HEADER SIGNALING PROTEIN 22-OCT-12 2YOA TITLE SYNAPTOTAGMIN-1 C2B DOMAIN WITH PHOSPHOSERINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN-1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C2B DOMAIN, RESIDUES 271-421; COMPND 5 SYNONYM: SYNAPTOTAGMIN I, SYTI, P65; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY 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_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET-28A KEYWDS SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.HONIGMANN,G.VAN DEN BOGAART,E.IRAHETA,H.J.RISSELADA,D.MILOVANOVIC, AUTHOR 2 V.MUELLER,S.MUELLAR,U.DIEDERICHSEN,D.FASSHAUER,H.GRUBMULLER, AUTHOR 3 S.W.HELL,C.EGGELING,K.KUHNEL,R.JAHN REVDAT 6 20-DEC-23 2YOA 1 REMARK LINK REVDAT 5 23-AUG-17 2YOA 1 REMARK REVDAT 4 19-JUN-13 2YOA 1 JRNL REVDAT 3 29-MAY-13 2YOA 1 JRNL REVDAT 2 15-MAY-13 2YOA 1 JRNL REVDAT 1 20-MAR-13 2YOA 0 JRNL AUTH A.HONIGMANN,G.VAN DEN BOGAART,E.IRAHETA,H.J.RISSELADA, JRNL AUTH 2 D.MILOVANOVIC,V.MUELLER,S.MUELLAR,U.DIEDERICHSEN, JRNL AUTH 3 D.FASSHAUER,H.GRUBMULLER,S.W.HELL,C.EGGELING,K.KUHNEL,R.JAHN JRNL TITL PHOSPHATIDYLINOSITOL 4,5-BISPHOSPHATE CLUSTERS ACT AS JRNL TITL 2 MOLECULAR BEACONS FOR VESICLE RECRUITMENT JRNL REF NAT.STRUCT.MOL.BIOL. V. 20 679 2013 JRNL REFN ISSN 1545-9993 JRNL PMID 23665582 JRNL DOI 10.1038/NSMB.2570 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 63497 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3342 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3865 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1710 REMARK 3 BIN FREE R VALUE SET COUNT : 203 REMARK 3 BIN FREE R VALUE : 0.2220 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2385 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 256 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.12000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.24000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.073 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.064 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.743 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.953 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2517 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3363 ; 1.229 ; 1.976 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 304 ; 6.050 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 106 ;37.956 ;25.094 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 476 ;11.875 ;15.063 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;12.956 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 379 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1812 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1105 ; 0.252 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1725 ; 0.304 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 167 ; 0.098 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 11 ; 0.094 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 88 ; 0.481 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 23 ; 0.083 ; 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): 1550 ; 0.961 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2472 ; 1.584 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 967 ; 2.448 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 891 ; 3.711 ; 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): 2517 ; 1.467 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 260 ; 4.277 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2456 ; 2.898 ; 3.000 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : 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 2YOA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1290054535. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-AUG-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99998 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 66840 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 43.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.26000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 7.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: BALBES REMARK 200 STARTING MODEL: PDB ENTRY 1UOV REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M KSCN, 20 % PEG 600 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 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 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 48.50000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 48.50000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 48.50000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 48.50000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 48.50000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.50000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 48.50000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.50000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 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: B 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 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 HOH A2102 LIES ON A SPECIAL POSITION. 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 VAL A 419 REMARK 465 LYS A 420 REMARK 465 LYS A 421 REMARK 465 MET B 270 REMARK 465 LYS B 420 REMARK 465 LYS B 421 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 294 -62.21 -92.23 REMARK 500 LEU A 307 -124.12 -117.94 REMARK 500 LEU B 294 -61.56 -90.29 REMARK 500 LEU B 307 -128.22 -116.51 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 A1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET A 302 O REMARK 620 2 ASP A 303 OD1 83.2 REMARK 620 3 ASP A 363 OD2 91.3 76.0 REMARK 620 4 ASP A 365 OD1 152.3 70.5 74.4 REMARK 620 5 ASP A 365 OD2 157.2 118.7 99.7 50.5 REMARK 620 6 ASP A 371 OD2 85.5 162.1 90.5 117.7 74.6 REMARK 620 7 HOH A2023 O 94.2 87.8 162.1 93.3 81.4 106.9 REMARK 620 N 1 2 3 4 5 6 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 303 OD1 REMARK 620 2 ASP A 303 OD2 53.9 REMARK 620 3 ASP A 309 OD2 126.7 74.2 REMARK 620 4 ASP A 363 OD1 98.0 91.0 93.4 REMARK 620 5 ASP A 363 OD2 63.3 94.2 139.1 46.8 REMARK 620 6 TYR A 364 O 149.3 156.3 83.8 81.4 96.8 REMARK 620 7 ASP A 365 OD1 71.2 124.5 152.8 104.7 64.7 79.2 REMARK 620 8 SEP A1004 O 88.3 89.6 79.7 172.7 140.4 95.2 80.8 REMARK 620 N 1 2 3 4 5 6 7 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 ASP A 365 OD2 REMARK 620 2 LYS A 369 O 93.6 REMARK 620 3 ASP A 371 OD1 89.3 88.3 REMARK 620 4 HOH A2070 O 89.2 91.7 178.5 REMARK 620 5 HOH A2071 O 84.0 173.1 98.1 81.9 REMARK 620 6 HOH A2076 O 173.6 92.5 92.8 88.7 89.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1002 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 MET B 302 O REMARK 620 2 ASP B 303 OD1 81.0 REMARK 620 3 ASP B 363 OD2 93.5 78.7 REMARK 620 4 ASP B 365 OD1 150.6 70.9 73.0 REMARK 620 5 ASP B 365 OD2 158.2 119.0 98.7 51.1 REMARK 620 6 ASP B 371 OD2 84.5 162.7 92.9 121.3 76.9 REMARK 620 7 HOH B2027 O 92.6 85.5 162.0 93.7 81.3 104.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1001 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 303 OD1 REMARK 620 2 ASP B 303 OD2 52.3 REMARK 620 3 ASP B 309 OD2 126.4 75.0 REMARK 620 4 ASP B 363 OD1 98.1 92.5 92.6 REMARK 620 5 ASP B 363 OD2 63.9 95.0 138.5 46.9 REMARK 620 6 TYR B 364 O 149.2 158.0 84.3 80.8 95.6 REMARK 620 7 ASP B 365 OD1 70.6 121.9 153.0 106.5 65.5 80.1 REMARK 620 8 SEP B1004 O 89.3 89.5 80.3 171.9 140.7 94.5 79.1 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B1003 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 365 OD2 REMARK 620 2 LYS B 369 O 91.3 REMARK 620 3 ASP B 371 OD1 90.1 88.6 REMARK 620 4 HOH B2075 O 89.2 91.0 179.2 REMARK 620 5 HOH B2076 O 86.6 172.7 98.4 81.9 REMARK 620 6 HOH B2082 O 176.6 91.9 91.1 89.6 90.0 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 A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SEP A 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 1005 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN A 1006 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN A 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 1003 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SEP B 1004 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN B 1007 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN B 1008 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN B 1009 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BYN RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF THE CALCIUM-BOUND FIRST C2- DOMAIN OF REMARK 900 SYNAPTOTAGMIN I REMARK 900 RELATED ID: 1K5W RELATED DB: PDB REMARK 900 THREE-DIMENSIONAL STRUCTURE OF THE SYNAPTOTAGMIN 1 C2B- DOMAIN: REMARK 900 SYNAPTOTAGMIN 1 AS A PHOSPHOLIPID BINDING MACHINE REMARK 900 RELATED ID: 1RSY RELATED DB: PDB REMARK 900 SYNAPTOTAGMIN I (FIRST C2 DOMAIN) (CALB) REMARK 900 RELATED ID: 1TJM RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC IDENTIFICATION OF SR2+ COORDINATION SITEIN REMARK 900 SYNAPTOTAGMIN I C2B DOMAIN REMARK 900 RELATED ID: 1TJX RELATED DB: PDB REMARK 900 CRYSTALLOGRAPHIC IDENTIFICATION OF CA2+ COORDINATION SITESIN REMARK 900 SYNAPTOTAGMIN I C2B DOMAIN REMARK 900 RELATED ID: 1UOV RELATED DB: PDB REMARK 900 CALCIUM BINDING DOMAIN C2B REMARK 900 RELATED ID: 1UOW RELATED DB: PDB REMARK 900 CALCIUM BINDING DOMAIN C2B DBREF 2YOA A 271 421 UNP P21707 SYT1_RAT 271 421 DBREF 2YOA B 271 421 UNP P21707 SYT1_RAT 271 421 SEQADV 2YOA MET A 270 UNP P21707 EXPRESSION TAG SEQADV 2YOA MET B 270 UNP P21707 EXPRESSION TAG SEQRES 1 A 152 MET GLU LYS LEU GLY ASP ILE CYS PHE SER LEU ARG TYR SEQRES 2 A 152 VAL PRO THR ALA GLY LYS LEU THR VAL VAL ILE LEU GLU SEQRES 3 A 152 ALA LYS ASN LEU LYS LYS MET ASP VAL GLY GLY LEU SER SEQRES 4 A 152 ASP PRO TYR VAL LYS ILE HIS LEU MET GLN ASN GLY LYS SEQRES 5 A 152 ARG LEU LYS LYS LYS LYS THR THR ILE LYS LYS ASN THR SEQRES 6 A 152 LEU ASN PRO TYR TYR ASN GLU SER PHE SER PHE GLU VAL SEQRES 7 A 152 PRO PHE GLU GLN ILE GLN LYS VAL GLN VAL VAL VAL THR SEQRES 8 A 152 VAL LEU ASP TYR ASP LYS ILE GLY LYS ASN ASP ALA ILE SEQRES 9 A 152 GLY LYS VAL PHE VAL GLY TYR ASN SER THR GLY ALA GLU SEQRES 10 A 152 LEU ARG HIS TRP SER ASP MET LEU ALA ASN PRO ARG ARG SEQRES 11 A 152 PRO ILE ALA GLN TRP HIS THR LEU GLN VAL GLU GLU GLU SEQRES 12 A 152 VAL ASP ALA MET LEU ALA VAL LYS LYS SEQRES 1 B 152 MET GLU LYS LEU GLY ASP ILE CYS PHE SER LEU ARG TYR SEQRES 2 B 152 VAL PRO THR ALA GLY LYS LEU THR VAL VAL ILE LEU GLU SEQRES 3 B 152 ALA LYS ASN LEU LYS LYS MET ASP VAL GLY GLY LEU SER SEQRES 4 B 152 ASP PRO TYR VAL LYS ILE HIS LEU MET GLN ASN GLY LYS SEQRES 5 B 152 ARG LEU LYS LYS LYS LYS THR THR ILE LYS LYS ASN THR SEQRES 6 B 152 LEU ASN PRO TYR TYR ASN GLU SER PHE SER PHE GLU VAL SEQRES 7 B 152 PRO PHE GLU GLN ILE GLN LYS VAL GLN VAL VAL VAL THR SEQRES 8 B 152 VAL LEU ASP TYR ASP LYS ILE GLY LYS ASN ASP ALA ILE SEQRES 9 B 152 GLY LYS VAL PHE VAL GLY TYR ASN SER THR GLY ALA GLU SEQRES 10 B 152 LEU ARG HIS TRP SER ASP MET LEU ALA ASN PRO ARG ARG SEQRES 11 B 152 PRO ILE ALA GLN TRP HIS THR LEU GLN VAL GLU GLU GLU SEQRES 12 B 152 VAL ASP ALA MET LEU ALA VAL LYS LYS HET CA A1001 1 HET CA A1002 1 HET CA A1003 1 HET SEP A1004 11 HET CA A1005 1 HET SCN A1006 3 HET SCN A1007 3 HET CA B1001 1 HET CA B1002 1 HET CA B1003 1 HET SEP B1004 11 HET SCN B1007 3 HET SCN B1008 3 HET SCN B1009 3 HETNAM CA CALCIUM ION HETNAM SEP PHOSPHOSERINE HETNAM SCN THIOCYANATE ION HETSYN SEP PHOSPHONOSERINE FORMUL 3 CA 7(CA 2+) FORMUL 6 SEP 2(C3 H8 N O6 P) FORMUL 8 SCN 5(C N S 1-) FORMUL 17 HOH *256(H2 O) HELIX 1 1 PRO A 284 ALA A 286 5 3 HELIX 2 2 PRO A 348 GLN A 353 1 6 HELIX 3 3 THR A 383 ASN A 396 1 14 HELIX 4 4 VAL A 409 ALA A 418 1 10 HELIX 5 5 PRO B 284 ALA B 286 5 3 HELIX 6 6 PRO B 348 GLN B 353 5 6 HELIX 7 7 THR B 383 ASN B 396 1 14 HELIX 8 8 VAL B 409 ALA B 418 1 10 SHEET 1 AA 4 TYR A 338 GLU A 346 0 SHEET 2 AA 4 LYS A 288 LYS A 297 -1 O LEU A 289 N PHE A 345 SHEET 3 AA 4 ASP A 275 VAL A 283 -1 O ASP A 275 N LYS A 297 SHEET 4 AA 4 ILE A 401 THR A 406 -1 O ILE A 401 N LEU A 280 SHEET 1 AB 4 LYS A 321 LYS A 327 0 SHEET 2 AB 4 PRO A 310 GLN A 318 -1 O ILE A 314 N LYS A 326 SHEET 3 AB 4 VAL A 355 ASP A 363 -1 O GLN A 356 N MET A 317 SHEET 4 AB 4 ASP A 371 GLY A 379 -1 O ASP A 371 N ASP A 363 SHEET 1 BA 4 TYR B 338 GLU B 346 0 SHEET 2 BA 4 LYS B 288 LYS B 297 -1 O LEU B 289 N PHE B 345 SHEET 3 BA 4 ASP B 275 VAL B 283 -1 O ASP B 275 N LYS B 297 SHEET 4 BA 4 ILE B 401 THR B 406 -1 O ILE B 401 N LEU B 280 SHEET 1 BB 4 LYS B 321 LYS B 327 0 SHEET 2 BB 4 PRO B 310 GLN B 318 -1 O ILE B 314 N LYS B 326 SHEET 3 BB 4 VAL B 355 ASP B 363 -1 O GLN B 356 N MET B 317 SHEET 4 BB 4 ASP B 371 GLY B 379 -1 O ASP B 371 N ASP B 363 LINK O MET A 302 CA CA A1002 1555 1555 2.33 LINK OD1 ASP A 303 CA CA A1001 1555 1555 2.40 LINK OD2 ASP A 303 CA CA A1001 1555 1555 2.36 LINK OD1 ASP A 303 CA CA A1002 1555 1555 2.34 LINK OD2 ASP A 309 CA CA A1001 1555 1555 2.35 LINK OD1 ASP A 363 CA CA A1001 1555 1555 2.37 LINK OD2 ASP A 363 CA CA A1001 1555 1555 2.98 LINK OD2 ASP A 363 CA CA A1002 1555 1555 2.32 LINK O TYR A 364 CA CA A1001 1555 1555 2.34 LINK OD1 ASP A 365 CA CA A1001 1555 1555 2.42 LINK OD1 ASP A 365 CA CA A1002 1555 1555 2.52 LINK OD2 ASP A 365 CA CA A1002 1555 1555 2.61 LINK OD2 ASP A 365 CA CA A1003 1555 1555 2.33 LINK O LYS A 369 CA CA A1003 1555 1555 2.34 LINK OD2 ASP A 371 CA CA A1002 1555 1555 2.33 LINK OD1 ASP A 371 CA CA A1003 1555 1555 2.32 LINK CA CA A1001 O SEP A1004 1555 1555 2.34 LINK CA CA A1002 O HOH A2023 1555 1555 2.33 LINK CA CA A1003 O HOH A2070 1555 1555 2.35 LINK CA CA A1003 O HOH A2071 1555 1555 2.33 LINK CA CA A1003 O HOH A2076 1555 1555 2.29 LINK CA CA A1005 O HOH A2027 1555 1555 3.04 LINK O MET B 302 CA CA B1002 1555 1555 2.33 LINK OD1 ASP B 303 CA CA B1001 1555 1555 2.58 LINK OD2 ASP B 303 CA CA B1001 1555 1555 2.37 LINK OD1 ASP B 303 CA CA B1002 1555 1555 2.33 LINK OD2 ASP B 309 CA CA B1001 1555 1555 2.40 LINK OD1 ASP B 363 CA CA B1001 1555 1555 2.37 LINK OD2 ASP B 363 CA CA B1001 1555 1555 2.95 LINK OD2 ASP B 363 CA CA B1002 1555 1555 2.31 LINK O TYR B 364 CA CA B1001 1555 1555 2.32 LINK OD1 ASP B 365 CA CA B1001 1555 1555 2.34 LINK OD1 ASP B 365 CA CA B1002 1555 1555 2.57 LINK OD2 ASP B 365 CA CA B1002 1555 1555 2.56 LINK OD2 ASP B 365 CA CA B1003 1555 1555 2.42 LINK O LYS B 369 CA CA B1003 1555 1555 2.33 LINK OD2 ASP B 371 CA CA B1002 1555 1555 2.34 LINK OD1 ASP B 371 CA CA B1003 1555 1555 2.33 LINK CA CA B1001 O SEP B1004 1555 1555 2.34 LINK CA CA B1002 O HOH B2027 1555 1555 2.31 LINK CA CA B1003 O HOH B2075 1555 1555 2.31 LINK CA CA B1003 O HOH B2076 1555 1555 2.29 LINK CA CA B1003 O HOH B2082 1555 1555 2.29 SITE 1 AC1 6 ASP A 303 ASP A 309 ASP A 363 TYR A 364 SITE 2 AC1 6 ASP A 365 SEP A1004 SITE 1 AC2 6 MET A 302 ASP A 303 ASP A 363 ASP A 365 SITE 2 AC2 6 ASP A 371 HOH A2023 SITE 1 AC3 6 ASP A 365 LYS A 369 ASP A 371 HOH A2070 SITE 2 AC3 6 HOH A2071 HOH A2076 SITE 1 AC4 12 ASP A 303 ASP A 309 TYR A 364 ASP A 365 SITE 2 AC4 12 LYS A 366 CA A1001 HOH A2025 HOH A2072 SITE 3 AC4 12 HOH A2130 ASN B 319 HOH B2038 HOH B2068 SITE 1 AC5 3 ASP A 309 TYR A 364 HOH A2027 SITE 1 AC6 4 LYS A 272 TYR A 311 LYS A 327 HOH A2131 SITE 1 AC7 4 THR A 334 ASN A 336 TYR A 338 ARG A 398 SITE 1 AC8 6 ASP B 303 ASP B 309 ASP B 363 TYR B 364 SITE 2 AC8 6 ASP B 365 SEP B1004 SITE 1 AC9 6 MET B 302 ASP B 303 ASP B 363 ASP B 365 SITE 2 AC9 6 ASP B 371 HOH B2027 SITE 1 BC1 6 ASP B 365 LYS B 369 ASP B 371 HOH B2075 SITE 2 BC1 6 HOH B2076 HOH B2082 SITE 1 BC2 13 ASN A 319 LYS A 321 ASP B 303 ASP B 309 SITE 2 BC2 13 TYR B 364 ASP B 365 LYS B 366 CA B1001 SITE 3 BC2 13 HOH B2029 HOH B2047 HOH B2077 HOH B2123 SITE 4 BC2 13 HOH B2124 SITE 1 BC3 5 PRO A 284 VAL B 283 PRO B 397 ARG B 398 SITE 2 BC3 5 HOH B2017 SITE 1 BC4 5 THR B 334 ASN B 336 TYR B 338 ARG B 398 SITE 2 BC4 5 HOH B2048 SITE 1 BC5 3 LYS B 272 TYR B 311 LYS B 327 CRYST1 97.000 97.000 89.010 90.00 90.00 90.00 P 4 21 2 16 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 0.010309 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010309 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011235 0.00000