PDB Short entry for 2KAP HEADER SIGNALING PROTEIN 12-NOV-08 2KAP TITLE SOLUTION STRUCTURE OF DLC1-SAM COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHO GTPASE-ACTIVATING PROTEIN 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: STERILE ALPHA MOTIF (SAM) DOMAIN, UNP RESIDUES 17-76; COMPND 5 SYNONYM: RHO-TYPE GTPASE-ACTIVATING PROTEIN 7, DELETED IN LIVER COMPND 6 CANCER 1 PROTEIN, DLC-1, STAR-RELATED LIPID TRANSFER PROTEIN 12, COMPND 7 START DOMAIN-CONTAINING PROTEIN 12, STARD12, HP PROTEIN; 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: DLC1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET32A-DERIVED KEYWDS SOLUTION STRUCTURE, SAM DOMAIN, DLC-1, CYTOPLASM, GTPASE ACTIVATION, KEYWDS 2 PHOSPHOPROTEIN, POLYMORPHISM, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR S.YANG,D.YANG REVDAT 2 16-MAR-22 2KAP 1 REMARK REVDAT 1 20-OCT-09 2KAP 0 JRNL AUTH S.YANG,C.G.NOBLE,D.YANG JRNL TITL CHARACTERIZATION OF DLC1-SAM EQUILIBRIUM UNFOLDING AT THE JRNL TITL 2 AMINO ACID RESIDUE LEVEL JRNL REF BIOCHEMISTRY V. 48 4040 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19317456 JRNL DOI 10.1021/BI9000936 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER, TALOS REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLM (AMBER), CORNILESCU, REMARK 3 DELAGLIO AND BAX (TALOS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1000100887. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM DLC1-SAM, 50MM SODIUM REMARK 210 PHOSPHATE, 3MM DTT, 5% [U-100% REMARK 210 2H] D2O, 95% H2O/5% D2O; 1MM [U- REMARK 210 100% 15N] DLC1-SAM, 50MM SODIUM REMARK 210 PHOSPHATE, 3MM DTT, 5% [U-100% REMARK 210 2H] D2O, 95% H2O/5% D2O; 1MM [U- REMARK 210 100% 13C; U-100% 15N] DLC1-SAM, REMARK 210 50MM SODIUM PHOSPHATE, 3MM DTT, REMARK 210 5% [U-100% 2H] D2O, 95% H2O/5% REMARK 210 D2O; 1MM DLC1-SAM, 50MM SODIUM REMARK 210 PHOSPHATE, 3MM DTT, 100 % D2O, REMARK 210 100% D2O; 1MM [U-100% 13C; U-100% REMARK 210 15N] DLC1-SAM, 50MM SODIUM REMARK 210 PHOSPHATE, 3MM DTT, 100% D2O, REMARK 210 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1D 1H SPECTRUM; 2D 1H-15N HSQC; REMARK 210 2D 1H-13C HSQC; 2D DQF-COSY; 2D REMARK 210 1H-1H NOESY; 2D 1H-1H TOCSY; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 15N TOCSY; 3D 1H-13C NOESY; 3D REMARK 210 H(CCO)NH; 3D CC(CO)NH 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 : CYANA, MOLMOL, NMRDRAW, NMRPIPE, REMARK 210 NMRVIEW, PROCHECKNMR, XWINNMR 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: 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: 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 2 ARG A 48 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 TYR A 15 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES REMARK 500 8 TYR A 15 CB - CG - CD2 ANGL. DEV. = -4.2 DEGREES REMARK 500 10 ASP A 21 CB - CG - OD1 ANGL. DEV. = 5.9 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 PHE A 12 62.65 -115.08 REMARK 500 1 ASP A 21 34.45 -92.75 REMARK 500 1 PHE A 22 4.60 -59.00 REMARK 500 1 MET A 59 62.78 -67.33 REMARK 500 2 PHE A 12 67.67 -112.57 REMARK 500 2 ASP A 21 34.93 -92.80 REMARK 500 2 PHE A 22 0.06 -56.27 REMARK 500 3 PHE A 12 63.50 -114.18 REMARK 500 3 ASP A 21 35.81 -96.72 REMARK 500 3 PHE A 22 -3.40 -52.36 REMARK 500 4 PHE A 12 62.10 -114.07 REMARK 500 4 ASP A 21 37.45 -93.14 REMARK 500 4 PHE A 22 1.99 -56.78 REMARK 500 4 ASP A 36 31.89 -78.35 REMARK 500 4 MET A 59 44.95 -73.49 REMARK 500 5 PHE A 12 66.99 -114.64 REMARK 500 5 ASP A 21 46.19 -85.43 REMARK 500 5 PHE A 22 -8.30 -57.12 REMARK 500 6 PHE A 12 64.95 -112.20 REMARK 500 6 ASP A 21 37.10 -84.65 REMARK 500 6 PHE A 22 -6.95 -57.28 REMARK 500 6 MET A 59 82.19 -63.29 REMARK 500 7 PHE A 12 66.41 -114.77 REMARK 500 7 ASP A 21 37.12 -92.74 REMARK 500 7 PHE A 22 -0.96 -55.74 REMARK 500 7 MET A 59 99.00 -59.88 REMARK 500 8 PHE A 12 62.21 -114.34 REMARK 500 8 ASP A 21 35.64 -91.15 REMARK 500 8 PHE A 22 -3.61 -54.79 REMARK 500 9 PHE A 12 68.78 -114.71 REMARK 500 9 PHE A 22 -6.30 -51.52 REMARK 500 9 HIS A 35 66.06 -119.75 REMARK 500 10 PHE A 12 62.50 -117.71 REMARK 500 10 PHE A 22 -5.27 -53.09 REMARK 500 REMARK 500 REMARK: NULL DBREF 2KAP A 1 60 UNP Q96QB1 RHG07_HUMAN 17 76 SEQRES 1 A 60 LYS GLU ALA CYS ASP TRP LEU ARG ALA THR GLY PHE PRO SEQRES 2 A 60 GLN TYR ALA GLN LEU TYR GLU ASP PHE LEU PHE PRO ILE SEQRES 3 A 60 ASP ILE SER LEU VAL LYS ARG GLU HIS ASP PHE LEU ASP SEQRES 4 A 60 ARG ASP ALA ILE GLU ALA LEU CYS ARG ARG LEU ASN THR SEQRES 5 A 60 LEU ASN LYS CYS ALA VAL MET LYS HELIX 1 1 LYS A 1 GLY A 11 1 11 HELIX 2 2 PHE A 12 ASP A 21 1 10 HELIX 3 3 ASP A 27 HIS A 35 1 9 HELIX 4 4 ASP A 39 VAL A 58 1 20 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