HEADER EXOCYTOSIS 02-FEB-22 7TUA TITLE HUMAN SYNAPTOTAGMIN-1 C2B Y312F WITHOUT CA2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 269-419; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BRAIN; SOURCE 6 GENE: SYT1, HCG_2016754; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: P202 KEYWDS C2 DOMAIN, AD3, C2B, GREEK KEY, SYNAPTOTAGMIN, EXOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR M.J.DOMINGUEZ,S.KARMAKAR,K.L.FUSON,R.B.SUTTON REVDAT 2 25-OCT-23 7TUA 1 REMARK REVDAT 1 22-MAR-23 7TUA 0 JRNL AUTH M.J.DOMINGUEZ,S.KARMAKAR,K.L.FUSON,R.B.SUTTON JRNL TITL HUMAN SYNAPTOTAGMIN-1 C2B Y312F WITHOUT CA2+ JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 TITL TOWARDS AUTOMATED CRYSTALLOGRAPHIC STRUCTURE REFINEMENT WITH REMARK 1 TITL 2 PHENIX.REFINE. REMARK 1 REF ACTA CRYSTALLOGR., SECT. D: V. 68 352 2012 REMARK 1 REF 2 BIOL. CRYSTALLOGR. REMARK 1 REFN ISSN 0907-4449 REMARK 1 REFERENCE 2 REMARK 1 TITL MACROMOLECULAR STRUCTURE DETERMINATION USING X-RAYS, REMARK 1 TITL 2 NEUTRONS AND ELECTRONS: RECENT DEVELOPMENTS IN PHENIX REMARK 1 REF ACTA CRYSTALLOGR., SECT. D: V. 75 861 2019 REMARK 1 REF 2 BIOL. CRYSTALLOGR. REMARK 1 REFN ISSN 0907-4449 REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20_4459 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 39758 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.178 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 2003 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 34.6900 - 3.2500 1.00 2906 156 0.1742 0.1843 REMARK 3 2 3.2500 - 2.5800 1.00 2771 148 0.1830 0.2121 REMARK 3 3 2.5800 - 2.2600 1.00 2721 143 0.1560 0.1653 REMARK 3 4 2.2600 - 2.0500 1.00 2739 144 0.1546 0.1971 REMARK 3 5 2.0500 - 1.9000 1.00 2715 144 0.1534 0.1836 REMARK 3 6 1.9000 - 1.7900 1.00 2713 142 0.1514 0.1834 REMARK 3 7 1.7900 - 1.7000 1.00 2668 140 0.1732 0.1858 REMARK 3 8 1.7000 - 1.6300 1.00 2697 147 0.2099 0.2014 REMARK 3 9 1.6300 - 1.5600 1.00 2673 144 0.1994 0.2554 REMARK 3 10 1.5600 - 1.5100 1.00 2658 143 0.2008 0.2030 REMARK 3 11 1.5100 - 1.4600 1.00 2668 141 0.2131 0.2663 REMARK 3 12 1.4600 - 1.4200 1.00 2684 144 0.2352 0.2369 REMARK 3 13 1.4200 - 1.3800 1.00 2659 136 0.2848 0.3248 REMARK 3 14 1.3800 - 1.3500 0.93 2483 131 0.3590 0.4168 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.175 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.649 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.32 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 : 0.013 1364 REMARK 3 ANGLE : 1.343 1859 REMARK 3 CHIRALITY : 0.101 207 REMARK 3 PLANARITY : 0.010 241 REMARK 3 DIHEDRAL : 14.497 537 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 7TUA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1000262928. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.09717 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2, XDS REMARK 200 DATA SCALING SOFTWARE : XIA2, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39819 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 34.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 13.70 REMARK 200 R MERGE (I) : 0.06954 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.1 REMARK 200 DATA REDUNDANCY IN SHELL : 8.40 REMARK 200 R MERGE FOR SHELL (I) : 2.10400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.020 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 6TZ3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM SODIUM ACETATE PH 4.5,200 MM REMARK 280 AMMONIUM SULFATE, 50% W/V PEG 2000MME, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 69.38000 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 34.69000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 34.69000 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 69.38000 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 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 GLY A 266 REMARK 465 ASP A 267 REMARK 465 ILE A 268 REMARK 465 THR A 269 REMARK 465 HIS A 270 REMARK 465 MET A 271 REMARK 465 GLU A 272 REMARK 465 LYS A 421 REMARK 465 LYS A 422 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 ARG A 399 -10.47 77.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 752 DISTANCE = 7.19 ANGSTROMS REMARK 525 HOH A 753 DISTANCE = 8.12 ANGSTROMS DBREF 7TUA A 272 422 UNP J3KQA0 J3KQA0_HUMAN 269 419 SEQADV 7TUA GLY A 266 UNP J3KQA0 EXPRESSION TAG SEQADV 7TUA ASP A 267 UNP J3KQA0 EXPRESSION TAG SEQADV 7TUA ILE A 268 UNP J3KQA0 EXPRESSION TAG SEQADV 7TUA THR A 269 UNP J3KQA0 EXPRESSION TAG SEQADV 7TUA HIS A 270 UNP J3KQA0 EXPRESSION TAG SEQADV 7TUA MET A 271 UNP J3KQA0 EXPRESSION TAG SEQADV 7TUA PHE A 312 UNP J3KQA0 TYR 309 CONFLICT SEQRES 1 A 157 GLY ASP ILE THR HIS MET GLU LYS LEU GLY ASP ILE CYS SEQRES 2 A 157 PHE SER LEU ARG TYR VAL PRO THR ALA GLY LYS LEU THR SEQRES 3 A 157 VAL VAL ILE LEU GLU ALA LYS ASN LEU LYS LYS MET ASP SEQRES 4 A 157 VAL GLY GLY LEU SER ASP PRO PHE VAL LYS ILE HIS LEU SEQRES 5 A 157 MET GLN ASN GLY LYS ARG LEU LYS LYS LYS LYS THR THR SEQRES 6 A 157 ILE LYS LYS ASN THR LEU ASN PRO TYR TYR ASN GLU SER SEQRES 7 A 157 PHE SER PHE GLU VAL PRO PHE GLU GLN ILE GLN LYS VAL SEQRES 8 A 157 GLN VAL VAL VAL THR VAL LEU ASP TYR ASP LYS ILE GLY SEQRES 9 A 157 LYS ASN ASP ALA ILE GLY LYS VAL PHE VAL GLY TYR ASN SEQRES 10 A 157 SER THR GLY ALA GLU LEU ARG HIS TRP SER ASP MET LEU SEQRES 11 A 157 ALA ASN PRO ARG ARG PRO ILE ALA GLN TRP HIS THR LEU SEQRES 12 A 157 GLN VAL GLU GLU GLU VAL ASP ALA MET LEU ALA VAL LYS SEQRES 13 A 157 LYS HET SO4 A 501 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *153(H2 O) HELIX 1 AA1 GLN A 352 LYS A 355 5 4 HELIX 2 AA2 THR A 384 ASN A 397 1 14 HELIX 3 AA3 VAL A 410 ALA A 419 1 10 SHEET 1 AA1 4 TYR A 339 GLU A 347 0 SHEET 2 AA1 4 LYS A 289 LYS A 298 -1 N VAL A 292 O PHE A 344 SHEET 3 AA1 4 ASP A 276 VAL A 284 -1 N CYS A 278 O GLU A 296 SHEET 4 AA1 4 ILE A 402 THR A 407 -1 O HIS A 406 N ILE A 277 SHEET 1 AA2 4 LYS A 322 LYS A 328 0 SHEET 2 AA2 4 PRO A 311 GLN A 319 -1 N ILE A 315 O LYS A 327 SHEET 3 AA2 4 GLN A 357 ASP A 364 -1 O VAL A 359 N HIS A 316 SHEET 4 AA2 4 ASP A 372 GLY A 380 -1 O ILE A 374 N VAL A 362 CRYST1 54.440 54.440 104.070 90.00 90.00 120.00 P 32 2 1 6 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 0.018369 0.010605 0.000000 0.00000 SCALE2 0.000000 0.021211 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009609 0.00000