HEADER EXOCYTOSIS 26-AUG-19 6U4W TITLE 1.4 A STRUCTURE OF A PATHOGENIC HUMAN SYT 1 C2B (D366E) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SYNAPTOTAGMIN I,SYTI,P65; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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, SVP65, SYT; 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, C2B, GREEK KEY, BAKER-GORDON SYNDROME, EXOCYTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR M.J.DOMINGUEZ,M.M.BRADBERRY,E.R.CHAPMAN,R.B.SUTTON REVDAT 3 11-OCT-23 6U4W 1 REMARK REVDAT 2 22-JUL-20 6U4W 1 JRNL REVDAT 1 13-MAY-20 6U4W 0 JRNL AUTH M.M.BRADBERRY,N.A.COURTNEY,M.J.DOMINGUEZ,S.M.LOFQUIST, JRNL AUTH 2 A.T.KNOX,R.B.SUTTON,E.R.CHAPMAN JRNL TITL MOLECULAR BASIS FOR SYNAPTOTAGMIN-1-ASSOCIATED JRNL TITL 2 NEURODEVELOPMENTAL DISORDER. JRNL REF NEURON V. 107 52 2020 JRNL REFN ISSN 0896-6273 JRNL PMID 32362337 JRNL DOI 10.1016/J.NEURON.2020.04.003 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 35502 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.220 REMARK 3 FREE R VALUE TEST SET COUNT : 1854 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 27.9100 - 3.2900 0.99 2777 162 0.1824 0.1868 REMARK 3 2 3.2900 - 2.6100 1.00 2648 141 0.1971 0.2135 REMARK 3 3 2.6100 - 2.2800 1.00 2614 163 0.1614 0.1858 REMARK 3 4 2.2800 - 2.0700 1.00 2583 185 0.1509 0.1859 REMARK 3 5 2.0700 - 1.9300 1.00 2598 140 0.1420 0.1972 REMARK 3 6 1.9300 - 1.8100 1.00 2593 112 0.1410 0.2158 REMARK 3 7 1.8100 - 1.7200 1.00 2594 163 0.1587 0.2055 REMARK 3 8 1.7200 - 1.6500 0.99 2563 142 0.1762 0.1847 REMARK 3 9 1.6500 - 1.5800 0.99 2597 111 0.1919 0.2340 REMARK 3 10 1.5800 - 1.5300 0.99 2562 138 0.2153 0.2187 REMARK 3 11 1.5300 - 1.4800 0.99 2503 145 0.2362 0.3084 REMARK 3 12 1.4800 - 1.4400 0.98 2547 127 0.3367 0.4093 REMARK 3 13 1.4400 - 1.4000 0.96 2469 125 0.5682 0.7859 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.202 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.774 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.27 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.98 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 : 0.011 1333 REMARK 3 ANGLE : 1.116 1810 REMARK 3 CHIRALITY : 0.091 196 REMARK 3 PLANARITY : 0.009 230 REMARK 3 DIHEDRAL : 19.928 519 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 6U4W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-19. REMARK 100 THE DEPOSITION ID IS D_1000243850. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0 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) : 0.97946 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 : XDS, XIA2 REMARK 200 DATA SCALING SOFTWARE : XSCALE, XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35752 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 27.910 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 9.200 REMARK 200 R MERGE (I) : 0.07700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 9.40 REMARK 200 R MERGE FOR SHELL (I) : 1.41600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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 (%): 52.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.6 M AMMONIUM SULFATE, 0.1 M CITRATE, REMARK 280 PH 4.0, VAPOR DIFFUSION, HANGING 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 69.28667 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 34.64333 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 34.64333 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 69.28667 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 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 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 -5.64 75.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 504 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1UOW RELATED DB: PDB DBREF 6U4W A 272 422 UNP P21579 SYT1_HUMAN 272 422 SEQADV 6U4W GLY A 266 UNP P21579 EXPRESSION TAG SEQADV 6U4W ASP A 267 UNP P21579 EXPRESSION TAG SEQADV 6U4W ILE A 268 UNP P21579 EXPRESSION TAG SEQADV 6U4W THR A 269 UNP P21579 EXPRESSION TAG SEQADV 6U4W HIS A 270 UNP P21579 EXPRESSION TAG SEQADV 6U4W MET A 271 UNP P21579 EXPRESSION TAG SEQADV 6U4W GLU A 366 UNP P21579 ASP 366 ENGINEERED MUTATION 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 TYR 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 GLU 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 HET SO4 A 502 5 HET SO4 A 503 5 HET SO4 A 504 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 4(O4 S 2-) FORMUL 6 HOH *110(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 LEU A 290 O PHE A 346 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 LEU A 317 O LEU A 324 SHEET 3 AA2 4 GLN A 357 ASP A 364 -1 O GLN A 357 N MET A 318 SHEET 4 AA2 4 ASP A 372 GLY A 380 -1 O ILE A 374 N VAL A 362 SITE 1 AC1 4 THR A 335 LEU A 336 ASN A 337 HOH A 607 SITE 1 AC2 4 LYS A 314 HIS A 316 ARG A 323 LYS A 326 SITE 1 AC3 5 GLU A 272 ARG A 282 LYS A 289 ARG A 399 SITE 2 AC3 5 HOH A 609 SITE 1 AC4 7 TYR A 312 LYS A 314 LYS A 326 LYS A 328 SITE 2 AC4 7 ASN A 371 HOH A 601 HOH A 634 CRYST1 54.390 54.390 103.930 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 0.018386 0.010615 0.000000 0.00000 SCALE2 0.000000 0.021230 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009622 0.00000