HEADER SIGNALING PROTEIN/GTP BINDING 19-MAR-19 6OB3 TITLE CRYSTAL STRUCTURE OF G13D-KRAS (GMPPNP-BOUND) IN COMPLEX WITH GAP- TITLE 2 RELATED DOMAIN (GRD) OF NEUROFIBROMIN (NF1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTPASE KRAS; COMPND 3 CHAIN: A, C; COMPND 4 SYNONYM: K-RAS 2,KI-RAS,C-K-RAS,C-KI-RAS; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: NEUROFIBROMIN; COMPND 9 CHAIN: B, D; COMPND 10 SYNONYM: NEUROFIBROMATOSIS-RELATED PROTEIN NF-1; COMPND 11 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: KRAS, KRAS2, RASK2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 GENE: NF1; SOURCE 15 EXPRESSION_SYSTEM: UNIDENTIFIED BACULOVIRUS; SOURCE 16 EXPRESSION_SYSTEM_TAXID: 10469 KEYWDS KRAS, RAS, KRAS4B, NF1, GAP, NEUROFIBROMIN, G13D, SIGNALING PROTEIN- KEYWDS 2 GTP BINDING COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.H.TRAN,S.DHARMAIAH,D.K.SIMANSHU REVDAT 4 11-OCT-23 6OB3 1 LINK REVDAT 3 13-NOV-19 6OB3 1 JRNL REVDAT 2 30-OCT-19 6OB3 1 JRNL REVDAT 1 16-OCT-19 6OB3 0 JRNL AUTH D.RABARA,T.H.TRAN,S.DHARMAIAH,R.M.STEPHENS,F.MCCORMICK, JRNL AUTH 2 D.K.SIMANSHU,M.HOLDERFIELD JRNL TITL KRAS G13D SENSITIVITY TO NEUROFIBROMIN-MEDIATED GTP JRNL TITL 2 HYDROLYSIS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 116 22122 2019 JRNL REFN ESSN 1091-6490 JRNL PMID 31611389 JRNL DOI 10.1073/PNAS.1908353116 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.76 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 72678 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.450 REMARK 3 FREE R VALUE TEST SET COUNT : 1779 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 77.8158 - 4.9374 0.99 5741 144 0.1555 0.1722 REMARK 3 2 4.9374 - 3.9190 1.00 5541 139 0.1396 0.1767 REMARK 3 3 3.9190 - 3.4236 1.00 5514 138 0.1710 0.2240 REMARK 3 4 3.4236 - 3.1106 0.99 5438 136 0.1931 0.2133 REMARK 3 5 3.1106 - 2.8876 1.00 5444 137 0.2144 0.2540 REMARK 3 6 2.8876 - 2.7174 1.00 5445 137 0.2148 0.2798 REMARK 3 7 2.7174 - 2.5813 1.00 5450 136 0.2111 0.2851 REMARK 3 8 2.5813 - 2.4689 1.00 5402 137 0.2137 0.2673 REMARK 3 9 2.4689 - 2.3739 1.00 5430 136 0.2279 0.2775 REMARK 3 10 2.3739 - 2.2919 1.00 5386 135 0.2477 0.3209 REMARK 3 11 2.2919 - 2.2203 0.99 5338 135 0.2700 0.3400 REMARK 3 12 2.2203 - 2.1568 1.00 5356 133 0.2966 0.3369 REMARK 3 13 2.1568 - 2.1000 1.00 5414 136 0.3225 0.3926 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 28.180 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.66 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.60 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 16.8414 -12.7081 -19.4087 REMARK 3 T TENSOR REMARK 3 T11: 0.2786 T22: 0.5463 REMARK 3 T33: 0.2802 T12: 0.0204 REMARK 3 T13: -0.0032 T23: 0.0102 REMARK 3 L TENSOR REMARK 3 L11: 0.3915 L22: 0.7205 REMARK 3 L33: 0.3438 L12: 0.2950 REMARK 3 L13: -0.1613 L23: -0.2577 REMARK 3 S TENSOR REMARK 3 S11: -0.0306 S12: 0.1179 S13: 0.0002 REMARK 3 S21: -0.0472 S22: -0.0163 S23: -0.1056 REMARK 3 S31: -0.0219 S32: 0.0125 S33: 0.0529 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 2 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN A AND (RESID 1 THROUGH 30 OR REMARK 3 (RESID 31 AND (NAME N OR NAME CA OR NAME REMARK 3 C OR NAME O OR NAME CB )) OR RESID 32 REMARK 3 THROUGH 48 OR (RESID 49 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB )) REMARK 3 OR RESID 50 THROUGH 93 OR RESID 95 REMARK 3 THROUGH 106 OR (RESID 107 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB )) REMARK 3 OR RESID 108 THROUGH 117 OR RESID 119 REMARK 3 THROUGH 127 OR (RESID 128 AND (NAME N OR REMARK 3 NAME CA OR NAME C OR NAME O OR NAME CB )) REMARK 3 OR RESID 129 THROUGH 164 OR (RESID 165 REMARK 3 AND (NAME N OR NAME CA OR NAME C OR NAME REMARK 3 O OR NAME CB )) OR RESID 166)) REMARK 3 SELECTION : (CHAIN C AND (RESID 1 THROUGH 93 OR RESID REMARK 3 95 THROUGH 117 OR RESID 119 THROUGH 166)) REMARK 3 ATOM PAIRS NUMBER : 1499 REMARK 3 RMSD : NULL REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: (CHAIN B AND (RESID 1219 THROUGH 1268 OR REMARK 3 (RESID 1269 AND (NAME N OR NAME CA OR REMARK 3 NAME C OR NAME O OR NAME CB )) OR RESID REMARK 3 1270 THROUGH 1285 OR RESID 1287 THROUGH REMARK 3 1298 OR (RESID 1299 AND (NAME N OR NAME REMARK 3 CA OR NAME C OR NAME O OR NAME CB )) OR REMARK 3 RESID 1300 THROUGH 1362 OR RESID 1364 REMARK 3 THROUGH 1377 OR (RESID 1378 AND (NAME N REMARK 3 OR NAME CA OR NAME C OR NAME O OR NAME CB REMARK 3 )) OR RESID 1379 THROUGH 1437 OR (RESID REMARK 3 1438 AND (NAME N OR NAME CA OR NAME C OR REMARK 3 NAME O OR NAME CB )) OR RESID 1439 REMARK 3 THROUGH 1463)) REMARK 3 SELECTION : (CHAIN D AND (RESID 1219 THROUGH 1285 OR REMARK 3 RESID 1287 THROUGH 1312 OR (RESID 1313 REMARK 3 THROUGH 1317 AND (NAME N OR NAME CA OR REMARK 3 NAME C OR NAME O OR NAME CB )) OR RESID REMARK 3 1318 THROUGH 1332 OR (RESID 1333 THROUGH REMARK 3 1334 AND (NAME N OR NAME CA OR NAME C OR REMARK 3 NAME O OR NAME CB )) OR RESID 1335 REMARK 3 THROUGH 1344 OR (RESID 1345 AND (NAME N REMARK 3 OR NAME CA OR NAME C OR NAME O OR NAME CB REMARK 3 OR NAME CG OR NAME CD )) OR RESID 1346 REMARK 3 THROUGH 1362 OR RESID 1364 THROUGH 1463)) REMARK 3 ATOM PAIRS NUMBER : 2149 REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BASED ON VARIOUS PARAMETERS, THE REMARK 3 AUTHORS DECIDED TO CUT-OFF THE RESOLUTION TO 2.10 ANG, AND THAT REMARK 3 VALUE WAS USED FOR CALCULATING DATA COLLECTION STATISTICS AND REMARK 3 FOR THE STRUCTURE REFINEMENT REMARK 4 REMARK 4 6OB3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1000240354. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979180 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72838 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 97.169 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.811 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.2600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.89 REMARK 200 R MERGE FOR SHELL (I) : 0.67900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.680 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: 6OB2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MES PH 6.0 AND 25% REMARK 280 PENTAERYTHRITOL PROPOXYLATE (5/4 PO/OH), VAPOR DIFFUSION, REMARK 280 SITTING DROP, 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 40.83850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.76250 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.58450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 77.76250 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.83850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.58450 REMARK 290 SMTRY3 4 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: DIMERIC 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 B 1208 REMARK 465 VAL B 1209 REMARK 465 GLU B 1210 REMARK 465 LEU B 1211 REMARK 465 VAL B 1212 REMARK 465 THR B 1213 REMARK 465 MET B 1214 REMARK 465 MET B 1215 REMARK 465 GLY B 1216 REMARK 465 ASP B 1217 REMARK 465 GLN B 1218 REMARK 465 GLY C 0 REMARK 465 LYS C 167 REMARK 465 GLU C 168 REMARK 465 LYS C 169 REMARK 465 GLY D 1208 REMARK 465 VAL D 1209 REMARK 465 GLU D 1210 REMARK 465 LEU D 1211 REMARK 465 VAL D 1212 REMARK 465 THR D 1213 REMARK 465 MET D 1214 REMARK 465 MET D 1215 REMARK 465 GLY D 1216 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 31 CD OE1 OE2 REMARK 470 ASP B1313 CG OD1 OD2 REMARK 470 TRP B1314 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B1314 CZ3 CH2 REMARK 470 GLN B1315 CG CD OE1 NE2 REMARK 470 HIS B1316 CG ND1 CD2 CE1 NE2 REMARK 470 VAL B1317 CG1 CG2 REMARK 470 GLU B1333 CG CD OE1 OE2 REMARK 470 GLU B1334 CG CD OE1 OE2 REMARK 470 LYS B1345 CE NZ REMARK 470 GLU C 31 CG CD OE1 OE2 REMARK 470 GLU C 107 CG CD OE1 OE2 REMARK 470 LYS C 128 CG CD CE NZ REMARK 470 LYS C 165 CG CD CE NZ REMARK 470 ASP D1217 CG OD1 OD2 REMARK 470 GLN D1218 CG CD OE1 NE2 REMARK 470 ASP D1269 CG OD1 OD2 REMARK 470 LYS D1299 CG CD CE NZ REMARK 470 GLN D1378 CG CD OE1 NE2 REMARK 470 GLU D1438 CG CD OE1 OE2 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 B 1687 O HOH B 1697 2.15 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 ASP A 33 74.04 -157.12 REMARK 500 GLU A 37 119.80 -172.22 REMARK 500 ASP A 108 76.16 -118.75 REMARK 500 LYS A 117 30.67 73.62 REMARK 500 PHE B1392 -65.36 -141.62 REMARK 500 LYS B1436 -75.80 -99.63 REMARK 500 ASP C 33 76.43 -154.20 REMARK 500 LYS C 117 45.73 73.94 REMARK 500 SER C 122 84.10 43.65 REMARK 500 PHE D1392 -61.07 -133.48 REMARK 500 LYS D1436 -71.90 -95.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH D1691 DISTANCE = 6.56 ANGSTROMS 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 A 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 17 OG REMARK 620 2 THR A 35 OG1 80.6 REMARK 620 3 GNP A 201 O1G 170.6 90.1 REMARK 620 4 GNP A 201 O2B 87.2 167.8 102.1 REMARK 620 5 HOH A 328 O 80.7 86.3 97.8 91.3 REMARK 620 6 HOH A 332 O 85.6 92.2 95.9 87.3 166.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG C 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER C 17 OG REMARK 620 2 THR C 35 OG1 86.3 REMARK 620 3 GNP C 201 O1G 174.5 88.7 REMARK 620 4 GNP C 201 O2B 93.1 178.3 91.9 REMARK 620 5 HOH C 306 O 90.5 88.0 91.7 90.4 REMARK 620 6 HOH C 314 O 87.2 88.7 90.3 92.8 176.1 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 GNP A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 1502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES B 1503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES B 1504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES B 1505 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GNP C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES D 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MES D 1502 DBREF 6OB3 A 1 169 UNP P01116 RASK_HUMAN 1 169 DBREF 6OB3 B 1209 1463 UNP P21359 NF1_HUMAN 1209 1463 DBREF 6OB3 C 1 169 UNP P01116 RASK_HUMAN 1 169 DBREF 6OB3 D 1209 1463 UNP P21359 NF1_HUMAN 1209 1463 SEQADV 6OB3 GLY A 0 UNP P01116 EXPRESSION TAG SEQADV 6OB3 ASP A 13 UNP P01116 GLY 13 ENGINEERED MUTATION SEQADV 6OB3 GLY B 1208 UNP P21359 EXPRESSION TAG SEQADV 6OB3 GLY C 0 UNP P01116 EXPRESSION TAG SEQADV 6OB3 ASP C 13 UNP P01116 GLY 13 ENGINEERED MUTATION SEQADV 6OB3 GLY D 1208 UNP P21359 EXPRESSION TAG SEQRES 1 A 170 GLY MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY SEQRES 2 A 170 ASP VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 A 170 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 A 170 SER TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS SEQRES 5 A 170 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SEQRES 6 A 170 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 A 170 PHE LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 A 170 GLU ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 A 170 LYS ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 A 170 LYS CYS ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN SEQRES 11 A 170 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE SEQRES 12 A 170 GLU THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA SEQRES 13 A 170 PHE TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU SEQRES 14 A 170 LYS SEQRES 1 B 256 GLY VAL GLU LEU VAL THR MET MET GLY ASP GLN GLY GLU SEQRES 2 B 256 LEU PRO ILE ALA MET ALA LEU ALA ASN VAL VAL PRO CYS SEQRES 3 B 256 SER GLN TRP ASP GLU LEU ALA ARG VAL LEU VAL THR LEU SEQRES 4 B 256 PHE ASP SER ARG HIS LEU LEU TYR GLN LEU LEU TRP ASN SEQRES 5 B 256 MET PHE SER LYS GLU VAL GLU LEU ALA ASP SER MET GLN SEQRES 6 B 256 THR LEU PHE ARG GLY ASN SER LEU ALA SER LYS ILE MET SEQRES 7 B 256 THR PHE CYS PHE LYS VAL TYR GLY ALA THR TYR LEU GLN SEQRES 8 B 256 LYS LEU LEU ASP PRO LEU LEU ARG ILE VAL ILE THR SER SEQRES 9 B 256 SER ASP TRP GLN HIS VAL SER PHE GLU VAL ASP PRO THR SEQRES 10 B 256 ARG LEU GLU PRO SER GLU SER LEU GLU GLU ASN GLN ARG SEQRES 11 B 256 ASN LEU LEU GLN MET THR GLU LYS PHE PHE HIS ALA ILE SEQRES 12 B 256 ILE SER SER SER SER GLU PHE PRO PRO GLN LEU ARG SER SEQRES 13 B 256 VAL CYS HIS CYS LEU TYR GLN VAL VAL SER GLN ARG PHE SEQRES 14 B 256 PRO GLN ASN SER ILE GLY ALA VAL GLY SER ALA MET PHE SEQRES 15 B 256 LEU ARG PHE ILE ASN PRO ALA ILE VAL SER PRO TYR GLU SEQRES 16 B 256 ALA GLY ILE LEU ASP LYS LYS PRO PRO PRO ARG ILE GLU SEQRES 17 B 256 ARG GLY LEU LYS LEU MET SER LYS ILE LEU GLN SER ILE SEQRES 18 B 256 ALA ASN HIS VAL LEU PHE THR LYS GLU GLU HIS MET ARG SEQRES 19 B 256 PRO PHE ASN ASP PHE VAL LYS SER ASN PHE ASP ALA ALA SEQRES 20 B 256 ARG ARG PHE PHE LEU ASP ILE ALA SER SEQRES 1 C 170 GLY MET THR GLU TYR LYS LEU VAL VAL VAL GLY ALA GLY SEQRES 2 C 170 ASP VAL GLY LYS SER ALA LEU THR ILE GLN LEU ILE GLN SEQRES 3 C 170 ASN HIS PHE VAL ASP GLU TYR ASP PRO THR ILE GLU ASP SEQRES 4 C 170 SER TYR ARG LYS GLN VAL VAL ILE ASP GLY GLU THR CYS SEQRES 5 C 170 LEU LEU ASP ILE LEU ASP THR ALA GLY GLN GLU GLU TYR SEQRES 6 C 170 SER ALA MET ARG ASP GLN TYR MET ARG THR GLY GLU GLY SEQRES 7 C 170 PHE LEU CYS VAL PHE ALA ILE ASN ASN THR LYS SER PHE SEQRES 8 C 170 GLU ASP ILE HIS HIS TYR ARG GLU GLN ILE LYS ARG VAL SEQRES 9 C 170 LYS ASP SER GLU ASP VAL PRO MET VAL LEU VAL GLY ASN SEQRES 10 C 170 LYS CYS ASP LEU PRO SER ARG THR VAL ASP THR LYS GLN SEQRES 11 C 170 ALA GLN ASP LEU ALA ARG SER TYR GLY ILE PRO PHE ILE SEQRES 12 C 170 GLU THR SER ALA LYS THR ARG GLN GLY VAL ASP ASP ALA SEQRES 13 C 170 PHE TYR THR LEU VAL ARG GLU ILE ARG LYS HIS LYS GLU SEQRES 14 C 170 LYS SEQRES 1 D 256 GLY VAL GLU LEU VAL THR MET MET GLY ASP GLN GLY GLU SEQRES 2 D 256 LEU PRO ILE ALA MET ALA LEU ALA ASN VAL VAL PRO CYS SEQRES 3 D 256 SER GLN TRP ASP GLU LEU ALA ARG VAL LEU VAL THR LEU SEQRES 4 D 256 PHE ASP SER ARG HIS LEU LEU TYR GLN LEU LEU TRP ASN SEQRES 5 D 256 MET PHE SER LYS GLU VAL GLU LEU ALA ASP SER MET GLN SEQRES 6 D 256 THR LEU PHE ARG GLY ASN SER LEU ALA SER LYS ILE MET SEQRES 7 D 256 THR PHE CYS PHE LYS VAL TYR GLY ALA THR TYR LEU GLN SEQRES 8 D 256 LYS LEU LEU ASP PRO LEU LEU ARG ILE VAL ILE THR SER SEQRES 9 D 256 SER ASP TRP GLN HIS VAL SER PHE GLU VAL ASP PRO THR SEQRES 10 D 256 ARG LEU GLU PRO SER GLU SER LEU GLU GLU ASN GLN ARG SEQRES 11 D 256 ASN LEU LEU GLN MET THR GLU LYS PHE PHE HIS ALA ILE SEQRES 12 D 256 ILE SER SER SER SER GLU PHE PRO PRO GLN LEU ARG SER SEQRES 13 D 256 VAL CYS HIS CYS LEU TYR GLN VAL VAL SER GLN ARG PHE SEQRES 14 D 256 PRO GLN ASN SER ILE GLY ALA VAL GLY SER ALA MET PHE SEQRES 15 D 256 LEU ARG PHE ILE ASN PRO ALA ILE VAL SER PRO TYR GLU SEQRES 16 D 256 ALA GLY ILE LEU ASP LYS LYS PRO PRO PRO ARG ILE GLU SEQRES 17 D 256 ARG GLY LEU LYS LEU MET SER LYS ILE LEU GLN SER ILE SEQRES 18 D 256 ALA ASN HIS VAL LEU PHE THR LYS GLU GLU HIS MET ARG SEQRES 19 D 256 PRO PHE ASN ASP PHE VAL LYS SER ASN PHE ASP ALA ALA SEQRES 20 D 256 ARG ARG PHE PHE LEU ASP ILE ALA SER HET GNP A 201 32 HET MG A 202 1 HET CL B1501 1 HET CL B1502 1 HET MES B1503 12 HET MES B1504 12 HET MES B1505 12 HET GNP C 201 32 HET MG C 202 1 HET CL C 203 1 HET MES D1501 12 HET MES D1502 12 HETNAM GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID FORMUL 5 GNP 2(C10 H17 N6 O13 P3) FORMUL 6 MG 2(MG 2+) FORMUL 7 CL 3(CL 1-) FORMUL 9 MES 5(C6 H13 N O4 S) FORMUL 17 HOH *313(H2 O) HELIX 1 AA1 GLY A 15 ASN A 26 1 12 HELIX 2 AA2 GLN A 61 ALA A 66 5 6 HELIX 3 AA3 MET A 67 GLY A 75 1 9 HELIX 4 AA4 ASN A 86 ASP A 105 1 20 HELIX 5 AA5 ASP A 126 GLY A 138 1 13 HELIX 6 AA6 GLY A 151 GLU A 168 1 18 HELIX 7 AA7 GLU B 1220 ASN B 1229 1 10 HELIX 8 AA8 VAL B 1230 VAL B 1231 5 2 HELIX 9 AA9 PRO B 1232 SER B 1234 5 3 HELIX 10 AB1 GLN B 1235 ARG B 1250 1 16 HELIX 11 AB2 LEU B 1252 ALA B 1268 1 17 HELIX 12 AB3 SER B 1270 LEU B 1274 5 5 HELIX 13 AB4 SER B 1279 THR B 1310 1 32 HELIX 14 AB5 TRP B 1314 SER B 1318 5 5 HELIX 15 AB6 ASP B 1322 LEU B 1326 5 5 HELIX 16 AB7 SER B 1331 SER B 1352 1 22 HELIX 17 AB8 SER B 1353 PHE B 1357 5 5 HELIX 18 AB9 PRO B 1358 GLN B 1374 1 17 HELIX 19 AC1 ARG B 1375 GLN B 1378 5 4 HELIX 20 AC2 ASN B 1379 ARG B 1391 1 13 HELIX 21 AC3 PHE B 1392 SER B 1399 1 8 HELIX 22 AC4 PRO B 1411 HIS B 1431 1 21 HELIX 23 AC5 GLU B 1437 PRO B 1442 5 6 HELIX 24 AC6 PHE B 1443 SER B 1463 1 21 HELIX 25 AC7 GLY C 15 ASN C 26 1 12 HELIX 26 AC8 GLN C 61 ALA C 66 5 6 HELIX 27 AC9 MET C 67 GLY C 75 1 9 HELIX 28 AD1 ASN C 86 LYS C 104 1 19 HELIX 29 AD2 ASP C 126 GLY C 138 1 13 HELIX 30 AD3 GLY C 151 HIS C 166 1 16 HELIX 31 AD4 GLY D 1219 ASN D 1229 1 11 HELIX 32 AD5 VAL D 1230 VAL D 1231 5 2 HELIX 33 AD6 PRO D 1232 SER D 1234 5 3 HELIX 34 AD7 GLN D 1235 ARG D 1250 1 16 HELIX 35 AD8 LEU D 1252 ALA D 1268 1 17 HELIX 36 AD9 PHE D 1275 ASN D 1278 5 4 HELIX 37 AE1 SER D 1279 SER D 1311 1 33 HELIX 38 AE2 SER D 1312 GLN D 1315 5 4 HELIX 39 AE3 ASP D 1322 LEU D 1326 5 5 HELIX 40 AE4 SER D 1331 SER D 1352 1 22 HELIX 41 AE5 SER D 1353 PHE D 1357 5 5 HELIX 42 AE6 PRO D 1358 PHE D 1376 1 19 HELIX 43 AE7 ASN D 1379 PHE D 1392 1 14 HELIX 44 AE8 PHE D 1392 SER D 1399 1 8 HELIX 45 AE9 PRO D 1411 HIS D 1431 1 21 HELIX 46 AF1 GLU D 1437 PRO D 1442 5 6 HELIX 47 AF2 PHE D 1443 SER D 1449 1 7 HELIX 48 AF3 ASN D 1450 SER D 1463 1 14 SHEET 1 AA1 6 GLU A 37 ILE A 46 0 SHEET 2 AA1 6 GLU A 49 THR A 58 -1 O LEU A 53 N LYS A 42 SHEET 3 AA1 6 THR A 2 VAL A 9 1 N TYR A 4 O ASP A 54 SHEET 4 AA1 6 GLY A 77 ALA A 83 1 O VAL A 81 N VAL A 9 SHEET 5 AA1 6 MET A 111 ASN A 116 1 O ASN A 116 N PHE A 82 SHEET 6 AA1 6 PHE A 141 GLU A 143 1 O ILE A 142 N LEU A 113 SHEET 1 AA2 6 GLU C 37 ILE C 46 0 SHEET 2 AA2 6 GLU C 49 THR C 58 -1 O CYS C 51 N VAL C 44 SHEET 3 AA2 6 THR C 2 GLY C 10 1 N THR C 2 O LEU C 52 SHEET 4 AA2 6 GLY C 77 ALA C 83 1 O LEU C 79 N VAL C 9 SHEET 5 AA2 6 MET C 111 ASN C 116 1 O VAL C 114 N CYS C 80 SHEET 6 AA2 6 PHE C 141 GLU C 143 1 O ILE C 142 N LEU C 113 LINK OG SER A 17 MG MG A 202 1555 1555 2.21 LINK OG1 THR A 35 MG MG A 202 1555 1555 2.15 LINK O1G GNP A 201 MG MG A 202 1555 1555 1.95 LINK O2B GNP A 201 MG MG A 202 1555 1555 2.03 LINK MG MG A 202 O HOH A 328 1555 1555 2.04 LINK MG MG A 202 O HOH A 332 1555 1555 2.07 LINK OG SER C 17 MG MG C 202 1555 1555 2.03 LINK OG1 THR C 35 MG MG C 202 1555 1555 2.11 LINK O1G GNP C 201 MG MG C 202 1555 1555 2.01 LINK O2B GNP C 201 MG MG C 202 1555 1555 2.07 LINK MG MG C 202 O HOH C 306 1555 1555 2.19 LINK MG MG C 202 O HOH C 314 1555 1555 2.07 SITE 1 AC1 28 GLY A 12 ASP A 13 VAL A 14 GLY A 15 SITE 2 AC1 28 LYS A 16 SER A 17 ALA A 18 PHE A 28 SITE 3 AC1 28 VAL A 29 ASP A 30 PRO A 34 THR A 35 SITE 4 AC1 28 GLY A 60 GLN A 61 ASN A 116 LYS A 117 SITE 5 AC1 28 ASP A 119 SER A 145 ALA A 146 LYS A 147 SITE 6 AC1 28 MG A 202 HOH A 323 HOH A 328 HOH A 329 SITE 7 AC1 28 HOH A 332 HOH A 346 HOH A 364 ARG B1276 SITE 1 AC2 5 SER A 17 THR A 35 GNP A 201 HOH A 328 SITE 2 AC2 5 HOH A 332 SITE 1 AC3 4 PHE B1376 PRO B1377 GLN B1378 ASN B1379 SITE 1 AC4 1 HOH B1691 SITE 1 AC5 2 ASP B1248 HOH B1654 SITE 1 AC6 2 TRP B1258 GLU D1333 SITE 1 AC7 5 GLN B1336 ARG B1337 LEU B1340 HOH B1604 SITE 2 AC7 5 LYS D1408 SITE 1 AC8 28 GLY C 12 ASP C 13 VAL C 14 GLY C 15 SITE 2 AC8 28 LYS C 16 SER C 17 ALA C 18 PHE C 28 SITE 3 AC8 28 VAL C 29 ASP C 30 PRO C 34 THR C 35 SITE 4 AC8 28 GLY C 60 ASN C 116 LYS C 117 ASP C 119 SITE 5 AC8 28 LEU C 120 SER C 145 ALA C 146 LYS C 147 SITE 6 AC8 28 MG C 202 HOH C 306 HOH C 310 HOH C 311 SITE 7 AC8 28 HOH C 313 HOH C 314 HOH C 315 HOH C 327 SITE 1 AC9 5 SER C 17 THR C 35 GNP C 201 HOH C 306 SITE 2 AC9 5 HOH C 314 SITE 1 AD1 1 ARG C 68 SITE 1 AD2 7 GLN A 22 PHE A 28 LYS A 147 THR A 148 SITE 2 AD2 7 ASP D1248 HIS D1251 HOH D1639 SITE 1 AD3 4 LEU D1340 PRO D1442 ASP D1445 HOH D1609 CRYST1 81.677 97.169 155.525 90.00 90.00 90.00 P 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 0.012243 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010291 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006430 0.00000