PDB Short entry for 1I35 HEADER TRANSFERASE 13-FEB-01 1I35 TITLE SOLUTION STRUCTURE OF THE RAS-BINDING DOMAIN OF THE PROTEIN KINASE TITLE 2 BYR2 FROM SCHIZOSACCHAROMYCES POMBE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN KINASE BYR2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RAS-BINDING DOMAIN; COMPND 5 EC: 2.7.1.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 GENE: BYR2 (AMINO ACIDS 71 - 165); SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B121 DE3; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX4T3 (PHARMACIA) KEYWDS UBIQUITIN SUPERFOLD, TRANSFERASE EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR W.GRONWALD,F.HUBER,P.GRUNEWALD,M.SPORNER,S.WOHLGEMUTH,C.HERRMANN, AUTHOR 2 H.R.KALBITZER REVDAT 3 23-FEB-22 1I35 1 REMARK REVDAT 2 24-FEB-09 1I35 1 VERSN REVDAT 1 12-DEC-01 1I35 0 JRNL AUTH W.GRONWALD,F.HUBER,P.GRUNEWALD,M.SPORNER,S.WOHLGEMUTH, JRNL AUTH 2 C.HERRMANN,H.R.KALBITZER JRNL TITL SOLUTION STRUCTURE OF THE RAS BINDING DOMAIN OF THE PROTEIN JRNL TITL 2 KINASE BYR2 FROM SCHIZOSACCHAROMYCES POMBE. JRNL REF STRUCTURE V. 9 1029 2001 JRNL REFN ISSN 0969-2126 JRNL PMID 11709167 JRNL DOI 10.1016/S0969-2126(01)00671-2 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH W.GRONWALD,E.BRUNNER,F.HUBER,M.WENZLER,C.HERRMANN, REMARK 1 AUTH 2 H.R.KALBITZER REMARK 1 TITL OVERCOMING THE PROBLEMS ASSOCIATED WITH POOR SPECTRA QUALITY REMARK 1 TITL 2 OF THE PROTEIN KINASE BYR2 USING RESIDUAL DIPOLAR COUPLINGS REMARK 1 REF PROTEIN SCI. V. 10 1260 2001 REMARK 1 REFN ISSN 0961-8368 REMARK 1 DOI 10.1110/PS.43201 REMARK 1 REFERENCE 2 REMARK 1 AUTH F.HUBER,W.GRONWALD,S.WOHLGEMUTH,C.HERRMANN,M.GEYER, REMARK 1 AUTH 2 A.WITTINGHOFER,H.R.KALBITZER REMARK 1 TITL LETTER TO THE EDITOR: SEQUENTIAL NMR ASSIGNMENT OF THE REMARK 1 TITL 2 RAS-BINDING DOMAIN OF BYR2 REMARK 1 REF J.BIOMOL.NMR V. 16 355 2000 REMARK 1 REFN ISSN 0925-2738 REMARK 1 DOI 10.1023/A:1008335420475 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : UXNMR 2.6, CNS 1.0 REMARK 3 AUTHORS : BRUKER SOFTWARE DEPARTMENT (UXNMR), BRUENGER, REMARK 3 A.T., ADAMS, P.D., CLORE, G.M., DELANO, W.L., GROS, REMARK 3 P., GROSSE-KUNSTLEVE, JIANG, R.W., KUSZEWSKI, J., REMARK 3 NILGES, M., PANNU, N.S., READ, R.J., RICE, L.M., REMARK 3 SIMONSON, T. & WARREN, G.L. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 824 NOE-RESTRAINTS, 88 BACKBONE REMARK 3 DIHEDRAL ANGLE RESTRAINS, 29 HYDROGEN REMARK 3 BONDS AND 28 RESIDUAL DIPOLAR REMARK 3 COUPLINGS REMARK 4 REMARK 4 1I35 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000012844. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 298; 298; 298; 298; 305 REMARK 210 PH : 6.9; 6.9; 6.9; 6.9; 6.9; 6.9 REMARK 210 IONIC STRENGTH : 200 MM DEUTERATED GLYCINE, 20 MM REMARK 210 PHOSPHATE BUFFER; 200 MM REMARK 210 DEUTERATED GLYCINE, 20 MM REMARK 210 PHOSPHATE BUFFER; 200 MM REMARK 210 DEUTERATED GLYCINE, 20 MM REMARK 210 PHOSPHATE BUFFER; 200 MM REMARK 210 DEUTERATED GLYCINE, 20 MM REMARK 210 PHOSPHATE BUFFER; 200 MM REMARK 210 DEUTERATED GLYCINE, 20 MM REMARK 210 PHOSPHATE BUFFER; 200 MM REMARK 210 DEUTERATED GLYCINE, 20 MM REMARK 210 PHOSPHATE BUFFER REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT; REMARK 210 AMBIENT; AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM BYR2 UNLABELED,25 MM DTE, REMARK 210 200 MM DEUTERATED GLYCINE, 20 MM REMARK 210 PHOSPHATE BUFFER, 0.5 MM EDTA, REMARK 210 0.5 MM NAN3, 0.1 MM DSS, 90% H2O/ REMARK 210 10% D2O; 1.2 MM BYR2 UNLABELED, REMARK 210 25 MM DTE, 200 MM DEUTERATED REMARK 210 GLYCINE, 20 MM PHOSPHATE BUFFER, REMARK 210 0.5 MM EDTA, 0.5 MM NAN3, 0.1 MM REMARK 210 DSS, 100% D2O; 1.0 MM BYR2 15N- REMARK 210 LABELED,25 MM DTE, 200 MM REMARK 210 DEUTERATED GLYCINE, 20 MM REMARK 210 PHOSPHATE BUFFER, 0.5 MM EDTA, REMARK 210 0.5 MM NAN3, 0.1 MM DSS, 90% H2O/ REMARK 210 10% D2O; 1.0 MM BYR2 15N-13C- REMARK 210 LABELED,25 MM DTE, 200 MM REMARK 210 DEUTERATED GLYCINE, 20 MM REMARK 210 PHOSPHATE BUFFER, 0.5 MM EDTA, REMARK 210 0.5 MM NAN3, 0.1 MM DSS, 90% H2O/ REMARK 210 10% D2O; 0.7 MM BYR2 15N-13C- REMARK 210 LABELED,25 MM DTE, 200 MM REMARK 210 DEUTERATED GLYCINE, 20 MM REMARK 210 PHOSPHATE BUFFER, 0.5 MM EDTA, REMARK 210 0.5 MM NAN3, 0.1 MM DSS, 100% REMARK 210 D2O; 1.0 MM BYR2 15N-LABELED,25 REMARK 210 MM DTE, 200 MM DEUTERATED REMARK 210 GLYCINE, 20 MM PHOSPHATE BUFFER, REMARK 210 0.5 MM EDTA, 0.5 MM NAN3, 0.1 MM REMARK 210 DSS, 5 WT.-% PHOSPHOLIPID REMARK 210 BICELLES, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA; 3D_13C- REMARK 210 SEPARATED_NOESY; 2D-HSQC WITH NO REMARK 210 DECOUPLING OF 1H DURING REMARK 210 T1(MEASUREMENT OF RESIDUAL REMARK 210 DIPOLAR COUPLINGS) REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : UXNMR 2.6, AURELIA 2.7.1, REMARK 210 AUREMOL 0.6, CNS 1.0 REMARK 210 METHOD USED : HIGH TEMPERATURE TORSION ANGLE REMARK 210 DYNAMICS. FIRST COOLING STAGE REMARK 210 USING TORSION ANGLE DYNAMICS. REMARK 210 SECOND COOLING STAGE USING REMARK 210 CARTESIAN DYNAMICS. FINAL ENERGY REMARK 210 MINIMIZATION. REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : THE SUBMITTED CONFORMER MODELS REMARK 210 ARE THE 10 STRUCTURES WITH THE REMARK 210 LOWEST TOTAL ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 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 O THR A 24 HB3 ALA A 28 1.30 REMARK 500 O ILE A 6 HA ILE A 74 1.40 REMARK 500 O ALA A 28 HB2 PHE A 32 1.52 REMARK 500 H SER A 45 OD2 ASP A 87 1.53 REMARK 500 O GLN A 22 H ALA A 26 1.55 REMARK 500 O ARG A 4 O ASP A 71 2.08 REMARK 500 O LYS A 30 O LEU A 34 2.11 REMARK 500 O PHE A 5 O ARG A 13 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 1 CYS A 8 179.01 66.01 REMARK 500 1 ARG A 18 -11.78 165.95 REMARK 500 1 ASP A 20 163.88 73.40 REMARK 500 1 LEU A 34 -147.61 -136.93 REMARK 500 1 ASP A 36 56.42 81.37 REMARK 500 1 PHE A 40 166.92 -37.68 REMARK 500 1 GLN A 46 -89.27 -127.30 REMARK 500 1 SER A 47 -89.51 -118.43 REMARK 500 1 THR A 54 -135.87 -89.12 REMARK 500 1 GLU A 55 -96.12 -83.94 REMARK 500 1 ASN A 64 -28.18 -32.31 REMARK 500 1 SER A 66 79.02 85.92 REMARK 500 1 GLU A 69 -176.93 37.08 REMARK 500 1 ASP A 71 -92.05 -158.38 REMARK 500 1 ARG A 72 62.37 -38.29 REMARK 500 1 LYS A 80 108.77 -167.93 REMARK 500 1 PRO A 81 -160.06 -71.92 REMARK 500 1 CYS A 82 -37.69 164.24 REMARK 500 1 SER A 84 -39.71 177.40 REMARK 500 1 PHE A 85 -7.44 -56.99 REMARK 500 1 SER A 91 -27.30 -152.38 REMARK 500 1 GLU A 93 -138.26 -63.61 REMARK 500 2 CYS A 8 -136.44 34.55 REMARK 500 2 GLN A 11 -113.33 -64.16 REMARK 500 2 GLN A 16 87.53 -60.63 REMARK 500 2 ASP A 20 128.99 57.42 REMARK 500 2 LEU A 34 -152.13 -124.08 REMARK 500 2 ASP A 36 74.27 52.60 REMARK 500 2 SER A 47 -158.19 55.79 REMARK 500 2 THR A 54 -92.29 -89.45 REMARK 500 2 GLU A 55 -80.79 -135.34 REMARK 500 2 ASN A 64 84.26 67.86 REMARK 500 2 SER A 65 -78.10 66.12 REMARK 500 2 SER A 66 -101.14 -160.78 REMARK 500 2 SER A 67 148.71 55.86 REMARK 500 2 GLU A 69 -146.38 94.36 REMARK 500 2 ARG A 70 -162.57 55.47 REMARK 500 2 ASP A 71 171.02 166.47 REMARK 500 2 ARG A 72 147.22 -21.70 REMARK 500 2 LYS A 78 -12.18 55.50 REMARK 500 2 LYS A 80 102.26 167.81 REMARK 500 2 PRO A 81 -158.99 -68.32 REMARK 500 2 PRO A 83 -86.04 -69.02 REMARK 500 2 SER A 84 -32.53 168.44 REMARK 500 2 LEU A 88 -85.24 -93.30 REMARK 500 2 ARG A 89 -167.75 57.41 REMARK 500 2 SER A 91 56.91 -179.44 REMARK 500 2 TRP A 92 -8.92 71.73 REMARK 500 2 GLU A 93 -49.63 114.94 REMARK 500 3 CYS A 8 -165.75 62.95 REMARK 500 REMARK 500 THIS ENTRY HAS 249 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1I35 A 1 95 UNP P28829 BYR2_SCHPO 71 165 SEQRES 1 A 95 CYS ILE LEU ARG PHE ILE ALA CYS ASN GLY GLN THR ARG SEQRES 2 A 95 ALA VAL GLN SER ARG GLY ASP TYR GLN LYS THR LEU ALA SEQRES 3 A 95 ILE ALA LEU LYS LYS PHE SER LEU GLU ASP ALA SER LYS SEQRES 4 A 95 PHE ILE VAL CYS VAL SER GLN SER SER ARG ILE LYS LEU SEQRES 5 A 95 ILE THR GLU GLU GLU PHE LYS GLN ILE CYS PHE ASN SER SEQRES 6 A 95 SER SER PRO GLU ARG ASP ARG LEU ILE ILE VAL PRO LYS SEQRES 7 A 95 GLU LYS PRO CYS PRO SER PHE GLU ASP LEU ARG ARG SER SEQRES 8 A 95 TRP GLU ILE GLU HELIX 1 1 GLY A 19 SER A 33 1 15 HELIX 2 2 ASP A 36 PHE A 40 5 5 HELIX 3 3 GLU A 56 ASN A 64 1 9 HELIX 4 4 SER A 84 ARG A 89 1 6 SHEET 1 A 5 GLN A 11 GLN A 16 0 SHEET 2 A 5 ILE A 2 ALA A 7 -1 N LEU A 3 O VAL A 15 SHEET 3 A 5 LEU A 73 VAL A 76 1 O LEU A 73 N ILE A 6 SHEET 4 A 5 ILE A 41 SER A 45 -1 N ILE A 41 O VAL A 76 SHEET 5 A 5 ILE A 50 ILE A 53 -1 N LYS A 51 O VAL A 44 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