PDB Short entry for 2OS6 HEADER CELL ADHESION 05-FEB-07 2OS6 TITLE SOLUTION STRUCTURE OF LARG PDZ DOMAIN IN COMPLEX WITH C-TERMINAL OCTA- TITLE 2 PEPTIDE OF PLEXIN B1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 12; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: PDZ DOMAIN; COMPND 5 SYNONYM: LARG PROTEIN, LEUKEMIA-ASSOCIATED RHOGEF; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: C-TERMINAL PEPTIDE OF PLEXIN-B1; COMPND 9 CHAIN: B; COMPND 10 SYNONYM: SEMAPHORIN RECEPTOR SEP; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B (+); SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS KEYWDS NERVE SYSTEM DEVELOPMENT, CYTOSKELETON REARRANGEMENT, CELL ADHESION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.LIU,H.HUANG,Y.YANG REVDAT 3 16-MAR-22 2OS6 1 REMARK SEQADV REVDAT 2 24-FEB-09 2OS6 1 VERSN REVDAT 1 12-FEB-08 2OS6 0 JRNL AUTH J.LIU,H.HUANG,Y.YANG JRNL TITL SOLUTION STRUCTURE OF THE LARG PDZ DOMAIN IN COMPLEX WITH JRNL TITL 2 C-TERMINAL PEPTIDE OF PLEXIN B1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS CNS 1.1, CSI 1.0 CSI 1.0 REMARK 3 AUTHORS : BRUNGER A. T. ETALL (CNS), DAVID S. WISHART (CSI REMARK 3 1.0) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE COMPLEX STRUCTURE IS SOLVED USING A REMARK 3 TOTAL OF 1306 EXPERIMENTAL RESTRAINTS THAT INCLUDE 1155 REMARK 3 INTRAMOLECULAR NOES, 90 DIHEDRAL ANGLE RESTRAINTS AND 61 REMARK 3 INTERMOLECULAR NOES DERIVED FROM NMR SPECTROSCOPY REMARK 4 REMARK 4 2OS6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-FEB-07. REMARK 100 THE DEPOSITION ID IS D_1000041519. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 50 MM PHOSPHATE BUFFER, 50MM REMARK 210 NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8MM 15N, 13C-LABELED LARG PDZ REMARK 210 DOMAIN, 5MM EDTA, 1MM DTT, 7.6MM REMARK 210 SYNTHETIC PEPTIDE, 50MM REMARK 210 PHOSPHATE BUFFER, 90% H2O, 10% REMARK 210 D2O; 0.8MM 15N, 13C-LABELED LARG REMARK 210 PDZ DOMAIN, 5MM EDTA, 1MM DTT, REMARK 210 7.6MM SYNTHETIC PEPTIDE, 50MM REMARK 210 PHOSPHATE BUFFER, 99.9% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; 2D, 13C, 15N- REMARK 210 FILTERED, 13C-EDITED NOESY; DQF- REMARK 210 COSY; 2D TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : DMX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE NMRPIPE 2.2, SPARKY 3 REMARK 210 SPARKY 3, MOLMOL 2K.2 MOLMOL 2K.2 REMARK 210 METHOD USED : DISTANCE GEOMETRY, SIMULATED REMARK 210 ANNEALING, MOLECULAR DYNAMICS, REMARK 210 TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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: 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: 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 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 HIS A 3 94.56 67.41 REMARK 500 1 ASN A 28 -92.33 30.46 REMARK 500 1 VAL A 60 30.24 -91.26 REMARK 500 1 HIS A 62 -50.07 -154.74 REMARK 500 1 GLU B 91 111.17 -161.05 REMARK 500 1 LYS B 93 42.18 -150.77 REMARK 500 2 HIS A 3 24.70 -141.38 REMARK 500 2 MET A 4 31.88 -158.99 REMARK 500 2 LEU A 6 74.63 -156.62 REMARK 500 2 ASP A 16 -166.89 -128.92 REMARK 500 2 ASP A 27 -94.66 -132.09 REMARK 500 2 GLN A 33 -79.11 -83.40 REMARK 500 2 LYS A 36 92.47 -59.73 REMARK 500 2 VAL A 60 35.45 -92.98 REMARK 500 2 GLU B 91 163.48 71.66 REMARK 500 3 ASN A 28 -91.08 30.30 REMARK 500 3 VAL A 60 37.45 -93.12 REMARK 500 3 HIS A 62 63.98 -175.81 REMARK 500 3 ASN B 92 38.26 -141.07 REMARK 500 4 HIS A 3 -61.68 -175.33 REMARK 500 4 MET A 4 160.17 66.25 REMARK 500 4 ASP A 27 -84.18 -127.12 REMARK 500 4 GLN A 33 -75.03 -80.17 REMARK 500 5 MET A 4 -177.58 66.28 REMARK 500 5 ASP A 27 -79.54 -133.38 REMARK 500 5 SER A 34 131.11 179.99 REMARK 500 5 VAL A 60 30.75 -94.10 REMARK 500 5 ARG A 85 -61.45 -176.21 REMARK 500 5 LYS B 93 50.28 -157.33 REMARK 500 6 SER A 2 -75.69 69.29 REMARK 500 6 HIS A 3 174.09 62.42 REMARK 500 6 MET A 4 177.77 62.79 REMARK 500 6 LEU A 6 100.76 63.15 REMARK 500 6 ASN A 28 -86.78 21.87 REMARK 500 6 VAL A 30 153.10 -49.82 REMARK 500 6 GLN A 33 -64.79 -91.54 REMARK 500 6 ARG A 51 82.90 -69.89 REMARK 500 6 GLU B 91 -161.80 -67.94 REMARK 500 7 LEU A 6 -179.87 59.76 REMARK 500 7 ASP A 27 -84.76 -128.37 REMARK 500 7 HIS A 62 52.49 -171.74 REMARK 500 7 GLU B 91 86.59 62.68 REMARK 500 7 LYS B 93 48.48 -146.01 REMARK 500 8 HIS A 3 123.84 -173.32 REMARK 500 8 ASP A 27 -79.53 -133.15 REMARK 500 8 ASP A 38 51.67 -119.50 REMARK 500 8 ASN B 92 169.82 67.82 REMARK 500 9 SER A 2 42.58 -147.61 REMARK 500 9 LEU A 6 156.85 66.59 REMARK 500 9 ASP A 27 -82.65 -124.60 REMARK 500 REMARK 500 THIS ENTRY HAS 109 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OMJ RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH C-TERMINAL PEPTIDE OF PLEXIN B1 DBREF 2OS6 A 5 89 UNP Q9NZN5 ARHGC_HUMAN 67 151 DBREF 2OS6 B 90 97 UNP O43157 PLXB1_HUMAN 2128 2135 SEQADV 2OS6 GLY A 1 UNP Q9NZN5 EXPRESSION TAG SEQADV 2OS6 SER A 2 UNP Q9NZN5 EXPRESSION TAG SEQADV 2OS6 HIS A 3 UNP Q9NZN5 EXPRESSION TAG SEQADV 2OS6 MET A 4 UNP Q9NZN5 EXPRESSION TAG SEQRES 1 A 89 GLY SER HIS MET GLY LEU VAL GLN ARG CYS VAL ILE ILE SEQRES 2 A 89 GLN LYS ASP ASP ASN GLY PHE GLY LEU THR VAL SER GLY SEQRES 3 A 89 ASP ASN PRO VAL PHE VAL GLN SER VAL LYS GLU ASP GLY SEQRES 4 A 89 ALA ALA MET ARG ALA GLY VAL GLN THR GLY ASP ARG ILE SEQRES 5 A 89 ILE LYS VAL ASN GLY THR LEU VAL THR HIS SER ASN HIS SEQRES 6 A 89 LEU GLU VAL VAL LYS LEU ILE LYS SER GLY SER TYR VAL SEQRES 7 A 89 ALA LEU THR VAL GLN GLY ARG PRO PRO GLY SER SEQRES 1 B 8 VAL GLU ASN LYS VAL THR ASP LEU HELIX 1 1 GLY A 39 ALA A 44 1 6 HELIX 2 2 ASN A 64 SER A 74 1 11 SHEET 1 A 4 VAL A 7 ILE A 13 0 SHEET 2 A 4 VAL A 78 GLY A 84 -1 O VAL A 82 N ARG A 9 SHEET 3 A 4 ARG A 51 VAL A 55 -1 N LYS A 54 O THR A 81 SHEET 4 A 4 THR A 58 LEU A 59 -1 O THR A 58 N VAL A 55 SHEET 1 B 3 PHE A 31 VAL A 35 0 SHEET 2 B 3 LEU A 22 SER A 25 -1 N THR A 23 O SER A 34 SHEET 3 B 3 VAL B 94 ASP B 96 -1 O THR B 95 N VAL A 24 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