2KAP - Header Asymmetric Unit

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 COMPND 5 17-76; COMPND 6 SYNONYM: RHO-TYPE GTPASE-ACTIVATING PROTEIN 7, DELETED IN COMPND 7 LIVER CANCER 1 PROTEIN, DLC-1, STAR-RELATED LIPID TRANSFER COMPND 8 PROTEIN 12, START DOMAIN-CONTAINING PROTEIN 12, STARD12, HP COMPND 9 PROTEIN; COMPND 10 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 KEYWDS 2 ACTIVATION, PHOSPHOPROTEIN, POLYMORPHISM, SIGNALING PROTEIN

EXPDTA SOLUTION NMR

NUMMDL 10

AUTHOR S.YANG,D.YANG

REVDAT 1 20-OCT-09 2KAP 0

JRNL AUTH S.YANG,C.G.NOBLE,D.YANG JRNL TITL CHARACTERIZATION OF DLC1-SAM EQUILIBRIUM UNFOLDING JRNL TITL 2 AT THE 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 1

REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.

REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TALOS REMARK 3 AUTHORS : CORNILESCU, DELAGLIO AND BAX REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL

REMARK 4 REMARK 4 2KAP COMPLIES WITH FORMAT V. 3.20, 01-DEC-08

REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-NOV-08. REMARK 100 THE RCSB ID CODE IS RCSB100887.

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 REMARK 210 [U-100% 15N] DLC1-SAM, 50MM REMARK 210 SODIUM PHOSPHATE, 3MM DTT, 5% REMARK 210 [U-100% 2H] D2O, 95% H2O/5% REMARK 210 D2O; 1MM [U-100% 13C; U-100% REMARK 210 15N] DLC1-SAM, 50MM SODIUM REMARK 210 PHOSPHATE, 3MM DTT, 5% [U-100% REMARK 210 2H] D2O, 95% H2O/5% D2O; 1MM REMARK 210 DLC1-SAM, 50MM SODIUM REMARK 210 PHOSPHATE, 3MM DTT, 100 % D2O, REMARK 210 100% D2O; 1MM [U-100% 13C; U- REMARK 210 100% 15N] DLC1-SAM, 50MM REMARK 210 SODIUM PHOSPHATE, 3MM DTT, REMARK 210 100% D2O, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 1D 1H SPECTRUM; 2D 1H-15N REMARK 210 HSQC; 2D 1H-13C HSQC; 2D DQF- REMARK 210 COSY; 2D 1H-1H NOESY; 2D 1H-1H REMARK 210 TOCSY; 3D CBCA(CO)NH; 3D REMARK 210 HNCACB; 3D HCCH-TOCSY; 3D 1H- REMARK 210 15N NOESY; 3D 1H-15N TOCSY; 3D REMARK 210 1H-13C NOESY; 3D H(CCO)NH; 3D REMARK 210 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 : AMBER, CYANA, MOLMOL, REMARK 210 NMRDRAW, NMRPIPE, NMRVIEW, REMARK 210 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 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