HEADER METAL BINDING PROTEIN 16-AUG-16 5T0S TITLE SYNAPTOTAGMIN 1 C2B DOMAIN, CADMIUM-BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN-1; COMPND 3 CHAIN: A; 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: 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 5T0S 1 LINK REVDAT 2 05-JUL-17 5T0S 1 JRNL REVDAT 1 14-JUN-17 5T0S 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. 1.42 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.920 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 26889 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.430 REMARK 3 FREE R VALUE TEST SET COUNT : 3748 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 36.5555 - 4.2464 0.99 1725 146 0.1732 0.2134 REMARK 3 2 4.2464 - 3.3713 1.00 1758 152 0.1452 0.1716 REMARK 3 3 3.3713 - 2.9453 1.00 1725 143 0.1565 0.1674 REMARK 3 4 2.9453 - 2.6761 1.00 1759 139 0.1737 0.1980 REMARK 3 5 2.6761 - 2.4844 1.00 1759 141 0.1624 0.1821 REMARK 3 6 2.4844 - 2.3379 1.00 1750 131 0.1566 0.1884 REMARK 3 7 2.3379 - 2.2208 1.00 1738 156 0.1424 0.1800 REMARK 3 8 2.2208 - 2.1242 1.00 1752 128 0.1400 0.1909 REMARK 3 9 2.1242 - 2.0424 1.00 1758 143 0.1363 0.1870 REMARK 3 10 2.0424 - 1.9719 1.00 1736 139 0.1351 0.1684 REMARK 3 11 1.9719 - 1.9103 1.00 1756 133 0.1401 0.1971 REMARK 3 12 1.9103 - 1.8557 1.00 1758 134 0.1363 0.1773 REMARK 3 13 1.8557 - 1.8068 1.00 1765 140 0.1533 0.2058 REMARK 3 14 1.8068 - 1.7628 1.00 1737 148 0.1485 0.2063 REMARK 3 15 1.7628 - 1.7227 1.00 1750 138 0.1652 0.2549 REMARK 3 16 1.7227 - 1.6860 1.00 1739 142 0.1502 0.1853 REMARK 3 17 1.6860 - 1.6523 1.00 1772 143 0.1599 0.2330 REMARK 3 18 1.6523 - 1.6211 1.00 1743 130 0.1608 0.2094 REMARK 3 19 1.6211 - 1.5922 1.00 1758 134 0.1678 0.1944 REMARK 3 20 1.5922 - 1.5652 1.00 1733 142 0.1700 0.2176 REMARK 3 21 1.5652 - 1.5399 1.00 1772 133 0.1887 0.2386 REMARK 3 22 1.5399 - 1.5162 1.00 1733 152 0.1849 0.2569 REMARK 3 23 1.5162 - 1.4939 1.00 1733 148 0.2098 0.2712 REMARK 3 24 1.4939 - 1.4729 1.00 1766 135 0.2015 0.3282 REMARK 3 25 1.4729 - 1.4530 1.00 1756 141 0.2225 0.2153 REMARK 3 26 1.4530 - 1.4341 0.99 1723 134 0.2344 0.2865 REMARK 3 27 1.4341 - 1.4162 0.70 1219 103 0.2530 0.3102 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.70 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.880 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.10 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 : 0.006 1315 REMARK 3 ANGLE : 1.037 1783 REMARK 3 CHIRALITY : 0.082 198 REMARK 3 PLANARITY : 0.004 230 REMARK 3 DIHEDRAL : 22.213 514 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 5T0S 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_1000223405. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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 : 26944 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 41.950 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05100 REMARK 200 FOR THE DATA SET : 18.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.54400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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: 1UOW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 13.4% PEG 400, 10.05% PEG 1000, 0.15 M REMARK 280 POTASSIUM PHOSPHATE DIBASIC/SODIUM PHOSPHATE DIBASIC PH 6.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 20.49600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 40.32850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.97400 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 40.32850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.49600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.97400 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 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 -61.22 -90.44 REMARK 500 LEU A 307 -118.46 -112.64 REMARK 500 LEU A 323 -69.41 -125.55 REMARK 500 TYR A 339 -62.78 -106.32 REMARK 500 ASP A 365 -61.02 -131.97 REMARK 500 ARG A 398 -7.78 79.25 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 501 CD REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 309 OD2 REMARK 620 2 ASP A 363 OD1 103.5 REMARK 620 3 TYR A 364 O 78.0 85.1 REMARK 620 4 HOH A 695 O 87.2 169.3 96.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 502 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 383 O REMARK 620 2 THR A 383 OG1 64.7 REMARK 620 3 GLU A 386 OE2 76.9 140.2 REMARK 620 4 HOH A 642 O 75.9 52.9 109.0 REMARK 620 5 HOH A 730 O 80.0 81.8 102.4 134.4 REMARK 620 6 HOH A 761 O 143.5 149.0 70.8 130.6 90.5 REMARK 620 7 HOH A 779 O 154.5 91.9 122.8 81.8 108.0 61.9 REMARK 620 N 1 2 3 4 5 6 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5T0R RELATED DB: PDB DBREF 5T0S A 271 421 UNP P46096 SYT1_MOUSE 271 421 SEQRES 1 A 151 GLU LYS LEU GLY ASP ILE CYS PHE SER LEU ARG TYR VAL SEQRES 2 A 151 PRO THR ALA GLY LYS LEU THR VAL VAL ILE LEU GLU ALA SEQRES 3 A 151 LYS ASN LEU LYS LYS MET ASP VAL GLY GLY LEU SER ASP SEQRES 4 A 151 PRO TYR VAL LYS ILE HIS LEU MET GLN ASN GLY LYS ARG SEQRES 5 A 151 LEU LYS LYS LYS LYS THR THR ILE LYS LYS ASN THR LEU SEQRES 6 A 151 ASN PRO TYR TYR ASN GLU SER PHE SER PHE GLU VAL PRO SEQRES 7 A 151 PHE GLU GLN ILE GLN LYS VAL GLN VAL VAL VAL THR VAL SEQRES 8 A 151 LEU ASP TYR ASP LYS ILE GLY LYS ASN ASP ALA ILE GLY SEQRES 9 A 151 LYS VAL PHE VAL GLY TYR ASN SER THR GLY ALA GLU LEU SEQRES 10 A 151 ARG HIS TRP SER ASP MET LEU ALA ASN PRO ARG ARG PRO SEQRES 11 A 151 ILE ALA GLN TRP HIS THR LEU GLN VAL GLU GLU GLU VAL SEQRES 12 A 151 ASP ALA MET LEU ALA VAL LYS LYS HET CD A 501 1 HET NA A 502 1 HETNAM CD CADMIUM ION HETNAM NA SODIUM ION FORMUL 2 CD CD 2+ FORMUL 3 NA NA 1+ FORMUL 4 HOH *211(H2 O) HELIX 1 AA1 PRO A 348 ILE A 352 5 5 HELIX 2 AA2 THR A 383 ASN A 396 1 14 HELIX 3 AA3 VAL A 409 LEU A 417 1 9 SHEET 1 AA1 4 TYR A 338 GLU A 346 0 SHEET 2 AA1 4 LYS A 288 LYS A 297 -1 N LEU A 289 O PHE A 345 SHEET 3 AA1 4 ASP A 275 VAL A 283 -1 N CYS A 277 O GLU A 295 SHEET 4 AA1 4 ILE A 401 THR A 406 -1 O ILE A 401 N LEU A 280 SHEET 1 AA2 4 LYS A 321 LYS A 327 0 SHEET 2 AA2 4 PRO A 310 GLN A 318 -1 N LEU A 316 O LYS A 324 SHEET 3 AA2 4 GLN A 356 ASP A 363 -1 O VAL A 358 N HIS A 315 SHEET 4 AA2 4 ASP A 371 GLY A 379 -1 O ILE A 373 N VAL A 361 LINK OD2 ASP A 309 CD CD A 501 1555 1555 2.67 LINK OD1 ASP A 363 CD CD A 501 1555 1555 2.48 LINK O TYR A 364 CD CD A 501 1555 1555 2.56 LINK O THR A 383 NA NA A 502 1555 1555 3.09 LINK OG1 THR A 383 NA NA A 502 1555 1555 2.93 LINK OE2 GLU A 386 NA NA A 502 1555 1555 2.68 LINK CD CD A 501 O HOH A 695 1555 1555 2.26 LINK NA NA A 502 O HOH A 642 1555 1555 3.05 LINK NA NA A 502 O HOH A 730 1555 1555 2.77 LINK NA NA A 502 O HOH A 761 1555 1555 3.03 LINK NA NA A 502 O HOH A 779 1555 1555 2.52 SITE 1 AC1 5 ASP A 303 ASP A 309 ASP A 363 TYR A 364 SITE 2 AC1 5 HOH A 695 SITE 1 AC2 6 THR A 383 GLU A 386 HOH A 642 HOH A 730 SITE 2 AC2 6 HOH A 761 HOH A 779 CRYST1 40.992 41.948 80.657 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 0.024395 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023839 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012398 0.00000