PDB Short entry for 2GYT HEADER PROTEIN BINDING 10-MAY-06 2GYT TITLE SOLUTION STRUCTURE OF THE SAM (STERILE ALPHA MOTIF) DOMAIN OF DLC1 TITLE 2 (DELETED IN LIVER CANCER 1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DELETED IN LIVER CANCER 1 PROTEIN, ISOFORM 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: STERILE ALPHA MOTIF (SAM) DOMAIN; COMPND 5 SYNONYM: RHO-TYPE GTPASE-ACTIVATING PROTEIN 7, RHO-GTPASE-ACTIVATING COMPND 6 PROTEIN 7, DLC-1, HP PROTEIN, STAR-RELATED LIPID TRANSFER PROTEIN 12, COMPND 7 STARD12, START DOMAIN-CONTAINING PROTEIN 12; 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 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: PET-32U-DERIVED KEYWDS SAM DOMAIN, PROTEIN STRUCTURE, PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.YANG REVDAT 4 09-MAR-22 2GYT 1 REMARK REVDAT 3 20-OCT-09 2GYT 1 JRNL REVDAT 2 24-FEB-09 2GYT 1 VERSN REVDAT 1 24-APR-07 2GYT 0 JRNL AUTH D.ZHONG,J.ZHANG,S.YANG,U.J.K.SOH,J.P.BUSCHDORF,Y.T.ZHOU, JRNL AUTH 2 D.YANG,B.C.LOW JRNL TITL THE SAM DOMAIN OF THE RHOGAP DLC1 BINDS EF1A1 TO REGULATE JRNL TITL 2 CELL MIGRATION JRNL REF J.CELL.SCI. V. 122 414 2009 JRNL REFN ISSN 0021-9533 JRNL PMID 19158340 JRNL DOI 10.1242/JCS.027482 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, AMBER 7, TALOS 2003.027.13.05 REMARK 3 AUTHORS : BRUKER (XWINNMR), CASE, D.A. ET AL (AMBER), REMARK 3 CORNILESCU,G. ET AL (TALOS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2GYT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037715. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 50MM SODIUM PHOSPHATE REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1MM DLC1-SAM 15N, 13C-LABALED; REMARK 210 50MM SODIUM PHOSPHATE BUFFER(PH REMARK 210 7.0); 3MM DTT; 90% H2O, 10% D2O; REMARK 210 1MM DLC1-SAM 15N-LABALED; 50MM REMARK 210 SODIUM PHOSPHATE BUFFER(PH 7.0); REMARK 210 3MM DTT; 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRVIEW 5.2.2_01, NMRPIPE REMARK 210 2004.126.16.02, CYANA 1.0.5 REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 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 STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY. 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: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 10 GLU A 18 CD GLU A 18 OE1 -0.087 REMARK 500 10 GLU A 18 CD GLU A 18 OE2 0.084 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 10 PHE A 40 CB - CG - CD1 ANGL. DEV. = 4.4 DEGREES 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 ARG A 3 -56.12 -166.81 REMARK 500 1 PRO A 6 46.06 -74.85 REMARK 500 1 ASP A 7 -46.59 -154.90 REMARK 500 1 PHE A 28 56.00 -140.93 REMARK 500 1 PHE A 38 29.57 -164.78 REMARK 500 1 LEU A 39 80.95 49.30 REMARK 500 2 CYS A 2 177.19 52.40 REMARK 500 2 PRO A 6 44.56 -76.49 REMARK 500 2 ASP A 7 -61.17 -152.64 REMARK 500 2 PHE A 38 20.96 -165.48 REMARK 500 2 LEU A 39 85.99 54.81 REMARK 500 2 HIS A 51 48.71 -103.48 REMARK 500 3 CYS A 2 -53.82 -137.73 REMARK 500 3 LYS A 4 171.55 56.74 REMARK 500 3 PHE A 38 25.56 -168.16 REMARK 500 3 LEU A 39 91.68 53.41 REMARK 500 4 CYS A 2 74.13 47.00 REMARK 500 4 ARG A 3 -46.76 -135.22 REMARK 500 4 PHE A 28 59.57 -141.44 REMARK 500 4 PHE A 38 23.62 -169.15 REMARK 500 4 LEU A 39 89.04 54.64 REMARK 500 5 CYS A 2 41.48 -140.50 REMARK 500 5 ARG A 3 157.32 -48.81 REMARK 500 5 PRO A 6 -177.65 -68.17 REMARK 500 5 ASP A 7 33.28 -68.30 REMARK 500 5 PHE A 38 26.92 -165.49 REMARK 500 5 LEU A 39 83.93 51.86 REMARK 500 5 HIS A 51 -75.51 -72.38 REMARK 500 5 ASP A 52 36.25 39.62 REMARK 500 5 PHE A 53 -47.66 -134.04 REMARK 500 6 ARG A 3 -70.33 58.49 REMARK 500 6 THR A 8 -42.39 -131.37 REMARK 500 6 PHE A 38 20.62 -168.31 REMARK 500 6 LEU A 39 88.99 55.10 REMARK 500 6 HIS A 51 62.47 -119.86 REMARK 500 6 CYS A 72 3.34 -64.99 REMARK 500 7 CYS A 2 179.44 59.48 REMARK 500 7 ARG A 3 94.92 42.77 REMARK 500 7 LYS A 4 108.13 67.06 REMARK 500 7 ASP A 7 103.79 59.51 REMARK 500 7 PHE A 38 15.96 -164.99 REMARK 500 7 LEU A 39 93.53 58.58 REMARK 500 8 CYS A 2 117.14 54.52 REMARK 500 8 LYS A 4 61.94 39.35 REMARK 500 8 PHE A 38 15.39 -165.50 REMARK 500 8 LEU A 39 93.10 59.96 REMARK 500 8 HIS A 51 -71.84 -79.16 REMARK 500 8 ASP A 52 -25.92 50.64 REMARK 500 9 ARG A 3 43.07 -153.72 REMARK 500 9 ASP A 7 35.69 -70.89 REMARK 500 REMARK 500 THIS ENTRY HAS 60 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 TYR A 35 0.08 SIDE CHAIN REMARK 500 8 TYR A 35 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2GYT A 1 76 UNP Q96QB1 RHG07_HUMAN 1 76 SEQRES 1 A 76 MET CYS ARG LYS LYS PRO ASP THR MET ILE LEU THR GLN SEQRES 2 A 76 ILE GLU ALA LYS GLU ALA CYS ASP TRP LEU ARG ALA THR SEQRES 3 A 76 GLY PHE PRO GLN TYR ALA GLN LEU TYR GLU ASP PHE LEU SEQRES 4 A 76 PHE PRO ILE ASP ILE SER LEU VAL LYS ARG GLU HIS ASP SEQRES 5 A 76 PHE LEU ASP ARG ASP ALA ILE GLU ALA LEU CYS ARG ARG SEQRES 6 A 76 LEU ASN THR LEU ASN LYS CYS ALA VAL MET LYS HELIX 1 1 ASP A 7 GLY A 27 1 21 HELIX 2 2 PHE A 28 LEU A 39 1 12 HELIX 3 3 ASP A 43 HIS A 51 1 9 HELIX 4 4 ASP A 55 MET A 75 1 21 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