HEADER METAL BINDING PROTEIN 16-AUG-16 5T0R TITLE SYNAPTOTAGMIN 1 C2A DOMAIN, CADMIUM-BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C2A DOMAIN RESIDUES 140-265; COMPND 5 SYNONYM: SYNAPTOTAGMIN I,SYTI,P65; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: SYT1; 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: PET-SUMO KEYWDS METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.B.TAYLOR,P.J.HART,T.I.IGUMENOVA REVDAT 3 04-OCT-23 5T0R 1 REMARK REVDAT 2 05-JUL-17 5T0R 1 JRNL REVDAT 1 14-JUN-17 5T0R 0 JRNL AUTH S.KATTI,S.B.NYENHUIS,B.HER,A.K.SRIVASTAVA,A.B.TAYLOR, JRNL AUTH 2 P.J.HART,D.S.CAFISO,T.I.IGUMENOVA JRNL TITL NON-NATIVE METAL ION REVEALS THE ROLE OF ELECTROSTATICS IN JRNL TITL 2 SYNAPTOTAGMIN 1-MEMBRANE INTERACTIONS. JRNL REF BIOCHEMISTRY V. 56 3283 2017 JRNL REFN ISSN 1520-4995 JRNL PMID 28574251 JRNL DOI 10.1021/ACS.BIOCHEM.7B00188 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10_2155 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.910 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 10031 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.970 REMARK 3 FREE R VALUE TEST SET COUNT : 1779 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 38.0787 - 4.5895 0.98 1292 143 0.1603 0.1674 REMARK 3 2 4.5895 - 3.6438 0.99 1297 146 0.1445 0.1992 REMARK 3 3 3.6438 - 3.1834 0.99 1311 139 0.1635 0.2450 REMARK 3 4 3.1834 - 2.8925 0.99 1302 148 0.2114 0.2555 REMARK 3 5 2.8925 - 2.6852 0.99 1321 135 0.2225 0.3311 REMARK 3 6 2.6852 - 2.5269 0.98 1275 139 0.2223 0.2369 REMARK 3 7 2.5269 - 2.4004 0.98 1305 153 0.2050 0.2341 REMARK 3 8 2.4004 - 2.2959 0.95 1251 132 0.2032 0.2460 REMARK 3 9 2.2959 - 2.2075 0.95 1253 140 0.2025 0.2475 REMARK 3 10 2.2075 - 2.1314 0.94 1241 142 0.2160 0.2335 REMARK 3 11 2.1314 - 2.0647 0.92 1187 134 0.2253 0.2682 REMARK 3 12 2.0647 - 2.0057 0.92 1213 139 0.2386 0.2449 REMARK 3 13 2.0057 - 1.9529 0.61 819 89 0.2451 0.2881 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.530 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.19 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1042 REMARK 3 ANGLE : 1.134 1407 REMARK 3 CHIRALITY : 0.052 152 REMARK 3 PLANARITY : 0.006 181 REMARK 3 DIHEDRAL : 13.904 388 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 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5T0R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223381. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : CONFOCAL OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10075 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 38.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10700 REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.37300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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: 3F00 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M TRI-SODIUM CITRATE, 16% PEG REMARK 280 6000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 14.03200 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.07150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.63800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.07150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.03200 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.63800 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 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 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 140 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 LYS A 189 -21.01 73.63 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 CD A 301 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 172 OD2 REMARK 620 2 ASP A 178 OD2 76.8 REMARK 620 3 ASP A 230 OD1 97.0 106.2 REMARK 620 4 ASP A 230 OD2 106.5 157.5 51.5 REMARK 620 5 PHE A 231 O 162.5 85.8 88.6 89.9 REMARK 620 6 HOH A 403 O 91.0 90.8 162.4 111.2 88.4 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 CD A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5T0S RELATED DB: PDB DBREF 5T0R A 140 265 UNP P46096 SYT1_MOUSE 140 265 SEQRES 1 A 126 GLU LYS LEU GLY LYS LEU GLN TYR SER LEU ASP TYR ASP SEQRES 2 A 126 PHE GLN ASN ASN GLN LEU LEU VAL GLY ILE ILE GLN ALA SEQRES 3 A 126 ALA GLU LEU PRO ALA LEU ASP MET GLY GLY THR SER ASP SEQRES 4 A 126 PRO TYR VAL LYS VAL PHE LEU LEU PRO ASP LYS LYS LYS SEQRES 5 A 126 LYS PHE GLU THR LYS VAL HIS ARG LYS THR LEU ASN PRO SEQRES 6 A 126 VAL PHE ASN GLU GLN PHE THR PHE LYS VAL PRO TYR SER SEQRES 7 A 126 GLU LEU GLY GLY LYS THR LEU VAL MET ALA VAL TYR ASP SEQRES 8 A 126 PHE ASP ARG PHE SER LYS HIS ASP ILE ILE GLY GLU PHE SEQRES 9 A 126 LYS VAL PRO MET ASN THR VAL ASP PHE GLY HIS VAL THR SEQRES 10 A 126 GLU GLU TRP ARG ASP LEU GLN SER ALA HET CD A 301 1 HETNAM CD CADMIUM ION FORMUL 2 CD CD 2+ FORMUL 3 HOH *128(H2 O) HELIX 1 AA1 PRO A 215 GLY A 220 1 6 HELIX 2 AA2 ASN A 248 VAL A 250 5 3 SHEET 1 AA1 4 VAL A 205 LYS A 213 0 SHEET 2 AA1 4 GLN A 157 ALA A 166 -1 N VAL A 160 O PHE A 210 SHEET 3 AA1 4 LYS A 144 ASP A 152 -1 N ASP A 150 O LEU A 159 SHEET 4 AA1 4 THR A 256 ASP A 261 -1 O ARG A 260 N LEU A 145 SHEET 1 AA2 4 PHE A 193 GLU A 194 0 SHEET 2 AA2 4 PRO A 179 LEU A 186 -1 N VAL A 183 O PHE A 193 SHEET 3 AA2 4 THR A 223 ASP A 230 -1 O VAL A 225 N PHE A 184 SHEET 4 AA2 4 ILE A 239 PRO A 246 -1 O ILE A 240 N VAL A 228 LINK OD2 ASP A 172 CD CD A 301 1555 1555 2.42 LINK OD2 ASP A 178 CD CD A 301 1555 1555 2.40 LINK OD1 ASP A 230 CD CD A 301 1555 1555 2.44 LINK OD2 ASP A 230 CD CD A 301 1555 1555 2.61 LINK O PHE A 231 CD CD A 301 1555 1555 2.52 LINK CD CD A 301 O HOH A 403 1555 1555 2.57 CISPEP 1 LEU A 186 PRO A 187 0 7.46 SITE 1 AC1 5 ASP A 172 ASP A 178 ASP A 230 PHE A 231 SITE 2 AC1 5 HOH A 403 CRYST1 28.064 63.276 76.143 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.035633 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015804 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013133 0.00000