HEADER SIGNALING PROTEIN/GTP-BINDING PROTEIN 02-MAR-08 3CF6 TITLE STRUCTURE OF EPAC2 IN COMPLEX WITH CYCLIC-AMP AND RAP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAP GUANINE NUCLEOTIDE EXCHANGE FACTOR (GEF) 4; COMPND 3 CHAIN: E; COMPND 4 FRAGMENT: UNP RESIDUES 306-993; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RAS-RELATED PROTEIN RAP-1B; COMPND 8 CHAIN: R; COMPND 9 FRAGMENT: UNP RESIDUES 1-167; COMPND 10 SYNONYM: GTP-BINDING PROTEIN SMG P21B, RAP1B; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RAPGEF4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: CK600K; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T1; SOURCE 11 OTHER_DETAILS: GST FUSION; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: RAP1B; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 19 EXPRESSION_SYSTEM_STRAIN: CK600K; SOURCE 20 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 21 EXPRESSION_SYSTEM_PLASMID: PTAC KEYWDS EPAC, RAPGEF4, RAP, RAP1B, CAMP, SP-CAMPS, GEF, GUNANINE NUCLEOTIDE KEYWDS 2 EXCHANGE FACTOR, G-PROTEIN, GTP-BINDING, NUCLEOTIDE-BINDING, KEYWDS 3 SIGNALING PROTEIN REGULATOR-GTP-BINDING PROTEIN COMPLEX, SIGNALING KEYWDS 4 PROTEIN-GTP-BINDING PROTEIN COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.REHMANN,E.ARIAS-PALOMO,M.A.HADDERS,F.SCHWEDE,O.LLORCA,J.L.BOS REVDAT 6 01-NOV-23 3CF6 1 REMARK REVDAT 5 04-AUG-21 3CF6 1 REMARK SEQADV REVDAT 4 05-FEB-14 3CF6 1 REMARK VERSN REVDAT 3 24-FEB-09 3CF6 1 VERSN REVDAT 2 09-SEP-08 3CF6 1 JRNL REVDAT 1 29-JUL-08 3CF6 0 JRNL AUTH H.REHMANN,E.ARIAS-PALOMO,M.A.HADDERS,F.SCHWEDE,O.LLORCA, JRNL AUTH 2 J.L.BOS JRNL TITL STRUCTURE OF EPAC2 IN COMPLEX WITH A CYCLIC AMP ANALOGUE AND JRNL TITL 2 RAP1B JRNL REF NATURE V. 455 124 2008 JRNL REFN ISSN 0028-0836 JRNL PMID 18660803 JRNL DOI 10.1038/NATURE07187 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.REHMANN,J.DAS,P.KNIPSCHEER,A.WITTINGHOFER,J.L.BOS REMARK 1 TITL STRUCTURE OF THE CYCLIC-AMP-RESPONSIVE EXCHANGE FACTOR EPAC2 REMARK 1 TITL 2 IN ITS AUTO-INHIBITED STATE REMARK 1 REF NATURE V. 439 625 2006 REMARK 1 REFN ISSN 0028-0836 REMARK 1 PMID 16452984 REMARK 1 DOI 10.1038/NATURE04468 REMARK 1 REFERENCE 2 REMARK 1 AUTH H.REHMANN,B.PRAKASH,E.WOLF,A.RUEPPEL,J.DE ROOIJ,J.L.BOS, REMARK 1 AUTH 2 A.WITTINGHOFER REMARK 1 TITL STRUCTURE AND REGULATION OF THE CAMP-BINDING DOMAINS OF REMARK 1 TITL 2 EPAC2 REMARK 1 REF NAT.STRUCT.BIOL. V. 10 26 2003 REMARK 1 REFN ISSN 1072-8368 REMARK 1 PMID 12469113 REMARK 1 DOI 10.1038/NSB878 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.56 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 3 NUMBER OF REFLECTIONS : 100557 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.244 REMARK 3 R VALUE (WORKING SET) : 0.243 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 5214 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 REFLECTION IN BIN (WORKING SET) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6238 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 49 REMARK 3 SOLVENT ATOMS : 274 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.19 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.11000 REMARK 3 B22 (A**2) : 1.41000 REMARK 3 B33 (A**2) : -1.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; 0.012 ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; 1.418 ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; 0.096 ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; 0.005 ; NULL REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : NULL REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3CF6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-MAR-08. REMARK 100 THE DEPOSITION ID IS D_1000046700. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9732 REMARK 200 MONOCHROMATOR : SILICON (1 1 1) CHANNEL-CUT REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 102111 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 3.620 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.960 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2BYV, PDB ENTRY 1BKD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 77.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.4M (NH4)2SO4, 1.2M LI2SO4, 0.1M REMARK 280 CITRATE, PH 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y+1/2,Z REMARK 290 7555 -X+1/2,Y,-Z REMARK 290 8555 X,-Y,-Z+1/2 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 62.68350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 112.64550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 74.51250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 112.64550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 62.68350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 74.51250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 62.68350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 74.51250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 112.64550 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 74.51250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 62.68350 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 112.64550 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 67380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -97.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, R 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -112.64550 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 35410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -43.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, R 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH E 998 LIES ON A SPECIAL POSITION. 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 E 300 REMARK 465 SER E 301 REMARK 465 PRO E 302 REMARK 465 GLU E 303 REMARK 465 SER E 304 REMARK 465 PHE E 305 REMARK 465 PRO E 306 REMARK 465 ASP E 307 REMARK 465 ALA E 308 REMARK 465 HIS E 309 REMARK 465 PRO E 463 REMARK 465 ALA E 464 REMARK 465 GLY E 465 REMARK 465 ASN E 466 REMARK 465 ARG E 467 REMARK 465 ALA E 468 REMARK 465 ALA E 469 REMARK 465 ASN E 470 REMARK 465 GLN E 471 REMARK 465 GLY E 472 REMARK 465 ASN E 473 REMARK 465 SER E 474 REMARK 465 GLN E 475 REMARK 465 PRO E 476 REMARK 465 GLN E 477 REMARK 465 LYS E 613 REMARK 465 GLN E 614 REMARK 465 ILE E 615 REMARK 465 SER E 616 REMARK 465 GLU E 617 REMARK 465 ASP E 618 REMARK 465 ALA E 619 REMARK 465 LYS E 620 REMARK 465 ALA E 621 REMARK 465 PRO E 622 REMARK 465 GLN E 623 REMARK 465 LYS E 624 REMARK 465 LYS E 625 REMARK 465 HIS E 626 REMARK 465 LYS E 627 REMARK 465 VAL E 628 REMARK 465 LEU E 629 REMARK 465 LEU E 630 REMARK 465 GLN E 631 REMARK 465 GLN E 632 REMARK 465 PHE E 633 REMARK 465 ASN E 634 REMARK 465 THR E 635 REMARK 465 GLY E 636 REMARK 465 ASP E 637 REMARK 465 GLU E 638 REMARK 465 ARG E 639 REMARK 465 ALA E 640 REMARK 465 GLN E 641 REMARK 465 LYS E 642 REMARK 465 PRO E 953 REMARK 465 ASP E 954 REMARK 465 ALA E 955 REMARK 465 ALA E 956 REMARK 465 GLN E 957 REMARK 465 ALA E 958 REMARK 465 ASN E 959 REMARK 465 LYS E 960 REMARK 465 ASN E 961 REMARK 465 ARG E 991 REMARK 465 ARG E 992 REMARK 465 PRO E 993 REMARK 465 MET R 1 REMARK 465 ARG R 2 REMARK 465 GLU R 45 REMARK 465 VAL R 46 REMARK 465 ASP R 47 REMARK 465 ALA R 48 REMARK 465 GLN R 49 REMARK 465 ALA R 135 REMARK 465 ARG R 136 REMARK 465 GLN R 137 REMARK 465 TRP R 138 REMARK 465 ASN R 139 REMARK 465 ASN R 140 REMARK 465 CYS R 141 REMARK 465 ILE R 165 REMARK 465 ASN R 166 REMARK 465 ARG R 167 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 PRO E 900 C - N - CA ANGL. DEV. = 11.2 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 PRO E 318 -51.03 -27.84 REMARK 500 ASN E 424 74.99 59.18 REMARK 500 VAL E 442 -38.31 -130.60 REMARK 500 THR E 446 137.24 -39.72 REMARK 500 PRO E 900 -69.42 -11.40 REMARK 500 PRO E 901 86.32 -66.75 REMARK 500 GLN R 25 -55.58 -157.82 REMARK 500 PHE R 28 -15.44 67.61 REMARK 500 GLN R 87 -74.65 -12.68 REMARK 500 ARG R 102 -36.51 172.10 REMARK 500 THR R 106 -167.95 -129.26 REMARK 500 LYS R 151 58.55 39.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ALA R 86 GLN R 87 148.24 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 R 168 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SP1 E 2 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SP1 E 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BYV RELATED DB: PDB REMARK 900 INACTIVE EPAC2 DBREF 3CF6 E 306 993 UNP A2ASW3 A2ASW3_MOUSE 306 993 DBREF 3CF6 R 1 167 UNP P61224 RAP1B_HUMAN 1 167 SEQADV 3CF6 GLY E 300 UNP A2ASW3 EXPRESSION TAG SEQADV 3CF6 SER E 301 UNP A2ASW3 EXPRESSION TAG SEQADV 3CF6 PRO E 302 UNP A2ASW3 EXPRESSION TAG SEQADV 3CF6 GLU E 303 UNP A2ASW3 EXPRESSION TAG SEQADV 3CF6 SER E 304 UNP A2ASW3 EXPRESSION TAG SEQADV 3CF6 PHE E 305 UNP A2ASW3 EXPRESSION TAG SEQRES 1 E 694 GLY SER PRO GLU SER PHE PRO ASP ALA HIS MET ARG MET SEQRES 2 E 694 ILE LEU ARG LYS PRO PRO GLY GLN ARG THR VAL ASP ASP SEQRES 3 E 694 LEU GLU ILE ILE TYR ASP GLU LEU LEU HIS ILE LYS ALA SEQRES 4 E 694 LEU SER HIS LEU SER THR THR VAL LYS ARG GLU LEU ALA SEQRES 5 E 694 GLY VAL LEU ILE PHE GLU SER HIS ALA LYS GLY GLY THR SEQRES 6 E 694 VAL LEU PHE ASN GLN GLY GLU GLU GLY THR SER TRP TYR SEQRES 7 E 694 ILE ILE LEU LYS GLY SER VAL ASN VAL VAL ILE TYR GLY SEQRES 8 E 694 LYS GLY VAL VAL CYS THR LEU HIS GLU GLY ASP ASP PHE SEQRES 9 E 694 GLY LYS LEU ALA LEU VAL ASN ASP ALA PRO ARG ALA ALA SEQRES 10 E 694 SER ILE VAL LEU ARG GLU ASP ASN CYS HIS PHE LEU ARG SEQRES 11 E 694 VAL ASP LYS GLU ASP PHE ASN ARG ILE LEU ARG ASP VAL SEQRES 12 E 694 GLU ALA ASN THR VAL ARG LEU LYS GLU HIS ASP GLN ASP SEQRES 13 E 694 VAL LEU VAL LEU GLU LYS VAL PRO ALA GLY ASN ARG ALA SEQRES 14 E 694 ALA ASN GLN GLY ASN SER GLN PRO GLN GLN LYS TYR THR SEQRES 15 E 694 VAL MET SER GLY THR PRO GLU LYS ILE LEU GLU HIS PHE SEQRES 16 E 694 LEU GLU THR ILE ARG LEU GLU PRO SER LEU ASN GLU ALA SEQRES 17 E 694 THR ASP SER VAL LEU ASN ASP PHE VAL MET MET HIS CYS SEQRES 18 E 694 VAL PHE MET PRO ASN THR GLN LEU CYS PRO ALA LEU VAL SEQRES 19 E 694 ALA HIS TYR HIS ALA GLN PRO SER GLN GLY THR GLU GLN SEQRES 20 E 694 GLU ARG MET ASP TYR ALA LEU ASN ASN LYS ARG ARG VAL SEQRES 21 E 694 ILE ARG LEU VAL LEU GLN TRP ALA ALA MET TYR GLY ASP SEQRES 22 E 694 LEU LEU GLN GLU ASP ASP VAL ALA MET ALA PHE LEU GLU SEQRES 23 E 694 GLU PHE TYR VAL SER VAL SER ASP ASP ALA ARG MET MET SEQRES 24 E 694 ALA ALA PHE LYS GLU GLN LEU PRO GLU LEU GLU LYS ILE SEQRES 25 E 694 VAL LYS GLN ILE SER GLU ASP ALA LYS ALA PRO GLN LYS SEQRES 26 E 694 LYS HIS LYS VAL LEU LEU GLN GLN PHE ASN THR GLY ASP SEQRES 27 E 694 GLU ARG ALA GLN LYS ARG GLN PRO ILE ARG GLY SER ASP SEQRES 28 E 694 GLU VAL LEU PHE LYS VAL TYR CYS ILE ASP HIS THR TYR SEQRES 29 E 694 THR THR ILE ARG VAL PRO VAL ALA ALA SER VAL LYS GLU SEQRES 30 E 694 VAL ILE SER ALA VAL ALA ASP LYS LEU GLY SER GLY GLU SEQRES 31 E 694 GLY LEU ILE ILE VAL LYS MET ASN SER GLY GLY GLU LYS SEQRES 32 E 694 VAL VAL LEU LYS SER ASN ASP VAL SER VAL PHE THR THR SEQRES 33 E 694 LEU THR ILE ASN GLY ARG LEU PHE ALA CYS PRO ARG GLU SEQRES 34 E 694 GLN PHE ASP SER LEU THR PRO LEU PRO GLU GLN GLU GLY SEQRES 35 E 694 PRO THR THR GLY THR VAL GLY THR PHE GLU LEU MET SER SEQRES 36 E 694 SER LYS ASP LEU ALA TYR GLN MET THR THR TYR ASP TRP SEQRES 37 E 694 GLU LEU PHE ASN CYS VAL HIS GLU LEU GLU LEU ILE TYR SEQRES 38 E 694 HIS THR PHE GLY ARG HIS ASN PHE LYS LYS THR THR ALA SEQRES 39 E 694 ASN LEU ASP LEU PHE LEU ARG ARG PHE ASN GLU ILE GLN SEQRES 40 E 694 PHE TRP VAL VAL THR GLU VAL CYS LEU CYS SER GLN LEU SEQRES 41 E 694 SER LYS ARG VAL GLN LEU LEU LYS LYS PHE ILE LYS ILE SEQRES 42 E 694 ALA ALA HIS CYS LYS GLU TYR LYS ASN LEU ASN SER PHE SEQRES 43 E 694 PHE ALA ILE VAL MET GLY LEU SER ASN VAL ALA VAL SER SEQRES 44 E 694 ARG LEU ALA LEU THR TRP GLU LYS LEU PRO SER LYS PHE SEQRES 45 E 694 LYS LYS PHE TYR ALA GLU PHE GLU SER LEU MET ASP PRO SEQRES 46 E 694 SER ARG ASN HIS ARG ALA TYR ARG LEU THR ALA ALA LYS SEQRES 47 E 694 LEU GLU PRO PRO LEU ILE PRO PHE MET PRO LEU LEU ILE SEQRES 48 E 694 LYS ASP MET THR PHE THR HIS GLU GLY ASN LYS THR PHE SEQRES 49 E 694 ILE ASP ASN LEU VAL ASN PHE GLU LYS MET ARG MET ILE SEQRES 50 E 694 ALA ASN THR ALA ARG THR VAL ARG TYR TYR ARG SER GLN SEQRES 51 E 694 PRO PHE ASN PRO ASP ALA ALA GLN ALA ASN LYS ASN HIS SEQRES 52 E 694 GLN ASP VAL ARG SER TYR VAL ARG GLN LEU ASN VAL ILE SEQRES 53 E 694 ASP ASN GLN ARG THR LEU SER GLN MET SER HIS ARG LEU SEQRES 54 E 694 GLU PRO ARG ARG PRO SEQRES 1 R 167 MET ARG GLU TYR LYS LEU VAL VAL LEU GLY SER GLY GLY SEQRES 2 R 167 VAL GLY LYS SER ALA LEU THR VAL GLN PHE VAL GLN GLY SEQRES 3 R 167 ILE PHE VAL GLU LYS TYR ASP PRO THR ILE GLU ASP SER SEQRES 4 R 167 TYR ARG LYS GLN VAL GLU VAL ASP ALA GLN GLN CYS MET SEQRES 5 R 167 LEU GLU ILE LEU ASP THR ALA GLY THR GLU GLN PHE THR SEQRES 6 R 167 ALA MET ARG ASP LEU TYR MET LYS ASN GLY GLN GLY PHE SEQRES 7 R 167 ALA LEU VAL TYR SER ILE THR ALA GLN SER THR PHE ASN SEQRES 8 R 167 ASP LEU GLN ASP LEU ARG GLU GLN ILE LEU ARG VAL LYS SEQRES 9 R 167 ASP THR ASP ASP VAL PRO MET ILE LEU VAL GLY ASN LYS SEQRES 10 R 167 CYS ASP LEU GLU ASP GLU ARG VAL VAL GLY LYS GLU GLN SEQRES 11 R 167 GLY GLN ASN LEU ALA ARG GLN TRP ASN ASN CYS ALA PHE SEQRES 12 R 167 LEU GLU SER SER ALA LYS SER LYS ILE ASN VAL ASN GLU SEQRES 13 R 167 ILE PHE TYR ASP LEU VAL ARG GLN ILE ASN ARG HET SP1 E 2 22 HET SP1 E 3 22 HET SO4 R 168 5 HETNAM SP1 6-(6-AMINO-PURIN-9-YL)-2-THIOXO-TETRAHYDRO-2-FURO[3,2- HETNAM 2 SP1 D][1,3,2]DIOXAPHOSPHININE-2,7-DIOL HETNAM SO4 SULFATE ION HETSYN SP1 SP-ADENOSINE-3',5'-CYCLIC-MONOPHOSPHOROTHIOATE FORMUL 3 SP1 2(C10 H12 N5 O5 P S) FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *274(H2 O) HELIX 1 1 MET E 310 LYS E 316 1 7 HELIX 2 2 PRO E 317 ARG E 321 5 5 HELIX 3 3 THR E 322 LEU E 334 1 13 HELIX 4 4 HIS E 335 SER E 340 5 6 HELIX 5 5 SER E 343 GLY E 352 1 10 HELIX 6 6 GLY E 404 ASP E 411 1 8 HELIX 7 7 LYS E 432 LEU E 439 1 8 HELIX 8 8 THR E 486 THR E 497 1 12 HELIX 9 9 GLU E 501 SER E 503 5 3 HELIX 10 10 LEU E 504 MET E 523 1 20 HELIX 11 11 PRO E 524 HIS E 537 1 14 HELIX 12 12 THR E 544 GLY E 571 1 28 HELIX 13 13 ASP E 572 GLU E 576 5 5 HELIX 14 14 ASP E 577 ALA E 599 1 23 HELIX 15 15 GLU E 603 VAL E 612 1 10 HELIX 16 16 SER E 673 GLY E 686 1 14 HELIX 17 17 VAL E 712 LEU E 716 5 5 HELIX 18 18 GLU E 728 LEU E 733 5 6 HELIX 19 19 LEU E 736 GLU E 740 5 5 HELIX 20 20 THR E 746 GLU E 751 1 6 HELIX 21 21 SER E 754 CYS E 772 1 19 HELIX 22 22 HIS E 774 GLY E 784 1 11 HELIX 23 23 ARG E 785 PHE E 788 5 4 HELIX 24 24 THR E 792 LEU E 815 1 24 HELIX 25 25 GLN E 818 TYR E 839 1 22 HELIX 26 26 ASN E 841 SER E 853 1 13 HELIX 27 27 ASN E 854 ARG E 859 1 6 HELIX 28 28 LEU E 860 LYS E 866 1 7 HELIX 29 29 PRO E 868 LEU E 881 1 14 HELIX 30 30 PRO E 884 LEU E 898 1 15 HELIX 31 31 PHE E 905 ASN E 920 1 16 HELIX 32 32 PHE E 930 ARG E 947 1 18 HELIX 33 33 HIS E 962 ARG E 970 1 9 HELIX 34 34 ASN E 977 GLU E 989 1 13 HELIX 35 35 GLY R 15 GLN R 25 1 11 HELIX 36 36 PHE R 64 GLY R 75 1 12 HELIX 37 37 ALA R 86 ASP R 92 1 7 HELIX 38 38 ASP R 92 LYS R 104 1 13 HELIX 39 39 GLY R 127 LEU R 134 1 8 HELIX 40 40 ASN R 153 GLN R 164 1 12 SHEET 1 A 4 ILE E 355 HIS E 359 0 SHEET 2 A 4 CYS E 425 ASP E 431 -1 O ARG E 429 N ILE E 355 SHEET 3 A 4 SER E 375 LYS E 381 -1 N LEU E 380 O HIS E 426 SHEET 4 A 4 ASP E 402 PHE E 403 -1 O PHE E 403 N TYR E 377 SHEET 1 B 4 VAL E 365 PHE E 367 0 SHEET 2 B 4 SER E 417 LEU E 420 -1 O ILE E 418 N PHE E 367 SHEET 3 B 4 SER E 383 ILE E 388 -1 N ASN E 385 O VAL E 419 SHEET 4 B 4 GLY E 392 HIS E 398 -1 O CYS E 395 N VAL E 386 SHEET 1 C 5 VAL E 447 GLU E 451 0 SHEET 2 C 5 GLN E 454 LYS E 461 -1 O LEU E 457 N LEU E 449 SHEET 3 C 5 TYR E 480 GLY E 485 -1 O MET E 483 N VAL E 458 SHEET 4 C 5 LEU E 927 ASN E 929 -1 O VAL E 928 N GLY E 485 SHEET 5 C 5 PHE E 923 ILE E 924 -1 N ILE E 924 O LEU E 927 SHEET 1 D 2 GLU E 651 TYR E 657 0 SHEET 2 D 2 TYR E 663 PRO E 669 -1 O THR E 664 N VAL E 656 SHEET 1 E 3 LYS E 702 VAL E 704 0 SHEET 2 E 3 LEU E 691 MET E 696 -1 N LYS E 695 O VAL E 703 SHEET 3 E 3 ARG E 721 PRO E 726 -1 O PHE E 723 N VAL E 694 SHEET 1 F 6 ARG R 41 GLN R 43 0 SHEET 2 F 6 MET R 52 ASP R 57 -1 O LEU R 53 N LYS R 42 SHEET 3 F 6 TYR R 4 LEU R 9 1 N LEU R 6 O LEU R 56 SHEET 4 F 6 GLY R 77 SER R 83 1 O ALA R 79 N LEU R 9 SHEET 5 F 6 MET R 111 ASN R 116 1 O VAL R 114 N LEU R 80 SHEET 6 F 6 PHE R 143 GLU R 145 1 O LEU R 144 N GLY R 115 SITE 1 AC1 8 SER R 11 GLY R 12 GLY R 13 GLY R 15 SITE 2 AC1 8 LYS R 16 SER R 17 ALA R 59 HOH R 171 SITE 1 AC2 15 PHE E 367 ILE E 388 CYS E 395 PHE E 403 SITE 2 AC2 15 GLY E 404 LEU E 406 ALA E 407 ARG E 414 SITE 3 AC2 15 ALA E 415 LEU E 449 LYS E 450 GLU E 451 SITE 4 AC2 15 LYS E 489 HOH E1054 HOH E1077 SITE 1 AC3 12 ASN E 368 ILE E 388 GLY E 392 SER E 417 SITE 2 AC3 12 GLN E 539 SER E 541 LYS E 556 ASP E 594 SITE 3 AC3 12 MET E 597 MET E 598 HOH E1033 HOH E1052 CRYST1 125.367 149.025 225.291 90.00 90.00 90.00 I 21 21 21 8 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 0.007977 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004439 0.00000