PDB Short entry for 1RLF HEADER SIGNAL TRANSDUCTION PROTEIN 09-JUL-98 1RLF TITLE STRUCTURE DETERMINATION OF THE RAS-BINDING DOMAIN OF THE RAL-SPECIFIC TITLE 2 GUANINE NUCLEOTIDE EXCHANGE FACTOR RLF, NMR, 10 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: RLF; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RAS BINDING DOMAIN, RESIDUES 646 - 735; COMPND 5 SYNONYM: RLF-RBD; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PGEX4T3 KEYWDS SIGNAL TRANSDUCTION PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR D.ESSER,B.BAUER,R.M.F.WOLTHUIS,A.WITTINGHOFER,R.H.COOL,P.BAY REVDAT 3 02-MAR-22 1RLF 1 REMARK REVDAT 2 24-FEB-09 1RLF 1 VERSN REVDAT 1 16-FEB-99 1RLF 0 JRNL AUTH D.ESSER,B.BAUER,R.M.WOLTHUIS,A.WITTINGHOFER,R.H.COOL,P.BAYER JRNL TITL STRUCTURE DETERMINATION OF THE RAS-BINDING DOMAIN OF THE JRNL TITL 2 RAL-SPECIFIC GUANINE NUCLEOTIDE EXCHANGE FACTOR RLF. JRNL REF BIOCHEMISTRY V. 37 13453 1998 JRNL REFN ISSN 0006-2960 JRNL PMID 9753431 JRNL DOI 10.1021/BI9811664 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH R.M.WOLTHUIS,N.D.DE RUITER,R.H.COOL,J.L.BOS REMARK 1 TITL STIMULATION OF GENE INDUCTION AND CELL GROWTH BY THE RAS REMARK 1 TITL 2 EFFECTOR RLF REMARK 1 REF EMBO J. V. 16 6748 1997 REMARK 1 REFN ISSN 0261-4189 REMARK 1 REFERENCE 2 REMARK 1 AUTH R.M.WOLTHUIS,B.BAUER,L.J.VAN'T VEER,A.M.DE VRIES-SMITS, REMARK 1 AUTH 2 R.H.COOL,M.SPAARGAREN,A.WITTINGHOFER,B.M.BURGERING,J.L.BOS REMARK 1 TITL RALGDS-LIKE FACTOR (RLF) IS A NOVEL RAS AND RAP REMARK 1 TITL 2 1A-ASSOCIATING PROTEIN REMARK 1 REF ONCOGENE V. 13 353 1996 REMARK 1 REFN ISSN 0950-9232 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: TOTAL NUMBER OF NOE CONSTRAINTS 2287; REMARK 3 INTRARESIDUE NOE CONSTRAINTS 804; SEQUENTIAL INTERRESIDUE REMARK 3 CONSTRAINTS (|I-J|=1) 469; INTERRESIDUE CONSTRAINTS (1<|I-J|<5) REMARK 3 296; INTERRESIDUE CONSTRAINTS (|I-J|>=5) 718; BACKBONE RMSD FROM REMARK 3 TARGET DISTANCES (ASP4-ARG90) 0.2A (COMPARED TO AVERAGE REMARK 3 STRUCTURE) COORDINATE RMSD FROM THE AVERAGE FOR ALL HEAVY REMARK 3 ATOM0.6A; NUMBER OF STRUCTURES USED IN ABOVE STATISTICS 10S REMARK 4 REMARK 4 1RLF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176109. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : DQF-COSY; NOECLEAN-TOCSY; GS-15N REMARK 210 -HSQC; 15N-NOESY-HMQC; 15N-TOCSY- REMARK 210 HMQCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NDEE, X-PLOR 3.851 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TWO- AND THREE REMARK 210 -DIMENSIONAL NMR SPECTROSCOPY ON UNLABELED AND 15N LABELED RLF- REMARK 210 RBD 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 VAL A 684 H ASN A 688 1.51 REMARK 500 O PHE A 719 H ASP A 723 1.57 REMARK 500 H VAL A 655 O LYS A 667 1.57 REMARK 500 O ALA A 716 H VAL A 718 1.58 REMARK 500 H ARG A 654 O HIS A 727 1.58 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 LYS A 667 109.60 179.43 REMARK 500 1 SER A 692 -132.26 -97.11 REMARK 500 1 LEU A 703 130.13 86.69 REMARK 500 1 ASP A 707 -47.28 -147.66 REMARK 500 1 LEU A 710 56.47 -113.78 REMARK 500 1 ASN A 717 64.85 -66.59 REMARK 500 1 ALA A 725 -146.95 -95.06 REMARK 500 2 VAL A 665 -0.30 -144.55 REMARK 500 2 ASP A 691 -40.20 -130.97 REMARK 500 2 SER A 692 -140.69 -96.79 REMARK 500 2 ALA A 695 102.53 51.05 REMARK 500 2 LEU A 703 129.16 76.12 REMARK 500 2 ASP A 707 -53.40 -133.15 REMARK 500 2 ASN A 717 62.58 -69.26 REMARK 500 2 ALA A 725 -150.62 -93.56 REMARK 500 3 LYS A 667 127.78 -177.01 REMARK 500 3 SER A 692 -147.31 -96.72 REMARK 500 3 ALA A 695 107.31 58.11 REMARK 500 3 GLU A 697 71.41 -69.72 REMARK 500 3 LEU A 703 135.93 80.06 REMARK 500 3 ASP A 707 -57.97 -130.30 REMARK 500 4 LYS A 667 118.24 -170.57 REMARK 500 4 SER A 692 -149.84 -96.61 REMARK 500 4 ALA A 695 91.23 60.34 REMARK 500 4 LEU A 703 128.99 72.72 REMARK 500 4 ASP A 707 -50.20 -131.79 REMARK 500 4 PRO A 713 34.05 -67.90 REMARK 500 4 ALA A 725 -145.49 -94.00 REMARK 500 4 HIS A 727 77.71 -105.38 REMARK 500 4 GLN A 733 102.96 -55.78 REMARK 500 5 SER A 692 -133.36 -96.99 REMARK 500 5 VAL A 694 -85.19 -142.94 REMARK 500 5 LEU A 703 127.83 83.64 REMARK 500 5 ASP A 707 -48.66 -130.19 REMARK 500 5 LEU A 710 67.57 -117.72 REMARK 500 6 VAL A 665 11.24 -142.69 REMARK 500 6 SER A 692 -135.96 -99.74 REMARK 500 6 ALA A 695 110.47 53.04 REMARK 500 6 GLU A 697 69.78 -69.87 REMARK 500 6 LEU A 703 125.17 76.72 REMARK 500 6 ASP A 707 -47.83 -148.51 REMARK 500 6 PRO A 713 2.42 -62.22 REMARK 500 6 ASP A 723 -95.03 -60.45 REMARK 500 6 ALA A 725 -108.19 -91.57 REMARK 500 7 LYS A 667 119.40 -164.04 REMARK 500 7 SER A 692 -135.85 -98.74 REMARK 500 7 ALA A 695 105.62 49.38 REMARK 500 7 LEU A 703 127.40 83.66 REMARK 500 7 ASP A 707 -51.79 -134.43 REMARK 500 7 ALA A 725 -127.94 -96.62 REMARK 500 REMARK 500 THIS ENTRY HAS 74 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 651 0.17 SIDE CHAIN REMARK 500 1 ARG A 654 0.15 SIDE CHAIN REMARK 500 1 ARG A 683 0.13 SIDE CHAIN REMARK 500 1 ARG A 690 0.30 SIDE CHAIN REMARK 500 1 ARG A 708 0.32 SIDE CHAIN REMARK 500 1 ARG A 732 0.08 SIDE CHAIN REMARK 500 1 ARG A 734 0.30 SIDE CHAIN REMARK 500 1 ARG A 735 0.19 SIDE CHAIN REMARK 500 2 ARG A 651 0.22 SIDE CHAIN REMARK 500 2 ARG A 654 0.26 SIDE CHAIN REMARK 500 2 ARG A 683 0.11 SIDE CHAIN REMARK 500 2 ARG A 690 0.08 SIDE CHAIN REMARK 500 2 ARG A 708 0.17 SIDE CHAIN REMARK 500 2 ARG A 734 0.25 SIDE CHAIN REMARK 500 2 ARG A 735 0.17 SIDE CHAIN REMARK 500 3 ARG A 651 0.13 SIDE CHAIN REMARK 500 3 ARG A 654 0.22 SIDE CHAIN REMARK 500 3 ARG A 683 0.31 SIDE CHAIN REMARK 500 3 ARG A 690 0.19 SIDE CHAIN REMARK 500 3 ARG A 708 0.32 SIDE CHAIN REMARK 500 3 ARG A 732 0.24 SIDE CHAIN REMARK 500 3 ARG A 734 0.12 SIDE CHAIN REMARK 500 3 ARG A 735 0.26 SIDE CHAIN REMARK 500 4 ARG A 651 0.14 SIDE CHAIN REMARK 500 4 ARG A 654 0.19 SIDE CHAIN REMARK 500 4 ARG A 690 0.21 SIDE CHAIN REMARK 500 4 ARG A 732 0.31 SIDE CHAIN REMARK 500 4 ARG A 734 0.22 SIDE CHAIN REMARK 500 4 ARG A 735 0.31 SIDE CHAIN REMARK 500 5 ARG A 651 0.28 SIDE CHAIN REMARK 500 5 ARG A 654 0.20 SIDE CHAIN REMARK 500 5 ARG A 683 0.28 SIDE CHAIN REMARK 500 5 ARG A 708 0.22 SIDE CHAIN REMARK 500 5 ARG A 732 0.27 SIDE CHAIN REMARK 500 5 ARG A 734 0.32 SIDE CHAIN REMARK 500 5 ARG A 735 0.22 SIDE CHAIN REMARK 500 6 ARG A 651 0.22 SIDE CHAIN REMARK 500 6 ARG A 683 0.32 SIDE CHAIN REMARK 500 6 ARG A 690 0.29 SIDE CHAIN REMARK 500 6 ARG A 708 0.32 SIDE CHAIN REMARK 500 6 ARG A 732 0.31 SIDE CHAIN REMARK 500 6 ARG A 734 0.31 SIDE CHAIN REMARK 500 6 ARG A 735 0.31 SIDE CHAIN REMARK 500 7 ARG A 651 0.14 SIDE CHAIN REMARK 500 7 ARG A 654 0.23 SIDE CHAIN REMARK 500 7 ARG A 683 0.32 SIDE CHAIN REMARK 500 7 ARG A 690 0.30 SIDE CHAIN REMARK 500 7 ARG A 708 0.27 SIDE CHAIN REMARK 500 7 ARG A 732 0.31 SIDE CHAIN REMARK 500 7 ARG A 734 0.28 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 71 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL DBREF 1RLF A 646 735 UNP Q61193 RGL2_MOUSE 646 735 SEQRES 1 A 90 GLY SER SER ASP CYS ARG ILE ILE ARG VAL GLN MET GLU SEQRES 2 A 90 LEU GLY GLU ASP GLY SER VAL TYR LYS SER ILE LEU VAL SEQRES 3 A 90 THR SER GLN ASP LYS ALA PRO SER VAL ILE SER ARG VAL SEQRES 4 A 90 LEU LYS LYS ASN ASN ARG ASP SER ALA VAL ALA SER GLU SEQRES 5 A 90 PHE GLU LEU VAL GLN LEU LEU PRO GLY ASP ARG GLU LEU SEQRES 6 A 90 THR ILE PRO HIS SER ALA ASN VAL PHE TYR ALA MET ASP SEQRES 7 A 90 GLY ALA SER HIS ASP PHE LEU LEU ARG GLN ARG ARG HELIX 1 1 VAL A 680 LYS A 687 1 8 HELIX 2 2 PHE A 719 MET A 722 1 4 SHEET 1 A 4 SER A 668 THR A 672 0 SHEET 2 A 4 CYS A 650 MET A 657 -1 N ILE A 653 O ILE A 669 SHEET 3 A 4 HIS A 727 GLN A 733 1 N HIS A 727 O ARG A 654 SHEET 4 A 4 PHE A 698 GLN A 702 -1 N VAL A 701 O LEU A 730 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