HEADER PROTEIN TRANSPORT 04-MAY-06 2CM6 TITLE CRYSTAL STRUCTURE OF THE C2B DOMAIN OF RABPHILIN3A COMPND MOL_ID: 1; COMPND 2 MOLECULE: RABPHILIN-3A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: C2B DOMAIN AND LINKER, RESIDUES 519-684; COMPND 5 SYNONYM: EXOPHILIN-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX-2T; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX-2T-RABPHILIN3A-519-684 KEYWDS PROTEIN TRANSPORT, ZINC-FINGER, RABPHILIN3A, CA2+ BINDING, METAL- KEYWDS 2 BINDING, SYNAPTIC EXOCYTOSIS, C2A-C2B LINKER FRAGMENT, C2B, ZINC, KEYWDS 3 SYNAPSE, C2 DOMAIN, TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR C.SCHLICKER,P.MONTAVILLE,G.M.SHELDRICK,S.BECKER REVDAT 5 13-DEC-23 2CM6 1 LINK REVDAT 4 24-FEB-09 2CM6 1 VERSN REVDAT 3 20-FEB-07 2CM6 1 JRNL REVDAT 2 02-JAN-07 2CM6 1 JRNL REVDAT 1 04-DEC-06 2CM6 0 JRNL AUTH P.MONTAVILLE,C.SCHLICKER,A.LEONOV,M.ZWECKSTETTER, JRNL AUTH 2 G.M.SHELDRICK,S.BECKER JRNL TITL THE C2A-C2B LINKER DEFINES THE HIGH AFFINITY CA2+ BINDING JRNL TITL 2 MODE OF RABPHILIN-3A. JRNL REF J.BIOL.CHEM. V. 282 5015 2007 JRNL REFN ISSN 0021-9258 JRNL PMID 17166855 JRNL DOI 10.1074/JBC.M606746200 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.76 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.198 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.195 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.268 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1270 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 25345 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 21013 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2312 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 76 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : 9466 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 ANGLE DISTANCES (A) : 0.021 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.005 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.027 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.029 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.038 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.275 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.080 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CM6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1290028563. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-05 REMARK 200 TEMPERATURE (KELVIN) : 89.7 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9536 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25345 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 43.760 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.390 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 6.440 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.43 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.070 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: PDB ENTRY 2CM5 REMARK 200 REMARK 200 REMARK: FRAGMENT CONTAINING RESIDUES 540-677 OF 2CM5 WAS USED AS REMARK 200 SEARCH MODEL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES PH 7.6, 25 % PEG 8000, 200 REMARK 280 MM CA REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 29.80300 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PQS 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 519 REMARK 465 SER A 520 REMARK 465 ALA A 521 REMARK 465 ARG A 522 REMARK 465 GLY A 523 REMARK 465 GLY A 536 REMARK 465 ASP A 537 REMARK 465 ILE A 538 REMARK 465 ASP A 587 REMARK 465 MET A 588 REMARK 465 GLY A 589 REMARK 465 ASN A 679 REMARK 465 HIS A 680 REMARK 465 VAL A 681 REMARK 465 SER A 682 REMARK 465 SER A 683 REMARK 465 ASP A 684 REMARK 465 GLY B 1519 REMARK 465 SER B 1520 REMARK 465 ALA B 1521 REMARK 465 ARG B 1522 REMARK 465 GLY B 1523 REMARK 465 MET B 1524 REMARK 465 GLU B 1533 REMARK 465 ARG B 1534 REMARK 465 ILE B 1535 REMARK 465 GLY B 1536 REMARK 465 ASP B 1537 REMARK 465 ILE B 1538 REMARK 465 ASN B 1679 REMARK 465 HIS B 1680 REMARK 465 VAL B 1681 REMARK 465 SER B 1682 REMARK 465 SER B 1683 REMARK 465 ASP B 1684 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 GLU A 533 CB CG CD OE1 OE2 REMARK 470 ILE A 535 CB CG1 CG2 CD1 REMARK 470 GLU A 539 CB CG CD OE1 OE2 REMARK 470 GLU A 540 CB CG CD OE1 OE2 REMARK 470 LYS A 543 CE NZ REMARK 470 GLN A 553 CG CD OE1 NE2 REMARK 470 MET A 570 CE REMARK 470 LYS A 585 CD CE NZ REMARK 470 LYS A 590 CB CG CD CE NZ REMARK 470 LYS A 591 CD CE NZ REMARK 470 LYS A 593 CE NZ REMARK 470 LYS A 595 CE NZ REMARK 470 GLN A 597 CD OE1 NE2 REMARK 470 LYS A 600 CE NZ REMARK 470 LYS A 601 CE NZ REMARK 470 ASP A 614 OD1 OD2 REMARK 470 LYS A 616 CE NZ REMARK 470 SER A 624 CB OG REMARK 470 ASP A 626 CG OD1 OD2 REMARK 470 LYS A 651 CD CE NZ REMARK 470 ARG A 654 CD NE CZ NH1 NH2 REMARK 470 LYS A 656 CE NZ REMARK 470 LYS A 663 CD CE NZ REMARK 470 LYS A 667 CD CE NZ REMARK 470 ALA B1525 CB REMARK 470 GLU B1539 CB CG CD OE1 OE2 REMARK 470 GLU B1540 CG CD OE1 OE2 REMARK 470 GLN B1553 CG CD OE1 NE2 REMARK 470 MET B1570 CE REMARK 470 LYS B1581 CD CE NZ REMARK 470 LYS B1590 CB CG CD CE NZ REMARK 470 LYS B1591 CG CD CE NZ REMARK 470 GLU B1606 CD OE1 OE2 REMARK 470 SER B1618 OG REMARK 470 LYS B1622 CG CD CE NZ REMARK 470 LYS B1656 CG CD CE NZ REMARK 470 LYS B1663 CE NZ REMARK 470 LYS B1667 CD CE NZ REMARK 470 LYS B1668 CE NZ REMARK 470 GLU B1678 CB CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 534 C - N - CA ANGL. DEV. = 15.3 DEGREES 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 ARG A 534 114.85 68.19 REMARK 500 GLU A 540 46.47 81.79 REMARK 500 TYR A 575 -167.85 -123.99 REMARK 500 ASP A 577 74.63 -115.55 REMARK 500 GLU B1540 41.31 -174.54 REMARK 500 LYS B1601 60.32 62.42 REMARK 500 ASN B1677 86.19 -65.63 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 CA A1680 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 530 O REMARK 620 2 MET A 570 O 88.8 REMARK 620 3 ASP A 571 OD1 92.5 76.2 REMARK 620 4 ASP A 631 OD2 177.0 88.4 85.7 REMARK 620 5 ASP A 633 OD1 106.3 144.6 71.5 75.4 REMARK 620 6 ASP A 633 OD2 82.9 161.2 120.9 100.1 54.2 REMARK 620 7 ASP A 639 OD2 90.6 84.8 160.6 90.3 125.7 78.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A1679 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 571 OD2 REMARK 620 2 ASP A 571 OD1 49.9 REMARK 620 3 ASP A 577 OD2 79.2 128.9 REMARK 620 4 ASP A 631 OD1 93.9 93.2 94.2 REMARK 620 5 ASP A 631 OD2 88.2 58.7 133.8 42.1 REMARK 620 6 TYR A 632 O 165.1 144.2 86.9 81.8 97.7 REMARK 620 7 ASP A 633 OD1 113.8 64.5 161.6 97.7 62.2 81.0 REMARK 620 8 HOH A2004 O 82.6 86.0 83.2 176.0 139.3 101.2 85.6 REMARK 620 N 1 2 3 4 5 6 7 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2680 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B1530 O REMARK 620 2 MET B1570 O 81.3 REMARK 620 3 ASP B1571 OD1 91.9 79.1 REMARK 620 4 ASP B1631 OD2 168.4 88.0 81.9 REMARK 620 5 ASP B1633 OD2 93.7 158.6 122.0 97.9 REMARK 620 6 ASP B1633 OD1 105.9 149.4 71.1 81.3 51.9 REMARK 620 7 ASP B1639 OD1 89.1 83.3 162.1 93.9 75.8 125.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B2679 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B1571 OD2 REMARK 620 2 ASP B1571 OD1 47.6 REMARK 620 3 ASP B1577 OD2 77.3 124.5 REMARK 620 4 ASP B1631 OD1 89.6 91.4 94.7 REMARK 620 5 ASP B1631 OD2 89.1 61.3 134.9 41.7 REMARK 620 6 TYR B1632 O 162.7 149.4 86.0 87.1 99.6 REMARK 620 7 ASP B1633 OD1 115.4 68.9 156.8 104.4 67.1 81.8 REMARK 620 8 HOH B2004 O 92.1 89.4 86.1 178.3 137.8 91.4 74.5 REMARK 620 N 1 2 3 4 5 6 7 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1679 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A1680 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B2679 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B2680 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B2681 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1ZBD RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF RAB EFFECTOR SPECIFICITY : CRYSTALSTRUCTURE OF REMARK 900 THE SMALL G PROTEIN RAB3A COMPLEXED WITH THEEFFECTOR DOMAIN OF REMARK 900 RABPHILIN-3A REMARK 900 RELATED ID: 2CHD RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE C2A DOMAIN 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: 3RPB RELATED DB: PDB REMARK 900 THE C2B-DOMAIN OF RABPHILIN: STRUCTURAL VARIATIONS IN A JANUS-FACED REMARK 900 DOMAIN DBREF 2CM6 A 519 684 UNP P47709 RP3A_RAT 519 684 DBREF 2CM6 B 1519 1684 UNP P47709 RP3A_RAT 519 684 SEQRES 1 A 166 GLY SER ALA ARG GLY MET ALA LEU TYR GLU GLU GLU GLN SEQRES 2 A 166 VAL GLU ARG ILE GLY ASP ILE GLU GLU ARG GLY LYS ILE SEQRES 3 A 166 LEU VAL SER LEU MET TYR SER THR GLN GLN GLY GLY LEU SEQRES 4 A 166 ILE VAL GLY ILE ILE ARG CYS VAL HIS LEU ALA ALA MET SEQRES 5 A 166 ASP ALA ASN GLY TYR SER ASP PRO PHE VAL LYS LEU TRP SEQRES 6 A 166 LEU LYS PRO ASP MET GLY LYS LYS ALA LYS HIS LYS THR SEQRES 7 A 166 GLN ILE LYS LYS LYS THR LEU ASN PRO GLU PHE ASN GLU SEQRES 8 A 166 GLU PHE PHE TYR ASP ILE LYS HIS SER ASP LEU ALA LYS SEQRES 9 A 166 LYS SER LEU ASP ILE SER VAL TRP ASP TYR ASP ILE GLY SEQRES 10 A 166 LYS SER ASN ASP TYR ILE GLY GLY CYS GLN LEU GLY ILE SEQRES 11 A 166 SER ALA LYS GLY GLU ARG LEU LYS HIS TRP TYR GLU CYS SEQRES 12 A 166 LEU LYS ASN LYS ASP LYS LYS ILE GLU ARG TRP HIS GLN SEQRES 13 A 166 LEU GLN ASN GLU ASN HIS VAL SER SER ASP SEQRES 1 B 166 GLY SER ALA ARG GLY MET ALA LEU TYR GLU GLU GLU GLN SEQRES 2 B 166 VAL GLU ARG ILE GLY ASP ILE GLU GLU ARG GLY LYS ILE SEQRES 3 B 166 LEU VAL SER LEU MET TYR SER THR GLN GLN GLY GLY LEU SEQRES 4 B 166 ILE VAL GLY ILE ILE ARG CYS VAL HIS LEU ALA ALA MET SEQRES 5 B 166 ASP ALA ASN GLY TYR SER ASP PRO PHE VAL LYS LEU TRP SEQRES 6 B 166 LEU LYS PRO ASP MET GLY LYS LYS ALA LYS HIS LYS THR SEQRES 7 B 166 GLN ILE LYS LYS LYS THR LEU ASN PRO GLU PHE ASN GLU SEQRES 8 B 166 GLU PHE PHE TYR ASP ILE LYS HIS SER ASP LEU ALA LYS SEQRES 9 B 166 LYS SER LEU ASP ILE SER VAL TRP ASP TYR ASP ILE GLY SEQRES 10 B 166 LYS SER ASN ASP TYR ILE GLY GLY CYS GLN LEU GLY ILE SEQRES 11 B 166 SER ALA LYS GLY GLU ARG LEU LYS HIS TRP TYR GLU CYS SEQRES 12 B 166 LEU LYS ASN LYS ASP LYS LYS ILE GLU ARG TRP HIS GLN SEQRES 13 B 166 LEU GLN ASN GLU ASN HIS VAL SER SER ASP HET CA A1679 1 HET CA A1680 1 HET CA B2679 1 HET CA B2680 1 HET PO4 B2681 5 HETNAM CA CALCIUM ION HETNAM PO4 PHOSPHATE ION FORMUL 3 CA 4(CA 2+) FORMUL 7 PO4 O4 P 3- FORMUL 8 HOH *76(H2 O) HELIX 1 1 LEU A 526 GLN A 531 5 6 HELIX 2 2 LYS A 616 ALA A 621 1 6 HELIX 3 3 LYS A 651 ASN A 664 1 14 HELIX 4 4 ALA B 1525 GLU B 1530 1 6 HELIX 5 5 MET B 1588 LYS B 1591 5 4 HELIX 6 6 LYS B 1616 ALA B 1621 1 6 HELIX 7 7 LYS B 1651 ASN B 1664 1 14 SHEET 1 AA 4 GLU A 606 ASP A 614 0 SHEET 2 AA 4 GLY A 556 VAL A 565 -1 O LEU A 557 N TYR A 613 SHEET 3 AA 4 LYS A 543 SER A 551 -1 O LYS A 543 N VAL A 565 SHEET 4 AA 4 ILE A 669 GLN A 674 -1 O ILE A 669 N LEU A 548 SHEET 1 AB 4 LYS A 593 LYS A 595 0 SHEET 2 AB 4 PRO A 578 LYS A 585 -1 O LEU A 582 N HIS A 594 SHEET 3 AB 4 SER A 624 ASP A 631 -1 O SER A 624 N LYS A 585 SHEET 4 AB 4 ASP A 639 GLY A 647 -1 O ASP A 639 N ASP A 631 SHEET 1 BA 4 GLU B1606 ASP B1614 0 SHEET 2 BA 4 GLY B1556 VAL B1565 -1 O LEU B1557 N TYR B1613 SHEET 3 BA 4 LYS B1543 SER B1551 -1 O LYS B1543 N VAL B1565 SHEET 4 BA 4 ILE B1669 GLN B1674 -1 O ILE B1669 N LEU B1548 SHEET 1 BB 4 LYS B1593 LYS B1595 0 SHEET 2 BB 4 PRO B1578 LYS B1585 -1 O LEU B1582 N HIS B1594 SHEET 3 BB 4 SER B1624 ASP B1631 -1 O SER B1624 N LYS B1585 SHEET 4 BB 4 ASP B1639 LEU B1646 -1 O ASP B1639 N ASP B1631 LINK O GLU A 530 CA CA A1680 1555 1555 2.29 LINK O MET A 570 CA CA A1680 1555 1555 2.18 LINK OD2 ASP A 571 CA CA A1679 1555 1555 2.16 LINK OD1 ASP A 571 CA CA A1679 1555 1555 2.82 LINK OD1 ASP A 571 CA CA A1680 1555 1555 2.10 LINK OD2 ASP A 577 CA CA A1679 1555 1555 2.29 LINK OD1 ASP A 631 CA CA A1679 1555 1555 2.36 LINK OD2 ASP A 631 CA CA A1679 1555 1555 3.27 LINK OD2 ASP A 631 CA CA A1680 1555 1555 2.32 LINK O TYR A 632 CA CA A1679 1555 1555 2.23 LINK OD1 ASP A 633 CA CA A1679 1555 1555 2.20 LINK OD1 ASP A 633 CA CA A1680 1555 1555 2.53 LINK OD2 ASP A 633 CA CA A1680 1555 1555 2.19 LINK OD2 ASP A 639 CA CA A1680 1555 1555 2.17 LINK CA CA A1679 O HOH A2004 1555 1555 2.41 LINK O GLU B1530 CA CA B2680 1555 1555 2.32 LINK O MET B1570 CA CA B2680 1555 1555 2.45 LINK OD2 ASP B1571 CA CA B2679 1555 1555 2.55 LINK OD1 ASP B1571 CA CA B2679 1555 1555 2.83 LINK OD1 ASP B1571 CA CA B2680 1555 1555 2.49 LINK OD2 ASP B1577 CA CA B2679 1555 1555 2.26 LINK OD1 ASP B1631 CA CA B2679 1555 1555 2.41 LINK OD2 ASP B1631 CA CA B2679 1555 1555 3.31 LINK OD2 ASP B1631 CA CA B2680 1555 1555 2.33 LINK O TYR B1632 CA CA B2679 1555 1555 2.24 LINK OD1 ASP B1633 CA CA B2679 1555 1555 2.39 LINK OD2 ASP B1633 CA CA B2680 1555 1555 2.32 LINK OD1 ASP B1633 CA CA B2680 1555 1555 2.63 LINK OD1 ASP B1639 CA CA B2680 1555 1555 2.13 LINK O HOH B2004 CA CA B2679 1555 1555 2.25 CISPEP 1 GLU A 533 ARG A 534 0 5.55 CISPEP 2 ARG A 534 ILE A 535 0 -0.56 CISPEP 3 GLU A 539 GLU A 540 0 -2.60 CISPEP 4 LYS A 585 PRO A 586 0 -2.99 CISPEP 5 LYS B 1585 PRO B 1586 0 -10.89 SITE 1 AC1 6 ASP A 571 ASP A 577 ASP A 631 TYR A 632 SITE 2 AC1 6 ASP A 633 HOH A2004 SITE 1 AC2 6 GLU A 530 MET A 570 ASP A 571 ASP A 631 SITE 2 AC2 6 ASP A 633 ASP A 639 SITE 1 AC3 6 ASP B1571 ASP B1577 ASP B1631 TYR B1632 SITE 2 AC3 6 ASP B1633 HOH B2004 SITE 1 AC4 6 GLU B1530 MET B1570 ASP B1571 ASP B1631 SITE 2 AC4 6 ASP B1633 ASP B1639 SITE 1 AC5 3 HIS B1594 PHE B1611 PHE B1612 CRYST1 40.069 59.606 66.385 90.00 103.89 90.00 P 1 21 1 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 0.024957 0.000000 0.006172 0.00000 SCALE2 0.000000 0.016777 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015517 0.00000