESIDUES 288-425; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PGEX-KG KEYWDS METAL BINDING PROTEIN, SYNAPTOTAGMIN, ENDOCYTOSIS/EXOCYTOSIS, KEYWDS 2 NEUROTRANSMITTER RELEASE, TRANSMEMBRANE EXPDTA X-RAY DIFFRACTION AUTHOR H.DAI,O.-H.SHIN,M.MACHIUS,D.R.TOMCHICK,T.C.SUDHOF,J.RIZO REVDAT 6 13-DEC-23 1W15 1 LINK REVDAT 5 08-MAY-19 1W15 1 REMARK REVDAT 4 13-JUL-11 1W15 1 VERSN REVDAT 3 24-FEB-09 1W15 1 VERSN REVDAT 2 15-JUN-05 1W15 1 JRNL REVDAT 1 13-AUG-04 1W15 0 JRNL AUTH H.DAI,O.-H.SHIN,M.MACHIUS,D.R.TOMCHICK,T.C.SUDHOF,J.RIZO JRNL TITL STRUCTURAL BASIS FOR THE EVOLUTIONARY INACTIVATION OF CA2+ JRNL TITL 2 BINDING TO SYNAPTOTAGMIN 4 JRNL REF NAT.STRUCT.MOL.BIOL. V. 11 844 2004 JRNL REFN ISSN 1545-9993 JRNL PMID 15311271 JRNL DOI 10.1038/NSMB817 REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 21854 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 + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1475 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1580 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.71 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 110 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1046 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.26000 REMARK 3 B22 (A**2) : 0.26000 REMARK 3 B33 (A**2) : -0.38000 REMARK 3 B12 (A**2) : 0.13000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.106 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.107 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.305 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.941 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1101 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1491 ; 1.821 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 137 ; 6.377 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 46 ;40.182 ;23.261 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 203 ;15.780 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;12.574 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 171 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 813 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 478 ; 0.260 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 733 ; 0.332 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 89 ; 0.200 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 7 ; 0.152 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 33 ; 0.215 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.209 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 678 ; 1.214 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1104 ; 2.218 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 436 ; 3.159 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 387 ; 5.166 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 273 A 300 REMARK 3 ORIGIN FOR THE GROUP (A): 41.4910 15.5260 45.9790 REMARK 3 T TENSOR REMARK 3 T11: .0231 T22: -.0328 REMARK 3 T33: -.1175 T12: -.0080 REMARK 3 T13: .0174 T23: .0523 REMARK 3 L TENSOR REMARK 3 L11: 11.8141 L22: 2.9823 REMARK 3 L33: 17.4147 L12: -1.5627 REMARK 3 L13: -11.8861 L23: -.5617 REMARK 3 S TENSOR REMARK 3 S11: -.2882 S12: .1351 S13: -.2541 REMARK 3 S21: -.1922 S22: -.0476 S23: -.0938 REMARK 3 S31: .3473 S32: .0227 S33: .3358 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 308 A 331 REMARK 3 ORIGIN FOR THE GROUP (A): 38.8400 13.4830 57.9630 REMARK 3 T TENSOR REMARK 3 T11: .0853 T22: -.0350 REMARK 3 T33: -.1245 T12: -.0185 REMARK 3 T13: .0352 T23: .0365 REMARK 3 L TENSOR REMARK 3 L11: 3.6312 L22: 4.7516 REMARK 3 L33: 4.0646 L12: -1.4647 REMARK 3 L13: -1.0775 L23: .3406 REMARK 3 S TENSOR REMARK 3 S11: -.1729 S12: -.1310 S13: .0770 REMARK 3 S21: .6471 S22: .1660 S23: .2303 REMARK 3 S31: .1607 S32: -.2863 S33: .0069 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 336 A 409 REMARK 3 ORIGIN FOR THE GROUP (A): 43.0290 9.7620 51.6930 REMARK 3 T TENSOR REMARK 3 T11: .0394 T22: -.0750 REMARK 3 T33: -.1389 T12: .0020 REMARK 3 T13: .0045 T23: .0111 REMARK 3 L TENSOR REMARK 3 L11: 1.3110 L22: 3.6168 REMARK 3 L33: 3.3558 L12: -.1172 REMARK 3 L13: .0140 L23: -1.5730 REMARK 3 S TENSOR REMARK 3 S11: -.0322 S12: .0053 S13: -.0511 REMARK 3 S21: .0556 S22: .0364 S23: -.0741 REMARK 3 S31: .2545 S32: -.0787 S33: -.0042 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1W15 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1290015598. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-NOV-03 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 7.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9876 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : CUSTOM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23368 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 REMARK 200 RESOLUTION RANGE LOW (A) : 37.684 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 41.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.96 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.50 REMARK 200 R MERGE FOR SHELL (I) : 0.71900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1K5W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 72.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE RAT SYNAPTOTAGMIN IV C2B DOMAIN REMARK 280 WAS CRYSTALLIZED BY THE VAPOR DIFFUSION METHOD (HANGING DROP) BY REMARK 280 MIXING 1 MICROLITER PROTEIN (IN 20 MM MES, 150 MM NACL AND 1 MM REMARK 280 EDTA, PH 6.32) WITH 1 MICROLITER RESERVOIR SOLUTION (2.5M NACL, REMARK 280 0.1M CACL2, 0.1M HEPES, PH 7.5) SUSPENDED OVER 500 MICROLITERS REMARK 280 RESERVOIR SOLUTION. HEXAGONAL CRYSTALS APPEARED OVERNIGHT AND REMARK 280 GREW TO A FINAL SIZE OF 0.1 X 0.1 X 0.2 MM WITHIN TWO DAYS. REMARK 280 PRIOR TO DATA COLLECTION, CRYSTALS WERE TRANSFERRED INTO REMARK 280 CRYSTALLIZATION SOLUTION CONTAINING 20% (V/V) ETHYLENE GLYCOL REMARK 280 FOR CRYSTALS GROWN IN 0.1 M CACL2, AND THEN COOLED IN LIQUID REMARK 280 PROPANE., PH 7.50, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 61.07100 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 61.07100 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 61.07100 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 61.07100 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 61.07100 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 61.07100 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PQS 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 45.74500 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 79.23266 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 91.49000 REMARK 350 BIOMT2 3 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 CL CL A3001 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 MAY BE INVOLVED IN CA(2+)-DEPENDENT EXOCYTOSIS OF REMARK 400 SECRETORY VESICLES THROUGH CA(2+) 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 273 REMARK 465 SER A 274 REMARK 465 PRO A 275 REMARK 465 GLY A 276 REMARK 465 ILE A 277 REMARK 465 SER A 278 REMARK 465 GLY A 279 REMARK 465 GLY A 280 REMARK 465 GLY A 281 REMARK 465 GLY A 282 REMARK 465 GLY A 283 REMARK 465 ILE A 284 REMARK 465 PRO A 285 REMARK 465 SER A 286 REMARK 465 GLY A 287 REMARK 465 LYS A 316 REMARK 465 SER A 317 REMARK 465 ASP A 318 REMARK 465 VAL A 319 REMARK 465 SER A 320 REMARK 465 GLY A 321 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 OE1 GLN A 415 O HOH A 2084 1.96 REMARK 500 CL CL A 3003 O HOH A 2018 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2042 O HOH A 2076 11655 2.15 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 LEU A 309 -64.60 -95.21 REMARK 500 ASP A 324 78.51 -118.31 REMARK 500 ALA A 334 -116.73 59.38 REMARK 500 ARG A 413 -0.21 75.82 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 CA A1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 324 OD2 REMARK 620 2 ASP A 378 OD2 140.8 REMARK 620 3 ASP A 378 OD1 101.5 41.6 REMARK 620 4 SER A 379 O 84.1 100.6 84.1 REMARK 620 5 GLU A 380 OE1 136.2 82.4 122.1 96.5 REMARK 620 6 HOH A2049 O 92.8 110.2 141.6 133.1 55.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 365 O REMARK 620 2 ASP A 410 OD1 148.4 REMARK 620 3 HOH A2010 O 68.9 80.5 REMARK 620 4 HOH A2042 O 87.1 108.9 131.6 REMARK 620 5 HOH A2071 O 136.9 73.8 144.0 81.3 REMARK 620 6 HOH A2072 O 84.0 104.3 90.7 129.1 72.2 REMARK 620 7 HOH A2076 O 89.0 79.0 81.7 55.6 116.6 171.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A2002 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 380 O REMARK 620 2 SER A 383 O 90.3 REMARK 620 3 ASN A 385 OD1 89.7 107.6 REMARK 620 4 HOH A2050 O 84.9 166.0 85.5 REMARK 620 5 HOH A2059 O 173.5 90.4 84.0 95.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 386 OE2 REMARK 620 2 ASP A 424 OD2 56.6 REMARK 620 3 ASP A 424 OD1 96.1 41.4 REMARK 620 4 GLY A 425 OXT 86.2 102.9 95.3 REMARK 620 5 HOH A2062 O 145.3 147.9 107.4 66.8 REMARK 620 6 HOH A2062 O 91.0 143.1 171.1 90.6 68.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A2001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A2002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A3002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A3003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A3004 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A3005 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A3006 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A3007 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A3009 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1W16 RELATED DB: PDB REMARK 900 RAT SYNAPTOTAGMIN 4 C2B DOMAIN IN THE ABSENCE OF CALCIUM DBREF 1W15 A 273 287 PDB 1W15 1W15 273 287 DBREF 1W15 A 288 425 UNP P50232 SYT4_RAT 288 425 SEQRES 1 A 153 GLY SER PRO GLY ILE SER GLY GLY GLY GLY GLY ILE PRO SEQRES 2 A 153 SER GLY ARG GLY GLU LEU LEU VAL SER LEU CYS TYR GLN SEQRES 3 A 153 SER THR THR ASN THR LEU THR VAL VAL VAL LEU LYS ALA SEQRES 4 A 153 ARG HIS LEU PRO LYS SER ASP VAL SER GLY LEU SER ASP SEQRES 5 A 153 PRO TYR VAL LYS VAL ASN LEU TYR HIS ALA LYS LYS ARG SEQRES 6 A 153 ILE SER LYS LYS LYS THR HIS VAL LYS LYS CYS THR PRO SEQRES 7 A 153 ASN ALA VAL PHE ASN GLU LEU PHE VAL PHE ASP ILE PRO SEQRES 8 A 153 CYS GLU SER LEU GLU GLU ILE SER VAL GLU PHE LEU VAL SEQRES 9 A 153 LEU ASP SER GLU ARG GLY SER ARG ASN GLU VAL ILE GLY SEQRES 10 A 153 ARG LEU VAL LEU GLY ALA THR ALA GLU GLY SER GLY GLY SEQRES 11 A 153 GLY HIS TRP LYS GLU ILE CYS ASP PHE PRO ARG ARG GLN SEQRES 12 A 153 ILE ALA LYS TRP HIS MET LEU CYS ASP GLY HET CA A1001 1 HET CA A1002 1 HET CA A1003 1 HET NA A2001 1 HET NA A2002 1 HET CL A3001 1 HET CL A3002 1 HET CL A3003 1 HET CL A3004 1 HET CL A3005 1 HET CL A3006 1 HET CL A3007 1 HET CL A3008 1 HET CL A3009 1 HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM CL CHLORIDE ION FORMUL 2 CA 3(CA 2+) FORMUL 5 NA 2(NA 1+) FORMUL 7 CL 9(CL 1-) FORMUL 16 HOH *93(H2 O) HELIX 1 1 GLY A 399 PHE A 411 1 13 SHEET 1 AA 4 ALA A 352 ASP A 361 0 SHEET 2 AA 4 THR A 303 ARG A 312 -1 O LEU A 304 N PHE A 360 SHEET 3 AA 4 GLU A 290 GLN A 298 -1 O GLU A 290 N ARG A 312 SHEET 4 AA 4 ILE A 416 MET A 421 -1 O ILE A 416 N LEU A 295 SHEET 1 AB 4 LYS A 336 LYS A 342 0 SHEET 2 AB 4 PRO A 325 HIS A 333 -1 O VAL A 329 N LYS A 341 SHEET 3 AB 4 ILE A 370 ASP A 378 -1 O SER A 371 N TYR A 332 SHEET 4 AB 4 GLU A 386 LEU A 393 -1 O GLU A 386 N ASP A 378 LINK OD2 ASP A 324 CA CA A1001 1555 1555 2.49 LINK O GLU A 365 CA CA A1002 1555 1555 2.50 LINK OD2 ASP A 378 CA CA A1001 1555 1555 3.15 LINK OD1 ASP A 378 CA CA A1001 1555 1555 2.68 LINK O SER A 379 CA CA A1001 1555 1555 2.67 LINK OE1 GLU A 380 CA CA A1001 1555 1555 2.58 LINK O GLU A 380 NA NA A2002 1555 1555 2.26 LINK O SER A 383 NA NA A2002 1555 1555 2.30 LINK OD1 ASN A 385 NA NA A2002 1555 1555 2.37 LINK OE2 GLU A 386 CA CA A1003 8556 1555 3.00 LINK OD1 ASP A 410 CA CA A1002 11655 1555 2.54 LINK OD2 ASP A 424 CA CA A1003 1555 1555 3.30 LINK OD1 ASP A 424 CA CA A1003 1555 1555 2.49 LINK OXT GLY A 425 CA CA A1003 1555 1555 2.41 LINK CA CA A1001 O HOH A2049 1555 1555 2.75 LINK CA CA A1002 O HOH A2010 1555 1555 2.32 LINK CA CA A1002 O HOH A2042 1555 1555 2.08 LINK CA CA A1002 O HOH A2071 1555 11655 2.52 LINK CA CA A1002 O HOH A2072 1555 11655 2.51 LINK CA CA A1002 O HOH A2076 1555 11655 2.48 LINK CA CA A1003 O HOH A2062 1555 1555 2.91 LINK CA CA A1003 O HOH A2062 1555 8556 2.48 LINK NA NA A2002 O HOH A2050 1555 1555 2.38 LINK NA NA A2002 O HOH A2059 1555 1555 2.52 SITE 1 AC1 5 ASP A 324 ASP A 378 SER A 379 GLU A 380 SITE 2 AC1 5 HOH A2049 SITE 1 AC2 7 GLU A 365 ASP A 410 HOH A2010 HOH A2042 SITE 2 AC2 7 HOH A2071 HOH A2072 HOH A2076 SITE 1 AC3 4 GLU A 386 ASP A 424 GLY A 425 HOH A2062 SITE 1 AC4 2 SER A 339 ASP A 361 SITE 1 AC5 6 GLU A 380 SER A 383 ASN A 385 HOH A2050 SITE 2 AC5 6 HOH A2054 HOH A2059 SITE 1 AC6 1 ASN A 355 SITE 1 AC7 4 VAL A 359 TRP A 419 HOH A2086 HOH A2087 SITE 1 AC8 4 TYR A 326 LYS A 328 ARG A 384 HOH A2018 SITE 1 AC9 4 LYS A 341 PHE A 358 VAL A 359 TRP A 419 SITE 1 BC1 3 LYS A 328 ASN A 330 ARG A 384 SITE 1 BC2 3 LYS A 328 ARG A 337 LYS A 340 SITE 1 BC3 3 ARG A 312 HIS A 313 HOH A2005 SITE 1 BC4 2 LEU A 367 HOH A2073 CRYST1 91.490 91.490 122.142 90.00 90.00 120.00 P 63 2 2 12 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 0.010930 0.006310 0.000000 0.00000 SCALE2 0.000000 0.012621 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008187 0.00000