HEADER PROTEIN TRANSPORT 21-NOV-13 4NP9 TITLE STRUCTURE OF RABPHILIN C2A DOMAIN BOUND TO IP3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RABPHILIN-3A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C2 DOMAIN, UNP RESIDUES 378-510; COMPND 5 SYNONYM: EXOPHILIN-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: BROWN RAT,RAT,RATS; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: RPH3A; 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: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS RABPHILIN-3A, C2 DOMAIN, C2A, CALCIUM BINDING, SYNAPTIC EXOCYTOSIS KEYWDS 2 METAL-BINDING, PROTEIN TRANSPORT, C-2 DOMAIN FOLD, EXOPHILIN-1 EXPDTA X-RAY DIFFRACTION AUTHOR J.GUILLEN,C.FERRER-ORTA,M.BUXADERAS,D.PEREZ-SANCHEZ,M.GUERRERO- AUTHOR 2 VALERO,G.LUENGO-GIL,J.POUS,P.GUERRA,J.C.GOMEZ-FERNANDEZ,N.VERDAGUER, AUTHOR 3 S.CORBALAN-GARCIA REVDAT 3 29-MAY-24 4NP9 1 REMARK REVDAT 2 24-AUG-22 4NP9 1 JRNL REMARK REVDAT 1 25-DEC-13 4NP9 0 JRNL AUTH J.GUILLEN,C.FERRER-ORTA,M.BUXADERAS,D.PEREZ-SANCHEZ, JRNL AUTH 2 M.GUERRERO-VALERO,G.LUENGO-GIL,J.POUS,P.GUERRA, JRNL AUTH 3 J.C.GOMEZ-FERNANDEZ,N.VERDAGUER,S.CORBALAN-GARCIA JRNL TITL STRUCTURAL INSIGHTS INTO THE CA2+ AND PI(4,5)P2 BINDING JRNL TITL 2 MODES OF THE C2 DOMAINS OF RABPHILIN 3A AND SYNAPTOTAGMIN 1. JRNL REF PROC.NATL.ACAD.SCI.USA V. 110 20503 2013 JRNL REFN ESSN 1091-6490 JRNL PMID 24302762 JRNL DOI 10.1073/PNAS.1316179110 REMARK 2 REMARK 2 RESOLUTION. 1.92 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1496) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.92 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.020 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 10754 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.211 REMARK 3 R VALUE (WORKING SET) : 0.209 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 520 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 29.5698 - 3.0470 1.00 2696 122 0.2068 0.2323 REMARK 3 2 3.0470 - 2.4188 1.00 2576 136 0.2019 0.2522 REMARK 3 3 2.4188 - 2.1132 0.98 2463 138 0.2178 0.2638 REMARK 3 4 2.1132 - 1.9200 0.98 2499 124 0.2209 0.2928 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.004 1080 REMARK 3 ANGLE : 0.903 1459 REMARK 3 CHIRALITY : 0.034 163 REMARK 3 PLANARITY : 0.003 184 REMARK 3 DIHEDRAL : 15.171 418 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 4NP9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083484. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.980110 REMARK 200 MONOCHROMATOR : MONOCHROMATOR SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10862 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 44.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 9.500 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : 0.08800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.1900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.0 REMARK 200 DATA REDUNDANCY IN SHELL : 50.80 REMARK 200 R MERGE FOR SHELL (I) : 0.30000 REMARK 200 R SYM FOR SHELL (I) : 0.35000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25-28% PEG 4K, 10-20MM AMMONIUM REMARK 280 SULFATE, 100MM HEPES PH 7.4, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 19.13500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.63000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.73500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.63000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.13500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.73500 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 ASP A 378 REMARK 465 GLN A 379 REMARK 465 ALA A 380 REMARK 465 THR A 381 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ILE A 510 CA C O CB CG1 CG2 CD1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 801 O HOH A 812 1.86 REMARK 500 O HOH A 822 O HOH A 825 1.87 REMARK 500 O HOH A 792 O HOH A 831 1.91 REMARK 500 O HOH A 820 O HOH A 827 1.98 REMARK 500 O LEU A 494 O HOH A 805 2.07 REMARK 500 OG1 THR A 382 O HOH A 766 2.08 REMARK 500 O HOH A 810 O HOH A 834 2.11 REMARK 500 O HOH A 759 O HOH A 813 2.13 REMARK 500 O HOH A 773 O HOH A 788 2.13 REMARK 500 O HOH A 732 O HOH A 790 2.15 REMARK 500 O HOH A 823 O HOH A 836 2.17 REMARK 500 O HOH A 770 O HOH A 805 2.17 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 ILE A 404 -70.08 -91.91 REMARK 500 MET A 412 -112.63 -119.86 REMARK 500 ASP A 419 77.81 -115.95 REMARK 500 ALA A 430 30.56 -77.16 REMARK 500 SER A 431 -177.73 57.34 REMARK 500 LYS A 432 -84.20 55.05 REMARK 500 HIS A 480 -167.48 -77.57 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 I3P A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 602 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NS0 RELATED DB: PDB REMARK 900 RELATED ID: 2CHD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE C2A DOMAIN OF RABPHILIN-3A REMARK 900 RELATED ID: 2K3H RELATED DB: PDB REMARK 900 STRUCTURAL DETERMINANTS FOR CA2+ AND PIP2 BINDING BY THE C2A DOMAIN REMARK 900 OF RABPHILIN-3A REMARK 900 RELATED ID: 2CM5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE C2B DOMAIN OF RABPHILIN REMARK 900 RELATED ID: 2CM6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE C2B DOMAIN OF RABPHILIN 3A DBREF 4NP9 A 378 510 UNP P47709 RP3A_RAT 378 510 SEQRES 1 A 133 ASP GLN ALA THR THR LEU GLY ALA LEU GLU PHE SER LEU SEQRES 2 A 133 LEU TYR ASP GLN ASP ASN SER ASN LEU GLN CYS THR ILE SEQRES 3 A 133 ILE ARG ALA LYS GLY LEU LYS PRO MET ASP SER ASN GLY SEQRES 4 A 133 LEU ALA ASP PRO TYR VAL LYS LEU HIS LEU LEU PRO GLY SEQRES 5 A 133 ALA SER LYS SER ASN LYS LEU ARG THR LYS THR LEU ARG SEQRES 6 A 133 ASN THR ARG ASN PRO VAL TRP ASN GLU THR LEU GLN TYR SEQRES 7 A 133 HIS GLY ILE THR GLU GLU ASP MET GLN ARG LYS THR LEU SEQRES 8 A 133 ARG ILE SER VAL CYS ASP GLU ASP LYS PHE GLY HIS ASN SEQRES 9 A 133 GLU PHE ILE GLY GLU THR ARG PHE SER LEU LYS LYS LEU SEQRES 10 A 133 LYS ALA ASN GLN ARG LYS ASN PHE ASN ILE CYS LEU GLU SEQRES 11 A 133 ARG VAL ILE HET I3P A 601 24 HET SO4 A 602 5 HETNAM I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE HETNAM SO4 SULFATE ION FORMUL 2 I3P C6 H15 O15 P3 FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *139(H2 O) HELIX 1 1 GLN A 394 ASN A 396 5 3 HELIX 2 2 SER A 431 SER A 433 5 3 HELIX 3 3 THR A 459 LYS A 466 1 8 HELIX 4 4 LYS A 492 LEU A 494 5 3 SHEET 1 A 4 VAL A 448 HIS A 456 0 SHEET 2 A 4 ASN A 398 LYS A 407 -1 N CYS A 401 O LEU A 453 SHEET 3 A 4 ALA A 385 ASP A 393 -1 N GLU A 387 O ARG A 405 SHEET 4 A 4 LYS A 500 CYS A 505 -1 O PHE A 502 N PHE A 388 SHEET 1 B 4 LYS A 435 ARG A 437 0 SHEET 2 B 4 PRO A 420 LEU A 427 -1 N LEU A 424 O LEU A 436 SHEET 3 B 4 THR A 467 GLU A 475 -1 O THR A 467 N LEU A 427 SHEET 4 B 4 ASN A 481 SER A 490 -1 O GLY A 485 N VAL A 472 CISPEP 1 LEU A 427 PRO A 428 0 -4.62 SITE 1 AC1 14 LYS A 410 PRO A 411 MET A 412 TYR A 421 SITE 2 AC1 14 LYS A 423 HIS A 425 LYS A 435 ARG A 437 SITE 3 AC1 14 ASN A 481 SO4 A 602 HOH A 702 HOH A 763 SITE 4 AC1 14 HOH A 764 HOH A 803 SITE 1 AC2 6 LYS A 423 ARG A 442 ARG A 469 SER A 471 SITE 2 AC2 6 PHE A 483 I3P A 601 CRYST1 38.270 39.470 89.260 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 0.026130 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025336 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011203 0.00000