HEADER METAL BINDING PROTEIN 08-AUG-11 2LHA TITLE SOLUTION STRUCTURE OF C2B WITH IP6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: SYNAPTOTAGMIN-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C2B DOMAIN, UNP RESIDUES 272-422; COMPND 5 SYNONYM: SYNAPTOTAGMIN I, SYTI, P65; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: SYT1, SVP65, SYT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PGEX4T1 KEYWDS PROTEIN-DRUG COMPLEX, BETA-SHEET PROTEIN, CALCIUM BINDING PROTEIN, KEYWDS 2 METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR M.JOUNG,S.K.MOHAN,C.YU REVDAT 4 14-JUN-23 2LHA 1 REMARK REVDAT 3 14-OCT-20 2LHA 1 REMARK HETSYN REVDAT 2 27-APR-16 2LHA 1 SEQRES REVDAT 1 02-MAY-12 2LHA 0 JRNL AUTH M.JOUNG,S.K.MOHAN,C.YU JRNL TITL MOLECULAR LEVEL INTERACTION OF INOSITOL HEXAPHOSPHATE WITH JRNL TITL 2 THE C2B DOMAIN OF HUMAN SYNAPTOTAGMIN I JRNL REF BIOCHEMISTRY 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 22475172 JRNL DOI 10.1021/BI300005W REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2, ARIA REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LHA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000102384. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.15 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-100% 13C; U-100% 15N] REMARK 210 PROTEIN-1, 1.1 MM INOSITOL REMARK 210 HEXAKISPHOSPHATE-2, 150 MM REMARK 210 SODIUM CHLORIDE-3, 20 MM MES-4, REMARK 210 2 MM DTT-5, 2 MM CALCIUM REMARK 210 CHLORIDE-6, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D C(CO)NH; 3D HNCO; 3D HNCA; 3D REMARK 210 HBHA(CO)NH; 3D HN(CO)CA; 3D REMARK 210 H(CCO)NH; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 3D REMARK 210 HCCH-COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : VARIAN REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY, VNMRJ REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLN A 270 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 HZ3 LYS A 375 OE1 GLU A 410 1.55 REMARK 500 HZ2 LYS A 369 OD2 ASP A 371 1.58 REMARK 500 OD2 ASP A 309 HZ2 LYS A 332 1.58 REMARK 500 REMARK 500 REMARK: NULL 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 1 ASP A 275 118.73 -171.21 REMARK 500 1 THR A 290 84.98 -156.57 REMARK 500 1 LEU A 294 -71.39 -76.01 REMARK 500 1 LYS A 301 94.53 -65.35 REMARK 500 1 LEU A 323 -72.54 -100.22 REMARK 500 1 ASN A 333 60.07 61.36 REMARK 500 1 PRO A 337 92.53 -61.99 REMARK 500 1 TYR A 339 -35.66 -167.18 REMARK 500 1 ASN A 340 85.91 70.80 REMARK 500 1 TYR A 364 73.55 -110.86 REMARK 500 1 ALA A 372 42.33 70.56 REMARK 500 1 TYR A 380 -80.93 -51.69 REMARK 500 1 SER A 382 -166.54 -105.66 REMARK 500 1 SER A 391 41.73 -77.93 REMARK 500 1 ASP A 392 -53.14 -139.50 REMARK 500 1 ASN A 396 -47.87 -166.03 REMARK 500 1 VAL A 419 85.83 57.09 REMARK 500 2 ASP A 275 130.50 -175.40 REMARK 500 2 ASN A 298 -18.36 -147.89 REMARK 500 2 LYS A 301 94.41 -62.69 REMARK 500 2 PRO A 337 86.19 -63.59 REMARK 500 2 TYR A 339 -39.71 -159.82 REMARK 500 2 ASN A 340 89.25 63.42 REMARK 500 2 TYR A 364 78.49 -110.89 REMARK 500 2 ASP A 365 106.00 -43.92 REMARK 500 2 ILE A 373 -82.30 -103.53 REMARK 500 2 TYR A 380 -71.00 -60.76 REMARK 500 2 SER A 391 34.21 -86.49 REMARK 500 2 ASP A 392 -46.25 -142.06 REMARK 500 2 ASN A 396 -54.37 -165.11 REMARK 500 2 VAL A 419 79.69 56.06 REMARK 500 3 LEU A 294 -75.02 -75.10 REMARK 500 3 ASN A 298 -46.49 -138.35 REMARK 500 3 PRO A 337 83.42 -61.51 REMARK 500 3 TYR A 339 -36.33 -157.10 REMARK 500 3 ASN A 340 77.59 68.51 REMARK 500 3 LYS A 354 16.03 -140.33 REMARK 500 3 TYR A 364 52.33 -116.85 REMARK 500 3 ASP A 365 107.65 -26.79 REMARK 500 3 ALA A 372 67.46 65.23 REMARK 500 3 TYR A 380 -71.11 -61.80 REMARK 500 3 SER A 391 35.47 -82.91 REMARK 500 3 ASP A 392 -41.11 -143.09 REMARK 500 3 ASN A 396 -49.23 -168.89 REMARK 500 3 VAL A 419 81.75 55.00 REMARK 500 4 ASP A 275 128.61 178.63 REMARK 500 4 ALA A 286 -33.38 -146.14 REMARK 500 4 LEU A 299 66.27 -104.06 REMARK 500 4 LYS A 301 101.30 -59.60 REMARK 500 4 LEU A 307 -153.20 -142.45 REMARK 500 REMARK 500 THIS ENTRY HAS 159 RAMACHANDRAN OUTLIERS. 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 IHP A 1 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17838 RELATED DB: BMRB DBREF 2LHA A 270 421 UNP P21579 SYT1_HUMAN 271 422 SEQRES 1 A 152 GLN 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 HET IHP A 1 42 HETNAM IHP INOSITOL HEXAKISPHOSPHATE HETSYN IHP MYO-INOSITOL HEXAKISPHOSPHATE; INOSITOL 1,2,3,4,5,6- HETSYN 2 IHP HEXAKISPHOSPHATE FORMUL 2 IHP C6 H18 O24 P6 HELIX 1 1 GLN A 351 LYS A 354 5 4 HELIX 2 2 ASP A 365 GLY A 368 5 4 HELIX 3 3 THR A 383 LEU A 394 1 12 HELIX 4 4 GLU A 410 ASP A 414 1 5 SHEET 1 A 3 TYR A 282 VAL A 283 0 SHEET 2 A 3 LYS A 288 ALA A 296 -1 O LYS A 288 N VAL A 283 SHEET 3 A 3 TYR A 338 GLU A 346 -1 O PHE A 345 N LEU A 289 SHEET 1 B 4 TYR A 282 VAL A 283 0 SHEET 2 B 4 LYS A 288 ALA A 296 -1 O LYS A 288 N VAL A 283 SHEET 3 B 4 ILE A 276 LEU A 280 -1 N SER A 279 O VAL A 292 SHEET 4 B 4 ILE A 401 GLN A 403 -1 O GLN A 403 N PHE A 278 SHEET 1 C 5 LYS A 321 LYS A 327 0 SHEET 2 C 5 PRO A 310 GLN A 318 -1 N LEU A 316 O LEU A 323 SHEET 3 C 5 GLN A 356 ASP A 363 -1 O VAL A 358 N HIS A 315 SHEET 4 C 5 GLY A 374 GLY A 379 -1 O VAL A 378 N VAL A 357 SHEET 5 C 5 GLN A 408 VAL A 409 -1 O GLN A 408 N LYS A 375 SITE 1 AC1 7 TYR A 311 THR A 329 ILE A 330 LYS A 332 SITE 2 AC1 7 TYR A 364 ILE A 367 GLY A 368 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1