PDB Short entry for 2L05 HEADER TRANSFERASE 30-JUN-10 2L05 TITLE SOLUTION NMR STRUCTURE OF THE RAS-BINDING DOMAIN OF SERINE/THREONINE- TITLE 2 PROTEIN KINASE B-RAF FROM HOMO SAPIENS, NORTHEAST STRUCTURAL GENOMICS TITLE 3 CONSORTIUM TARGET HR4694F COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE/THREONINE-PROTEIN KINASE B-RAF; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RBD DOMAIN RESIDUES 149-232; COMPND 5 SYNONYM: PROTO-ONCOGENE B-RAF, P94, V-RAF MURINE SARCOMA VIRAL COMPND 6 ONCOGENE HOMOLOG B1; COMPND 7 EC: 2.7.11.1; COMPND 8 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, BRAF1, RAFB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PMGK; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET 14-15C KEYWDS STRUCTURAL GENOMICS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), KEYWDS 2 PSI-2, PROTEIN STRUCTURE INITIATIVE, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,H.JANJUA,C.CICCOSANTI,R.SHASTRY,Y.J.HUANG,T.B.ACTON, AUTHOR 2 R.XIAO,J.K.EVERETT,G.T.MONTELIONE,NORTHEAST STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (NESG) REVDAT 3 14-JUN-23 2L05 1 REMARK REVDAT 2 05-FEB-20 2L05 1 REMARK SEQADV REVDAT 1 14-JUL-10 2L05 0 JRNL AUTH J.M.ARAMINI,H.JANJUA,C.CICCOSANTI,R.SHASTRY,Y.J.HUANG, JRNL AUTH 2 T.B.ACTON,R.XIAO,J.K.EVERETT,G.T.MONTELIONE JRNL TITL SOLUTION NMR STRUCTURE OF THE RAS-BINDING DOMAIN OF JRNL TITL 2 SERINE/THREONINE-PROTEIN KINASE B-RAF FROM HOMO SAPIENS, JRNL TITL 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET HR4694F JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2, CYANA 3.0 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 (CNS), GUNTERT, MUMENTHALER AND WUTHRICH (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL STRUCTURES ARE BASED ON A REMARK 3 TOTAL OF 1750 CONFORMATIONALLY-RESTRICTING NOE-DERIVED DISTANCE REMARK 3 CONSTRAINTS AND 125 DIHEDRAL ANGLE CONSTRAINTS; 0 HYDROGEN BOND REMARK 3 CONSTRAINTS (22.1 CONSTRAINTS PER RESIDUE, 6.4 LONG RANGE REMARK 3 CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 147 TO 232 BY REMARK 3 PSVS 1.4). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY REMARK 3 USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST REMARK 3 TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR REMARK 3 DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH REMARK 3 PARAM19. REMARK 4 REMARK 4 2L05 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-10. REMARK 100 THE DEPOSITION ID IS D_1000101789. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.5 REMARK 210 IONIC STRENGTH : 0.1 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.84 MM [U-100% 13C; U-100% 15N] REMARK 210 HR4694F, 20 MM AMMONIUM ACETATE, REMARK 210 100 MM SODIUM CHLORIDE-3, 5 MM REMARK 210 CALCIUM CHLORIDE, 10 MM DTT, REMARK 210 0.02 % SODIUM AZIDE, 50 UM DSS, REMARK 210 90% H2O/10% D2O; 0.69 MM [U-5% REMARK 210 13C; U-100% 15N] HR4694F, 20 MM REMARK 210 AMMONIUM ACETATE, 100 MM SODIUM REMARK 210 CHLORIDE, 5 MM CALCIUM CHLORIDE, REMARK 210 10 MM DTT, 0.02 % SODIUM AZIDE, REMARK 210 50 UM DSS-14, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 15N-NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC; 2D 1H-13C HSQC HIGH REMARK 210 RESOLUTION (L/V METHYL REMARK 210 STEREOASSIGNMENT); 3D HNCO; 3D REMARK 210 HN(CA)CO; 3D HN(CO)CA; 3D HNCA; REMARK 210 3D CBCA(CO)NH; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HCCH-TOCSY; 3D REMARK 210 HCCH-COSY; 3D CCH-TOCSY; 3D HNHA; REMARK 210 2D 1H-15N HETNOE; 1D 15N T1 AND REMARK 210 T2 REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, AUTOSTRUCTURE 2.2.1, REMARK 210 PSVS 1.4, NMRPIPE 2.3, REMARK 210 MOLPROBITY 3.17, TOPSPIN 2.1, REMARK 210 PDBSTAT 5.1, PINE 1.0, SPARKY REMARK 210 3.112, TALOS+ REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE PROTEIN IS MONOMERIC BY GEL FILTRATION CHROMATOGRAPHY, REMARK 210 STATIC LIGHT SCATTERING AND 15N T1/T2 RELAXATION. THE STRUCTURE REMARK 210 WAS DETERMINED USING TRIPLE RESONANCE NMR SPECTROSCOPY. SPECTRA REMARK 210 FOR BACKBONE AND SIDE CHAIN ASSIGNMENTS WERE OBTAINED ON A 1.7- REMARK 210 MM MICROCRYOPROBE AT 600 MHZ. ALL NOESY DATA WERE ACQUIRED AT REMARK 210 800 MHZ USING A 5-MM CROYOPROBE. BACKBONE ASSIGNMENTS WERE MADE REMARK 210 USING PINE, AND THE SIDE CHAIN ASSIGNMENTS WERE COMPLETED REMARK 210 MANUALLY. AUTOMATIC NOESY ASSIGNMENTS WERE DETERMINED USING REMARK 210 CYANA 3.0. BACKBONE (PHI/PSI) DIHEDRAL ANGLE CONSTRAINTS WERE REMARK 210 OBTAINED FROM TALOSPLUS. COMPLETENESS OF NMR ASSIGNMENTS REMARK 210 (EXCLUDING N-TERMINAL TAG): BACKBONE, 98.3%, SIDE CHAIN, 98.1%, REMARK 210 AROMATICS, 100%, STEREOSPECIFIC METHYL, 100%, STEREOSPECIFIC REMARK 210 SIDE CHAIN NH2: 100%. FINAL STRUCTURE QUALITY FACTORS (FOR REMARK 210 RESIDUES 147 TO 232, PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + REMARK 210 S(PSI) > 1.8] COMPRISE: 154-228: (A) RMSD (ORDERED RESIDUES): BB, REMARK 210 0.6, HEAVY ATOM, 1.0. (B) RAMACHANDRAN STATISTICS FOR ORDERED REMARK 210 RESIDUES: MOST FAVORED, 91.9%, ADDITIONALLY ALLOWED, 8.0%, REMARK 210 GENEROUSLY ALLOWED, 0.1%, DISALLOWED, 0.0%. (C) PROCHECK SCORES REMARK 210 FOR ORDERED RESIDUES (RAW/Z-): PHI-PSI, -0.36/-1.10, ALL, -0.15/- REMARK 210 0.89. (D) MOLPROBITY CLASH SCORE (RAW/Z-): 14.54/-0.97 (E) RPF REMARK 210 SCORES FOR GOODNESS OF FIT TO NOESY DATA (RESIDUES 147 TO 232): REMARK 210 RECALL, 0.979, PRECISION, 0.933, F-MEASURE, 0.956, DP-SCORE, REMARK 210 0.808. (F) NUMBER OF CLOSE CONTACTS PER 20 MODELS: 2. THE REMARK 210 MAJORITY OF THE N-TERMINAL HIS TAG RESIDUES OF THE PROTEIN REMARK 210 (MGHHHHHHS) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS AND REMARK 210 HAVE BEEN OMITTED FROM THIS DEPOSITION. REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 138 REMARK 465 GLY A 139 REMARK 465 HIS A 140 REMARK 465 HIS A 141 REMARK 465 HIS A 142 REMARK 465 HIS A 143 REMARK 465 HIS A 144 REMARK 465 HIS A 145 REMARK 465 SER A 146 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 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 1 PRO A 152 37.90 -88.50 REMARK 500 1 GLN A 153 32.71 -80.35 REMARK 500 1 THR A 218 108.42 -56.74 REMARK 500 2 MET A 148 118.27 70.63 REMARK 500 2 SER A 151 85.21 64.88 REMARK 500 2 VAL A 230 88.07 63.42 REMARK 500 4 PRO A 231 98.88 -66.21 REMARK 500 5 PRO A 149 72.57 -66.56 REMARK 500 5 SER A 151 87.24 -151.02 REMARK 500 5 PRO A 152 87.99 -67.61 REMARK 500 6 PRO A 149 85.80 -66.63 REMARK 500 6 LYS A 150 85.95 -63.14 REMARK 500 6 PRO A 162 153.62 -49.72 REMARK 500 7 GLN A 153 39.18 -82.16 REMARK 500 7 ASN A 163 54.43 74.50 REMARK 500 8 SER A 151 87.45 47.52 REMARK 500 8 PRO A 152 97.99 -69.44 REMARK 500 9 MET A 148 84.94 60.77 REMARK 500 9 SER A 151 108.15 -172.48 REMARK 500 11 LYS A 150 20.04 -76.80 REMARK 500 11 SER A 151 86.74 72.83 REMARK 500 11 THR A 218 109.43 -56.30 REMARK 500 12 MET A 148 149.44 66.27 REMARK 500 12 ASN A 163 65.60 72.57 REMARK 500 12 LEU A 227 -78.22 -76.92 REMARK 500 13 MET A 148 111.40 65.49 REMARK 500 13 ASP A 202 16.28 57.46 REMARK 500 14 GLN A 153 89.28 -65.52 REMARK 500 14 ASN A 163 46.82 75.96 REMARK 500 14 ASN A 229 27.37 -72.56 REMARK 500 15 MET A 148 102.47 66.82 REMARK 500 15 PRO A 162 172.20 -59.03 REMARK 500 15 THR A 218 109.98 -56.64 REMARK 500 15 LEU A 227 -71.77 -82.47 REMARK 500 16 MET A 148 149.76 65.18 REMARK 500 16 LYS A 150 93.39 -68.80 REMARK 500 16 ASN A 229 37.62 -78.10 REMARK 500 17 PRO A 149 107.61 -57.93 REMARK 500 17 THR A 218 108.35 -54.93 REMARK 500 17 LEU A 227 -72.39 -100.92 REMARK 500 18 GLN A 153 38.65 -81.72 REMARK 500 19 MET A 148 96.83 67.30 REMARK 500 19 GLN A 153 84.75 -69.57 REMARK 500 19 LEU A 227 -86.21 -106.96 REMARK 500 19 ASN A 229 42.29 -80.56 REMARK 500 20 GLN A 153 39.17 -79.31 REMARK 500 20 VAL A 230 80.00 57.28 REMARK 500 20 PRO A 231 -172.29 -65.66 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HR4694F RELATED DB: TARGETDB REMARK 900 RELATED ID: 17030 RELATED DB: BMRB DBREF 2L05 A 149 232 UNP P15056 BRAF_HUMAN 149 232 SEQADV 2L05 MET A 138 UNP P15056 EXPRESSION TAG SEQADV 2L05 GLY A 139 UNP P15056 EXPRESSION TAG SEQADV 2L05 HIS A 140 UNP P15056 EXPRESSION TAG SEQADV 2L05 HIS A 141 UNP P15056 EXPRESSION TAG SEQADV 2L05 HIS A 142 UNP P15056 EXPRESSION TAG SEQADV 2L05 HIS A 143 UNP P15056 EXPRESSION TAG SEQADV 2L05 HIS A 144 UNP P15056 EXPRESSION TAG SEQADV 2L05 HIS A 145 UNP P15056 EXPRESSION TAG SEQADV 2L05 SER A 146 UNP P15056 EXPRESSION TAG SEQADV 2L05 HIS A 147 UNP P15056 EXPRESSION TAG SEQADV 2L05 MET A 148 UNP P15056 EXPRESSION TAG SEQRES 1 A 95 MET GLY HIS HIS HIS HIS HIS HIS SER HIS MET PRO LYS SEQRES 2 A 95 SER PRO GLN LYS PRO ILE VAL ARG VAL PHE LEU PRO ASN SEQRES 3 A 95 LYS GLN ARG THR VAL VAL PRO ALA ARG CYS GLY VAL THR SEQRES 4 A 95 VAL ARG ASP SER LEU LYS LYS ALA LEU MET MET ARG GLY SEQRES 5 A 95 LEU ILE PRO GLU CYS CYS ALA VAL TYR ARG ILE GLN ASP SEQRES 6 A 95 GLY GLU LYS LYS PRO ILE GLY TRP ASP THR ASP ILE SER SEQRES 7 A 95 TRP LEU THR GLY GLU GLU LEU HIS VAL GLU VAL LEU GLU SEQRES 8 A 95 ASN VAL PRO LEU HELIX 1 1 THR A 176 GLY A 189 1 14 HELIX 2 2 ILE A 191 GLU A 193 5 3 HELIX 3 3 ASP A 213 THR A 218 5 6 SHEET 1 A 5 GLN A 165 PRO A 170 0 SHEET 2 A 5 ILE A 156 LEU A 161 -1 N VAL A 159 O THR A 167 SHEET 3 A 5 GLU A 221 VAL A 226 1 O LEU A 222 N PHE A 160 SHEET 4 A 5 CYS A 195 GLN A 201 -1 N ALA A 196 O GLU A 225 SHEET 5 A 5 GLU A 204 ILE A 208 -1 O ILE A 208 N VAL A 197 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000