HEADER SIGNALING PROTEIN 15-JUN-16 5KHO TITLE RASIP1 RA DOMAIN IN COMPLEX WITH RAP1B COMPND MOL_ID: 1; COMPND 2 MOLECULE: RAS-INTERACTING PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: RAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: RAS-RELATED PROTEIN RAP-1B; COMPND 8 CHAIN: C, D; COMPND 9 SYNONYM: GTP-BINDING PROTEIN SMG P21B; COMPND 10 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: RASIP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: RAP1B, OK/SW-CL.11; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS RASIP1, RAS-ASSOCIATION DOMAIN, RAP1B, COMPLEX, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.R.GINGRAS REVDAT 4 27-SEP-23 5KHO 1 LINK REVDAT 3 04-OCT-17 5KHO 1 REMARK REVDAT 2 15-FEB-17 5KHO 1 JRNL REVDAT 1 19-OCT-16 5KHO 0 JRNL AUTH A.R.GINGRAS,W.PUZON-MCLAUGHLIN,A.A.BOBKOV,M.H.GINSBERG JRNL TITL STRUCTURAL BASIS OF DIMERIC RASIP1 RA DOMAIN RECOGNITION OF JRNL TITL 2 THE RAS SUBFAMILY OF GTP-BINDING PROTEINS. JRNL REF STRUCTURE V. 24 2152 2016 JRNL REFN ISSN 1878-4186 JRNL PMID 27839947 JRNL DOI 10.1016/J.STR.2016.10.001 REMARK 2 REMARK 2 RESOLUTION. 2.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0151 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.24 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 15232 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 802 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.78 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1030 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.4260 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.4540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4046 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 14 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 89.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 91.41 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.32000 REMARK 3 B22 (A**2) : -3.62000 REMARK 3 B33 (A**2) : 3.95000 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): 0.422 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.392 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 20.821 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4176 ; 0.009 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5670 ; 1.397 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 532 ; 6.163 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;39.579 ;22.905 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 643 ;19.625 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;20.006 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 650 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3134 ; 0.004 ; 0.020 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): 2154 ; 4.998 ; 9.597 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2678 ; 8.087 ;14.373 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2019 ; 5.202 ; 9.669 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 : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 5KHO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979460 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN-COOLED DOUBLE REMARK 200 CRYSTAL SI(111) REMARK 200 OPTICS : MIRROR: RH COATED REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16034 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.780 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 (%) : 99.5 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 8.30 REMARK 200 R MERGE FOR SHELL (I) : 1.43900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.450 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: 4HDQ CHAIN B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16% PEG 8K, 200MM CALCIUM ACETATE, AND REMARK 280 100MM MES PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 50.77000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 77.38000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 50.77000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 77.38000 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 130 REMARK 465 ALA A 131 REMARK 465 MET A 132 REMARK 465 GLY A 133 REMARK 465 GLU A 134 REMARK 465 PRO A 135 REMARK 465 PRO A 136 REMARK 465 LEU A 137 REMARK 465 ALA A 138 REMARK 465 THR A 139 REMARK 465 ARG A 140 REMARK 465 ALA A 141 REMARK 465 THR A 142 REMARK 465 ALA A 186 REMARK 465 GLY A 187 REMARK 465 SER A 188 REMARK 465 PRO A 189 REMARK 465 GLY A 190 REMARK 465 GLY A 191 REMARK 465 GLY A 192 REMARK 465 PRO A 193 REMARK 465 GLY A 194 REMARK 465 GLU A 195 REMARK 465 SER A 196 REMARK 465 ALA A 212 REMARK 465 ALA A 213 REMARK 465 ALA A 214 REMARK 465 GLY A 215 REMARK 465 VAL A 216 REMARK 465 GLY A 217 REMARK 465 SER A 218 REMARK 465 GLY A 219 REMARK 465 GLU A 220 REMARK 465 GLU A 266 REMARK 465 ALA A 267 REMARK 465 PHE A 268 REMARK 465 GLY A 269 REMARK 465 ALA A 270 REMARK 465 ALA A 271 REMARK 465 ASP A 272 REMARK 465 SER A 273 REMARK 465 GLU A 274 REMARK 465 GLY A 275 REMARK 465 THR A 276 REMARK 465 GLY A 277 REMARK 465 ALA A 278 REMARK 465 PRO A 279 REMARK 465 SER A 280 REMARK 465 TRP A 281 REMARK 465 ARG A 282 REMARK 465 PRO A 283 REMARK 465 GLN A 284 REMARK 465 LYS A 285 REMARK 465 GLY B 130 REMARK 465 ALA B 131 REMARK 465 MET B 132 REMARK 465 GLY B 133 REMARK 465 GLU B 134 REMARK 465 PRO B 135 REMARK 465 PRO B 136 REMARK 465 LEU B 137 REMARK 465 ALA B 138 REMARK 465 THR B 139 REMARK 465 ARG B 140 REMARK 465 ALA B 141 REMARK 465 THR B 142 REMARK 465 ALA B 186 REMARK 465 GLY B 187 REMARK 465 SER B 188 REMARK 465 PRO B 189 REMARK 465 GLY B 190 REMARK 465 GLY B 191 REMARK 465 GLY B 192 REMARK 465 PRO B 193 REMARK 465 GLY B 194 REMARK 465 GLU B 195 REMARK 465 ALA B 212 REMARK 465 ALA B 213 REMARK 465 ALA B 214 REMARK 465 GLY B 215 REMARK 465 VAL B 216 REMARK 465 GLY B 217 REMARK 465 SER B 218 REMARK 465 GLY B 219 REMARK 465 GLU B 220 REMARK 465 PHE B 268 REMARK 465 GLY B 269 REMARK 465 ALA B 270 REMARK 465 ALA B 271 REMARK 465 ASP B 272 REMARK 465 SER B 273 REMARK 465 GLU B 274 REMARK 465 GLY B 275 REMARK 465 THR B 276 REMARK 465 GLY B 277 REMARK 465 ALA B 278 REMARK 465 PRO B 279 REMARK 465 SER B 280 REMARK 465 TRP B 281 REMARK 465 ARG B 282 REMARK 465 PRO B 283 REMARK 465 GLN B 284 REMARK 465 LYS B 285 REMARK 465 GLU C 62 REMARK 465 GLN C 63 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 ARG A 169 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 174 CG CD OE1 OE2 REMARK 470 GLU A 178 CG CD OE1 OE2 REMARK 470 CYS A 198 SG REMARK 470 PRO A 211 CG CD REMARK 470 ARG A 222 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 224 CG CD OE1 OE2 REMARK 470 GLU A 240 CG CD OE1 OE2 REMARK 470 GLU A 259 CG CD OE1 OE2 REMARK 470 GLN A 265 CG CD OE1 NE2 REMARK 470 SER B 196 OG REMARK 470 SER B 197 OG REMARK 470 CYS B 198 SG REMARK 470 ARG B 222 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 224 CG CD OE1 OE2 REMARK 470 ARG B 234 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 240 CG CD OE1 OE2 REMARK 470 GLU B 266 CG CD OE1 OE2 REMARK 470 GLU C 3 CG CD OE1 OE2 REMARK 470 LYS C 5 CG CD CE NZ REMARK 470 LYS C 31 CG CD CE NZ REMARK 470 GLU C 45 CG CD OE1 OE2 REMARK 470 THR C 61 OG1 CG2 REMARK 470 THR C 65 OG1 CG2 REMARK 470 MET C 67 CG SD CE REMARK 470 LEU C 70 CG CD1 CD2 REMARK 470 LYS C 73 CG CD CE NZ REMARK 470 GLU C 98 CG CD OE1 OE2 REMARK 470 ARG C 102 CG CD NE CZ NH1 NH2 REMARK 470 ASP C 107 CG OD1 OD2 REMARK 470 GLU C 121 CG CD OE1 OE2 REMARK 470 ASP C 122 CG OD1 OD2 REMARK 470 LYS C 128 CG CD CE NZ REMARK 470 GLU C 129 CG CD OE1 OE2 REMARK 470 ASN C 133 CG OD1 ND2 REMARK 470 ARG C 136 CG CD NE CZ NH1 NH2 REMARK 470 GLU D 3 CG CD OE1 OE2 REMARK 470 LYS D 5 CG CD CE NZ REMARK 470 GLU D 30 CG CD OE1 OE2 REMARK 470 LYS D 31 CG CD CE NZ REMARK 470 LYS D 42 CG CD CE NZ REMARK 470 GLU D 62 CG CD OE1 OE2 REMARK 470 GLN D 63 CG CD OE1 NE2 REMARK 470 PHE D 64 CG CD1 CD2 CE1 CE2 CZ REMARK 470 THR D 65 OG1 CG2 REMARK 470 MET D 67 CG SD CE REMARK 470 ASP D 69 CG OD1 OD2 REMARK 470 LYS D 73 CG CD CE NZ REMARK 470 ASN D 91 CG OD1 ND2 REMARK 470 GLN D 94 CG CD OE1 NE2 REMARK 470 GLU D 98 CG CD OE1 OE2 REMARK 470 GLN D 99 CG CD OE1 NE2 REMARK 470 LYS D 104 CG CD CE NZ REMARK 470 ASP D 107 CG OD1 OD2 REMARK 470 ASP D 108 CG OD1 OD2 REMARK 470 GLU D 121 CG CD OE1 OE2 REMARK 470 GLU D 129 CG CD OE1 OE2 REMARK 470 GLN D 132 CG CD OE1 NE2 REMARK 470 ASN D 133 CG OD1 ND2 REMARK 470 ARG D 136 CG CD NE CZ NH1 NH2 REMARK 470 ASN D 140 CG OD1 ND2 REMARK 470 LYS D 149 CG CD CE NZ REMARK 470 GLU D 156 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O ARG C 167 O ARG C 167 2455 2.01 REMARK 500 REMARK 500 REMARK: NULL 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 A 211 C - N - CA ANGL. DEV. = 10.4 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 ALA A 153 80.44 -64.70 REMARK 500 LEU A 155 -31.02 -138.97 REMARK 500 SER A 157 -122.18 54.45 REMARK 500 ASN A 160 -64.72 -120.10 REMARK 500 PRO B 145 66.02 -67.86 REMARK 500 ALA B 153 87.16 -57.28 REMARK 500 LEU B 155 -49.45 -134.53 REMARK 500 SER B 197 59.63 -101.96 REMARK 500 GLU C 37 102.27 -173.05 REMARK 500 ASP C 47 78.20 50.04 REMARK 500 ALA C 48 19.68 52.45 REMARK 500 LYS C 117 24.05 87.21 REMARK 500 GLU D 30 -93.75 -82.28 REMARK 500 PRO D 34 113.18 -34.67 REMARK 500 GLU D 37 118.91 -172.78 REMARK 500 VAL D 46 -76.28 -112.11 REMARK 500 ALA D 48 -9.46 62.13 REMARK 500 THR D 61 87.40 -58.64 REMARK 500 THR D 106 145.74 -172.20 REMARK 500 ASP D 108 50.85 -91.19 REMARK 500 ASN D 153 7.77 57.20 REMARK 500 ASN D 166 97.13 -64.43 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 MG C 200 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER C 17 OG REMARK 620 2 THR C 35 OG1 67.3 REMARK 620 3 GNP C 201 O2B 86.3 147.4 REMARK 620 4 GNP C 201 O2G 152.7 86.6 114.9 REMARK 620 5 HOH C 302 O 72.8 76.1 78.0 94.1 REMARK 620 6 HOH C 303 O 75.3 86.3 105.9 112.1 147.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG D 200 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER D 17 OG REMARK 620 2 THR D 35 OG1 88.7 REMARK 620 3 GNP D 201 O1G 167.2 79.1 REMARK 620 4 GNP D 201 O1B 83.0 154.8 106.6 REMARK 620 5 HOH D 301 O 85.9 80.1 88.4 75.6 REMARK 620 6 HOH D 302 O 106.9 103.2 79.8 101.9 166.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG D 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP D 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KHQ RELATED DB: PDB DBREF 5KHO A 134 285 UNP Q5U651 RAIN_HUMAN 134 285 DBREF 5KHO B 134 285 UNP Q5U651 RAIN_HUMAN 134 285 DBREF 5KHO C 1 167 UNP P61224 RAP1B_HUMAN 1 167 DBREF 5KHO D 1 167 UNP P61224 RAP1B_HUMAN 1 167 SEQADV 5KHO GLY A 130 UNP Q5U651 EXPRESSION TAG SEQADV 5KHO ALA A 131 UNP Q5U651 EXPRESSION TAG SEQADV 5KHO MET A 132 UNP Q5U651 EXPRESSION TAG SEQADV 5KHO GLY A 133 UNP Q5U651 EXPRESSION TAG SEQADV 5KHO GLY B 130 UNP Q5U651 EXPRESSION TAG SEQADV 5KHO ALA B 131 UNP Q5U651 EXPRESSION TAG SEQADV 5KHO MET B 132 UNP Q5U651 EXPRESSION TAG SEQADV 5KHO GLY B 133 UNP Q5U651 EXPRESSION TAG SEQRES 1 A 156 GLY ALA MET GLY GLU PRO PRO LEU ALA THR ARG ALA THR SEQRES 2 A 156 ALA PRO PRO GLY VAL LEU LYS ILE PHE GLY ALA GLY LEU SEQRES 3 A 156 ALA SER GLY ALA ASN TYR LYS SER VAL LEU ALA THR ALA SEQRES 4 A 156 ARG SER THR ALA ARG GLU LEU VAL ALA GLU ALA LEU GLU SEQRES 5 A 156 ARG TYR GLY LEU ALA GLY SER PRO GLY GLY GLY PRO GLY SEQRES 6 A 156 GLU SER SER CYS VAL ASP ALA PHE ALA LEU CYS ASP ALA SEQRES 7 A 156 LEU GLY ARG PRO ALA ALA ALA GLY VAL GLY SER GLY GLU SEQRES 8 A 156 TRP ARG ALA GLU HIS LEU ARG VAL LEU GLY ASP SER GLU SEQRES 9 A 156 ARG PRO LEU LEU VAL GLN GLU LEU TRP ARG ALA ARG PRO SEQRES 10 A 156 GLY TRP ALA ARG ARG PHE GLU LEU ARG GLY ARG GLU GLU SEQRES 11 A 156 ALA ARG ARG LEU GLU GLN GLU ALA PHE GLY ALA ALA ASP SEQRES 12 A 156 SER GLU GLY THR GLY ALA PRO SER TRP ARG PRO GLN LYS SEQRES 1 B 156 GLY ALA MET GLY GLU PRO PRO LEU ALA THR ARG ALA THR SEQRES 2 B 156 ALA PRO PRO GLY VAL LEU LYS ILE PHE GLY ALA GLY LEU SEQRES 3 B 156 ALA SER GLY ALA ASN TYR LYS SER VAL LEU ALA THR ALA SEQRES 4 B 156 ARG SER THR ALA ARG GLU LEU VAL ALA GLU ALA LEU GLU SEQRES 5 B 156 ARG TYR GLY LEU ALA GLY SER PRO GLY GLY GLY PRO GLY SEQRES 6 B 156 GLU SER SER CYS VAL ASP ALA PHE ALA LEU CYS ASP ALA SEQRES 7 B 156 LEU GLY ARG PRO ALA ALA ALA GLY VAL GLY SER GLY GLU SEQRES 8 B 156 TRP ARG ALA GLU HIS LEU ARG VAL LEU GLY ASP SER GLU SEQRES 9 B 156 ARG PRO LEU LEU VAL GLN GLU LEU TRP ARG ALA ARG PRO SEQRES 10 B 156 GLY TRP ALA ARG ARG PHE GLU LEU ARG GLY ARG GLU GLU SEQRES 11 B 156 ALA ARG ARG LEU GLU GLN GLU ALA PHE GLY ALA ALA ASP SEQRES 12 B 156 SER GLU GLY THR GLY ALA PRO SER TRP ARG PRO GLN LYS SEQRES 1 C 167 MET ARG GLU TYR LYS LEU VAL VAL LEU GLY SER GLY GLY SEQRES 2 C 167 VAL GLY LYS SER ALA LEU THR VAL GLN PHE VAL GLN GLY SEQRES 3 C 167 ILE PHE VAL GLU LYS TYR ASP PRO THR ILE GLU ASP SER SEQRES 4 C 167 TYR ARG LYS GLN VAL GLU VAL ASP ALA GLN GLN CYS MET SEQRES 5 C 167 LEU GLU ILE LEU ASP THR ALA GLY THR GLU GLN PHE THR SEQRES 6 C 167 ALA MET ARG ASP LEU TYR MET LYS ASN GLY GLN GLY PHE SEQRES 7 C 167 ALA LEU VAL TYR SER ILE THR ALA GLN SER THR PHE ASN SEQRES 8 C 167 ASP LEU GLN ASP LEU ARG GLU GLN ILE LEU ARG VAL LYS SEQRES 9 C 167 ASP THR ASP ASP VAL PRO MET ILE LEU VAL GLY ASN LYS SEQRES 10 C 167 CYS ASP LEU GLU ASP GLU ARG VAL VAL GLY LYS GLU GLN SEQRES 11 C 167 GLY GLN ASN LEU ALA ARG GLN TRP ASN ASN CYS ALA PHE SEQRES 12 C 167 LEU GLU SER SER ALA LYS SER LYS ILE ASN VAL ASN GLU SEQRES 13 C 167 ILE PHE TYR ASP LEU VAL ARG GLN ILE ASN ARG SEQRES 1 D 167 MET ARG GLU TYR LYS LEU VAL VAL LEU GLY SER GLY GLY SEQRES 2 D 167 VAL GLY LYS SER ALA LEU THR VAL GLN PHE VAL GLN GLY SEQRES 3 D 167 ILE PHE VAL GLU LYS TYR ASP PRO THR ILE GLU ASP SER SEQRES 4 D 167 TYR ARG LYS GLN VAL GLU VAL ASP ALA GLN GLN CYS MET SEQRES 5 D 167 LEU GLU ILE LEU ASP THR ALA GLY THR GLU GLN PHE THR SEQRES 6 D 167 ALA MET ARG ASP LEU TYR MET LYS ASN GLY GLN GLY PHE SEQRES 7 D 167 ALA LEU VAL TYR SER ILE THR ALA GLN SER THR PHE ASN SEQRES 8 D 167 ASP LEU GLN ASP LEU ARG GLU GLN ILE LEU ARG VAL LYS SEQRES 9 D 167 ASP THR ASP ASP VAL PRO MET ILE LEU VAL GLY ASN LYS SEQRES 10 D 167 CYS ASP LEU GLU ASP GLU ARG VAL VAL GLY LYS GLU GLN SEQRES 11 D 167 GLY GLN ASN LEU ALA ARG GLN TRP ASN ASN CYS ALA PHE SEQRES 12 D 167 LEU GLU SER SER ALA LYS SER LYS ILE ASN VAL ASN GLU SEQRES 13 D 167 ILE PHE TYR ASP LEU VAL ARG GLN ILE ASN ARG HET GOL A 301 6 HET MG C 200 1 HET GNP C 201 32 HET MG D 200 1 HET GNP D 201 32 HETNAM GOL GLYCEROL HETNAM MG MAGNESIUM ION HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL C3 H8 O3 FORMUL 6 MG 2(MG 2+) FORMUL 7 GNP 2(C10 H17 N6 O13 P3) FORMUL 10 HOH *14(H2 O) HELIX 1 AA1 THR A 171 GLU A 181 1 11 HELIX 2 AA2 CYS A 198 ASP A 200 5 3 HELIX 3 AA3 ARG A 234 LEU A 241 1 8 HELIX 4 AA4 ARG A 257 GLN A 265 1 9 HELIX 5 AA5 THR B 171 GLY B 184 1 14 HELIX 6 AA6 SER B 197 ASP B 200 5 4 HELIX 7 AA7 ARG B 234 LEU B 241 1 8 HELIX 8 AA8 ARG B 257 GLU B 266 1 10 HELIX 9 AA9 GLY C 15 GLN C 25 1 11 HELIX 10 AB1 THR C 65 GLY C 75 1 11 HELIX 11 AB2 ALA C 86 ASP C 92 1 7 HELIX 12 AB3 ASP C 92 ASP C 105 1 14 HELIX 13 AB4 LEU C 120 ARG C 124 5 5 HELIX 14 AB5 GLY C 127 TRP C 138 1 12 HELIX 15 AB6 ASN C 153 ASN C 166 1 14 HELIX 16 AB7 GLY D 15 GLY D 26 1 12 HELIX 17 AB8 MET D 67 GLY D 75 1 9 HELIX 18 AB9 ALA D 86 ASP D 92 1 7 HELIX 19 AC1 ASP D 92 LYS D 104 1 13 HELIX 20 AC2 LEU D 120 ARG D 124 5 5 HELIX 21 AC3 GLY D 127 TRP D 138 1 12 HELIX 22 AC4 ASN D 153 ASN D 166 1 14 SHEET 1 AA111 HIS A 225 VAL A 228 0 SHEET 2 AA111 PHE A 202 GLY A 209 -1 N ASP A 206 O ARG A 227 SHEET 3 AA111 ALA A 249 GLY A 256 -1 O ARG A 255 N ALA A 203 SHEET 4 AA111 GLY A 146 GLY A 152 1 N PHE A 151 O LEU A 254 SHEET 5 AA111 ALA A 159 ALA A 166 -1 O VAL A 164 N LEU A 148 SHEET 6 AA111 ASP C 38 GLU C 45 -1 O SER C 39 N TYR A 161 SHEET 7 AA111 GLN C 50 ASP C 57 -1 O LEU C 53 N LYS C 42 SHEET 8 AA111 ARG C 2 LEU C 9 1 N LEU C 6 O GLU C 54 SHEET 9 AA111 GLY C 77 SER C 83 1 O ALA C 79 N LEU C 9 SHEET 10 AA111 MET C 111 ASN C 116 1 O VAL C 114 N LEU C 80 SHEET 11 AA111 ALA C 142 SER C 146 1 O SER C 146 N GLY C 115 SHEET 1 AA2 2 TRP A 242 ALA A 244 0 SHEET 2 AA2 2 TRP B 242 ALA B 244 -1 O ARG B 243 N ARG A 243 SHEET 1 AA311 HIS B 225 VAL B 228 0 SHEET 2 AA311 PHE B 202 GLY B 209 -1 N ASP B 206 O ARG B 227 SHEET 3 AA311 ALA B 249 GLY B 256 -1 O ARG B 255 N ALA B 203 SHEET 4 AA311 VAL B 147 PHE B 151 1 N PHE B 151 O PHE B 252 SHEET 5 AA311 ALA B 159 LEU B 165 -1 O VAL B 164 N LEU B 148 SHEET 6 AA311 ASP D 38 GLU D 45 -1 O SER D 39 N TYR B 161 SHEET 7 AA311 GLN D 50 ASP D 57 -1 O CYS D 51 N VAL D 44 SHEET 8 AA311 GLU D 3 GLY D 10 1 N LEU D 6 O GLU D 54 SHEET 9 AA311 GLY D 77 SER D 83 1 O VAL D 81 N LEU D 9 SHEET 10 AA311 MET D 111 ASN D 116 1 O VAL D 114 N LEU D 80 SHEET 11 AA311 ALA D 142 GLU D 145 1 O ALA D 142 N LEU D 113 LINK OG SER C 17 MG MG C 200 1555 1555 2.50 LINK OG1 THR C 35 MG MG C 200 1555 1555 2.25 LINK MG MG C 200 O2B GNP C 201 1555 1555 1.92 LINK MG MG C 200 O2G GNP C 201 1555 1555 1.85 LINK MG MG C 200 O HOH C 302 1555 1555 2.18 LINK MG MG C 200 O HOH C 303 1555 1555 2.05 LINK OG SER D 17 MG MG D 200 1555 1555 2.13 LINK OG1 THR D 35 MG MG D 200 1555 1555 2.22 LINK MG MG D 200 O1G GNP D 201 1555 1555 2.08 LINK MG MG D 200 O1B GNP D 201 1555 1555 2.07 LINK MG MG D 200 O HOH D 301 1555 1555 1.98 LINK MG MG D 200 O HOH D 302 1555 1555 1.93 SITE 1 AC1 8 ASP A 206 ARG A 227 VAL A 238 TRP A 242 SITE 2 AC1 8 ARG A 250 ASP B 206 ARG B 227 TRP B 242 SITE 1 AC2 5 SER C 17 THR C 35 GNP C 201 HOH C 302 SITE 2 AC2 5 HOH C 303 SITE 1 AC3 24 GLU B 258 GLY C 13 VAL C 14 GLY C 15 SITE 2 AC3 24 LYS C 16 SER C 17 ALA C 18 PHE C 28 SITE 3 AC3 24 VAL C 29 GLU C 30 TYR C 32 PRO C 34 SITE 4 AC3 24 THR C 35 GLY C 60 ASN C 116 LYS C 117 SITE 5 AC3 24 ASP C 119 LEU C 120 SER C 147 ALA C 148 SITE 6 AC3 24 LYS C 149 MG C 200 HOH C 302 HOH C 303 SITE 1 AC4 5 SER D 17 THR D 35 GNP D 201 HOH D 301 SITE 2 AC4 5 HOH D 302 SITE 1 AC5 21 GLY D 13 VAL D 14 GLY D 15 LYS D 16 SITE 2 AC5 21 SER D 17 ALA D 18 PHE D 28 VAL D 29 SITE 3 AC5 21 GLU D 30 TYR D 32 THR D 35 GLY D 60 SITE 4 AC5 21 ASN D 116 LYS D 117 ASP D 119 LEU D 120 SITE 5 AC5 21 SER D 147 ALA D 148 MG D 200 HOH D 301 SITE 6 AC5 21 HOH D 302 CRYST1 101.540 154.760 38.800 90.00 90.00 90.00 P 21 21 2 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 0.009848 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006462 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025773 0.00000