HEADER PROTEIN BINDING 12-JUL-06 2DTC TITLE CRYSTAL STRUCTURE OF MS0666 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAL GUANINE NUCLEOTIDE EXCHANGE FACTOR RALGPS1A; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PLECKSTRIN HOMOLOGY DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 6 EXPRESSION_SYSTEM_PLASMID: PX051128-20; SOURCE 7 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS PH DOMAIN, PROTEIN BINDING, STRUCTURAL GENOMICS, NPPSFA, KEYWDS 2 NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL KEYWDS 3 ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, KEYWDS 4 RSGI EXPDTA X-RAY DIFFRACTION AUTHOR H.WANG,S.KISHISHITA,K.MURAYAMA,T.TERADA,M.SHIROUZU, AUTHOR 2 S.YOKOYAMA,RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE AUTHOR 3 (RSGI) REVDAT 2 24-FEB-09 2DTC 1 VERSN REVDAT 1 12-JAN-07 2DTC 0 JRNL AUTH H.WANG,S.KISHISHITA,K.MURAYAMA,T.TERADA,M.SHIROUZU, JRNL AUTH 2 S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF MS0666 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 187438.360 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.4 REMARK 3 NUMBER OF REFLECTIONS : 23256 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 SET) : 0.192 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1114 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3298 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE : 0.3040 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 155 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1873 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 288 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.64000 REMARK 3 B22 (A**2) : 4.24000 REMARK 3 B33 (A**2) : -1.61000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -4.07000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.19 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.13 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.70 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.94 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.37 REMARK 3 BSOL : 46.98 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DTC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 13-JUL-06. REMARK 100 THE RCSB ID CODE IS RCSB025819. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9700, 0.9790, 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24140 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 13.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26900 REMARK 200 FOR SHELL : 4.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, TRIS, PH 8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 30.53850 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLN A 117 REMARK 465 VAL A 118 REMARK 465 PRO A 119 REMARK 465 ALA A 120 REMARK 465 ASN A 121 REMARK 465 LEU A 122 REMARK 465 MSE A 123 REMARK 465 SER A 124 REMARK 465 PHE A 125 REMARK 465 GLU A 126 REMARK 465 PRO B 116 REMARK 465 GLN B 117 REMARK 465 VAL B 118 REMARK 465 PRO B 119 REMARK 465 ALA B 120 REMARK 465 ASN B 121 REMARK 465 LEU B 122 REMARK 465 MSE B 123 REMARK 465 SER B 124 REMARK 465 PHE B 125 REMARK 465 GLU B 126 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 SER A 43 -142.55 -146.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MMT008001402.1 RELATED DB: TARGETDB DBREF 2DTC A 1 126 UNP Q8BVR9 Q8BVR9_MOUSE 460 585 DBREF 2DTC B 1 126 UNP Q8BVR9 Q8BVR9_MOUSE 460 585 SEQADV 2DTC MSE A 3 UNP Q8BVR9 MET 462 MODIFIED RESIDUE SEQADV 2DTC MSE A 66 UNP Q8BVR9 MET 525 MODIFIED RESIDUE SEQADV 2DTC MSE A 123 UNP Q8BVR9 MET 582 MODIFIED RESIDUE SEQADV 2DTC MSE B 3 UNP Q8BVR9 MET 462 MODIFIED RESIDUE SEQADV 2DTC MSE B 66 UNP Q8BVR9 MET 525 MODIFIED RESIDUE SEQADV 2DTC MSE B 123 UNP Q8BVR9 MET 582 MODIFIED RESIDUE SEQRES 1 A 126 PRO THR MSE GLU GLY PRO LEU ARG ARG LYS THR LEU LEU SEQRES 2 A 126 LYS GLU GLY ARG LYS PRO ALA LEU SER SER TRP THR ARG SEQRES 3 A 126 TYR TRP VAL VAL LEU SER GLY ALA THR LEU LEU TYR TYR SEQRES 4 A 126 GLY ALA LYS SER LEU ARG GLY THR ASP ARG LYS HIS TYR SEQRES 5 A 126 LYS SER THR PRO GLY LYS LYS VAL SER ILE VAL GLY TRP SEQRES 6 A 126 MSE VAL GLN LEU PRO ASP ASP PRO GLU HIS PRO ASP ILE SEQRES 7 A 126 PHE GLN LEU ASN ASN PRO ASP LYS GLY ASN VAL TYR LYS SEQRES 8 A 126 PHE GLN THR GLY SER ARG PHE HIS ALA ILE LEU TRP HIS SEQRES 9 A 126 LYS HIS LEU ASP ASP ALA CYS LYS SER SER ARG PRO GLN SEQRES 10 A 126 VAL PRO ALA ASN LEU MSE SER PHE GLU SEQRES 1 B 126 PRO THR MSE GLU GLY PRO LEU ARG ARG LYS THR LEU LEU SEQRES 2 B 126 LYS GLU GLY ARG LYS PRO ALA LEU SER SER TRP THR ARG SEQRES 3 B 126 TYR TRP VAL VAL LEU SER GLY ALA THR LEU LEU TYR TYR SEQRES 4 B 126 GLY ALA LYS SER LEU ARG GLY THR ASP ARG LYS HIS TYR SEQRES 5 B 126 LYS SER THR PRO GLY LYS LYS VAL SER ILE VAL GLY TRP SEQRES 6 B 126 MSE VAL GLN LEU PRO ASP ASP PRO GLU HIS PRO ASP ILE SEQRES 7 B 126 PHE GLN LEU ASN ASN PRO ASP LYS GLY ASN VAL TYR LYS SEQRES 8 B 126 PHE GLN THR GLY SER ARG PHE HIS ALA ILE LEU TRP HIS SEQRES 9 B 126 LYS HIS LEU ASP ASP ALA CYS LYS SER SER ARG PRO GLN SEQRES 10 B 126 VAL PRO ALA ASN LEU MSE SER PHE GLU MODRES 2DTC MSE A 3 MET SELENOMETHIONINE MODRES 2DTC MSE A 66 MET SELENOMETHIONINE MODRES 2DTC MSE B 3 MET SELENOMETHIONINE MODRES 2DTC MSE B 66 MET SELENOMETHIONINE HET MSE A 3 8 HET MSE A 66 8 HET MSE B 3 8 HET MSE B 66 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 HOH *288(H2 O) HELIX 1 1 ASP A 48 TYR A 52 5 5 HELIX 2 2 SER A 96 LYS A 112 1 17 HELIX 3 3 ASP B 48 TYR B 52 5 5 HELIX 4 4 SER B 96 LYS B 112 1 17 SHEET 1 A 7 LYS A 58 SER A 61 0 SHEET 2 A 7 THR A 35 GLY A 40 -1 N LEU A 36 O VAL A 60 SHEET 3 A 7 THR A 25 SER A 32 -1 N VAL A 30 O LEU A 37 SHEET 4 A 7 MSE A 3 LEU A 13 -1 N MSE A 3 O LEU A 31 SHEET 5 A 7 VAL A 89 GLN A 93 -1 O GLN A 93 N ARG A 8 SHEET 6 A 7 ILE A 78 ASN A 82 -1 N LEU A 81 O TYR A 90 SHEET 7 A 7 MSE A 66 GLN A 68 -1 N MSE A 66 O ASN A 82 SHEET 1 B 7 LYS B 58 SER B 61 0 SHEET 2 B 7 THR B 35 GLY B 40 -1 N LEU B 36 O VAL B 60 SHEET 3 B 7 THR B 25 SER B 32 -1 N TRP B 28 O TYR B 39 SHEET 4 B 7 MSE B 3 LEU B 13 -1 N MSE B 3 O LEU B 31 SHEET 5 B 7 VAL B 89 GLN B 93 -1 O VAL B 89 N LEU B 12 SHEET 6 B 7 ILE B 78 ASN B 82 -1 N LEU B 81 O TYR B 90 SHEET 7 B 7 MSE B 66 GLN B 68 -1 N MSE B 66 O ASN B 82 LINK C THR A 2 N MSE A 3 1555 1555 1.33 LINK C MSE A 3 N GLU A 4 1555 1555 1.33 LINK C TRP A 65 N MSE A 66 1555 1555 1.33 LINK C MSE A 66 N VAL A 67 1555 1555 1.33 LINK C THR B 2 N MSE B 3 1555 1555 1.33 LINK C MSE B 3 N GLU B 4 1555 1555 1.34 LINK C TRP B 65 N MSE B 66 1555 1555 1.33 LINK C MSE B 66 N VAL B 67 1555 1555 1.33 CRYST1 43.680 61.077 43.939 90.00 104.72 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 0.022894 0.000000 0.006015 0.00000 SCALE2 0.000000 0.016373 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023531 0.00000