HEADER TRANSFERASE 10-MAY-17 5VR3 TITLE CRYSTAL STRUCTURE OF THE BRS DOMAIN OF BRAF COMPND MOL_ID: 1; COMPND 2 MOLECULE: BRAF; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 38-116; COMPND 5 EC: 2.7.11.1; COMPND 6 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: BRAF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX 2T KEYWDS BRAF, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR N.THEVAKUMARAN,P.MAISONNEUVE,I.KURINOV,H.LAVOIE,S.A.MARULLO,M.SAHMI, AUTHOR 2 T.JIN,M.THERRIEN,F.SICHERI REVDAT 4 13-MAR-24 5VR3 1 REMARK REVDAT 3 07-MAR-18 5VR3 1 JRNL REVDAT 2 28-FEB-18 5VR3 1 JRNL REVDAT 1 14-FEB-18 5VR3 0 JRNL AUTH H.LAVOIE,M.SAHMI,P.MAISONNEUVE,S.A.MARULLO,N.THEVAKUMARAN, JRNL AUTH 2 T.JIN,I.KURINOV,F.SICHERI,M.THERRIEN JRNL TITL MEK DRIVES BRAF ACTIVATION THROUGH ALLOSTERIC CONTROL OF KSR JRNL TITL 2 PROTEINS. JRNL REF NATURE V. 554 549 2018 JRNL REFN ESSN 1476-4687 JRNL PMID 29433126 JRNL DOI 10.1038/NATURE25478 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2155: ???) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.690 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.1 REMARK 3 NUMBER OF REFLECTIONS : 10045 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 492 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 35.9999 - 3.3353 1.00 2634 150 0.1874 0.1986 REMARK 3 2 3.3353 - 2.6476 1.00 2640 126 0.2419 0.2649 REMARK 3 3 2.6476 - 2.3130 0.97 2537 143 0.2683 0.3323 REMARK 3 4 2.3130 - 2.1015 0.65 1742 73 0.2617 0.3203 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.550 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 504 REMARK 3 ANGLE : 0.800 682 REMARK 3 CHIRALITY : 0.044 76 REMARK 3 PLANARITY : 0.004 87 REMARK 3 DIHEDRAL : 19.147 311 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 41 THROUGH 67 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.8142 18.2696 25.2149 REMARK 3 T TENSOR REMARK 3 T11: 0.3757 T22: 0.7816 REMARK 3 T33: 0.4035 T12: 0.0358 REMARK 3 T13: 0.0201 T23: -0.0909 REMARK 3 L TENSOR REMARK 3 L11: 6.7258 L22: 6.6366 REMARK 3 L33: 2.8447 L12: 0.7590 REMARK 3 L13: -1.2849 L23: -1.7336 REMARK 3 S TENSOR REMARK 3 S11: -0.2617 S12: -0.5871 S13: 0.4722 REMARK 3 S21: 0.2329 S22: -0.3308 S23: 0.2875 REMARK 3 S31: -1.3846 S32: 0.0638 S33: 0.4464 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 68 THROUGH 75 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.2518 14.9888 0.4258 REMARK 3 T TENSOR REMARK 3 T11: 1.5719 T22: 1.2934 REMARK 3 T33: 0.7442 T12: -0.3976 REMARK 3 T13: -0.0263 T23: -0.0239 REMARK 3 L TENSOR REMARK 3 L11: 5.4116 L22: 6.1855 REMARK 3 L33: 2.6682 L12: -5.4301 REMARK 3 L13: -2.0822 L23: 2.8874 REMARK 3 S TENSOR REMARK 3 S11: 0.7046 S12: 1.4469 S13: -0.8981 REMARK 3 S21: 1.3387 S22: -1.4478 S23: 1.2645 REMARK 3 S31: 0.0688 S32: -1.8249 S33: 0.7264 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 76 THROUGH 102 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.5438 9.5483 21.4006 REMARK 3 T TENSOR REMARK 3 T11: 0.8091 T22: 0.6852 REMARK 3 T33: 0.3882 T12: 0.0110 REMARK 3 T13: -0.0294 T23: -0.0290 REMARK 3 L TENSOR REMARK 3 L11: 4.6632 L22: 4.0870 REMARK 3 L33: 2.5280 L12: 2.3377 REMARK 3 L13: -2.9296 L23: -2.8261 REMARK 3 S TENSOR REMARK 3 S11: -0.7440 S12: -0.2282 S13: -0.0529 REMARK 3 S21: -0.4625 S22: 0.2954 S23: -0.1282 REMARK 3 S31: 1.9917 S32: -0.5776 S33: 0.3438 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5VR3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227879. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-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 : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97920 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5773 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 200 DATA REDUNDANCY : 21.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 75.0000 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) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 49.2 REMARK 200 DATA REDUNDANCY IN SHELL : 10.70 REMARK 200 R MERGE FOR SHELL (I) : 0.25400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.610 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO PHASING REMARK 200 SOFTWARE USED: ARCIMBOLDO REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5, 2.0 M AMMONIUM REMARK 280 SULPHATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.95167 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 65.90333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 65.90333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 32.95167 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 A 311 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 313 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 A 27 REMARK 465 ALA A 28 REMARK 465 MET A 29 REMARK 465 ASP A 30 REMARK 465 PRO A 31 REMARK 465 GLY A 32 REMARK 465 GLY A 33 REMARK 465 GLY A 34 REMARK 465 GLY A 35 REMARK 465 SER A 36 REMARK 465 SER A 37 REMARK 465 ALA A 38 REMARK 465 ALA A 39 REMARK 465 ASP A 40 REMARK 465 GLY A 69 REMARK 465 GLY A 70 REMARK 465 LEU A 103 REMARK 465 GLY A 104 REMARK 465 ASN A 105 REMARK 465 GLY A 106 REMARK 465 THR A 107 REMARK 465 ASP A 108 REMARK 465 PHE A 109 REMARK 465 SER A 110 REMARK 465 VAL A 111 REMARK 465 SER A 112 REMARK 465 SER A 113 REMARK 465 SER A 114 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 PRO A 41 CG CD REMARK 470 GLU A 71 CG CD OE1 OE2 REMARK 470 HIS A 72 CG ND1 CD2 CE1 NE2 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 66 8.30 -65.34 REMARK 500 ASN A 73 67.95 -114.43 REMARK 500 LEU A 100 39.05 -83.49 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 A 201 DBREF 5VR3 A 36 114 UNP G3RLM7 G3RLM7_GORGO 38 116 SEQADV 5VR3 GLY A 27 UNP G3RLM7 EXPRESSION TAG SEQADV 5VR3 ALA A 28 UNP G3RLM7 EXPRESSION TAG SEQADV 5VR3 MET A 29 UNP G3RLM7 EXPRESSION TAG SEQADV 5VR3 ASP A 30 UNP G3RLM7 EXPRESSION TAG SEQADV 5VR3 PRO A 31 UNP G3RLM7 EXPRESSION TAG SEQADV 5VR3 GLY A 32 UNP G3RLM7 EXPRESSION TAG SEQADV 5VR3 GLY A 33 UNP G3RLM7 EXPRESSION TAG SEQADV 5VR3 GLY A 34 UNP G3RLM7 EXPRESSION TAG SEQADV 5VR3 GLY A 35 UNP G3RLM7 EXPRESSION TAG SEQRES 1 A 88 GLY ALA MET ASP PRO GLY GLY GLY GLY SER SER ALA ALA SEQRES 2 A 88 ASP PRO ALA ILE PRO GLU GLU VAL TRP ASN ILE LYS GLN SEQRES 3 A 88 MET ILE LYS LEU THR GLN GLU HIS ILE GLU ALA LEU LEU SEQRES 4 A 88 ASP LYS PHE GLY GLY GLU HIS ASN PRO PRO SER ILE TYR SEQRES 5 A 88 LEU GLU ALA TYR GLU GLU TYR THR SER LYS LEU ASP ALA SEQRES 6 A 88 LEU GLN GLN ARG GLU GLN GLN LEU LEU GLU SER LEU GLY SEQRES 7 A 88 ASN GLY THR ASP PHE SER VAL SER SER SER HET SO4 A 201 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *13(H2 O) HELIX 1 AA1 PRO A 44 ASP A 66 1 23 HELIX 2 AA2 PRO A 75 LEU A 100 1 26 SITE 1 AC1 5 LYS A 51 LYS A 55 PRO A 75 SER A 76 SITE 2 AC1 5 HOH A 304 CRYST1 41.563 41.563 98.855 90.00 90.00 120.00 P 31 2 1 6 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 0.024060 0.013891 0.000000 0.00000 SCALE2 0.000000 0.027782 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010116 0.00000