PDB Short entry for 2RQT HEADER SIGNALING PROTEIN 14-DEC-09 2RQT TITLE SOLUTION STRUCTURE OF THE HUMAN DDEF1 SH3 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ARF-GAP WITH SH3 DOMAIN, ANK REPEAT AND PH DOMAIN- COMPND 3 CONTAINING PROTEIN 1; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: UNP RESIDUES 1069-1129; COMPND 6 SYNONYM: DDEF1_SH3, 130 KDA PHOSPHATIDYLINOSITOL 4,5-BIPHOSPHATE- COMPND 7 DEPENDENT ARF1 GTPASE-ACTIVATING PROTEIN, PIP2-DEPENDENT ARF1 GAP, COMPND 8 ADP-RIBOSYLATION FACTOR-DIRECTED GTPASE-ACTIVATING PROTEIN 1, ARF COMPND 9 GTPASE-ACTIVATING PROTEIN 1, DEVELOPMENT AND DIFFERENTIATION- COMPND 10 ENHANCING FACTOR 1, DIFFERENTIATION-ENHANCING FACTOR 1, DEF-1; 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 GENE: ASAP1, DDEF1, KIAA1249; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET32A KEYWDS SH3 DOMAIN, GAP, GTPASE ACTIVATION, MEMBRANE, SIGNALING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.KAIEDA,C.MATSUI,Y.MIMORI-KIYOSUE,T.IKEGAMI REVDAT 2 16-MAR-22 2RQT 1 REMARK REVDAT 1 07-JUL-10 2RQT 0 JRNL AUTH S.KAIEDA,C.MATSUI,Y.MIMORI-KIYOSUE,T.IKEGAMI JRNL TITL STRUCTURAL BASIS OF THE RECOGNITION OF THE SAMP MOTIF OF JRNL TITL 2 ADENOMATOUS POLYPOSIS COLI BY THE SRC-HOMOLOGY 3 DOMAIN. JRNL REF BIOCHEMISTRY V. 49 5143 2010 JRNL REFN ISSN 0006-2960 JRNL PMID 20509626 JRNL DOI 10.1021/BI100563Z REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, ARIA 2.2 REMARK 3 AUTHORS : BRUKER BIOSPIN (XWINNMR), RIEPING, HABECK, REMARK 3 BARDIAUX, BERNARD, MALLIAVIN, AND NILGES (ARIA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2RQT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1000150175. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-15N] DDEF1 SH3-1, 20 REMARK 210 MM SODIUM PHOSPHATE-2, 50 MM REMARK 210 SODIUM CHLORIDE-3, 0.02 % SODIUM REMARK 210 AZIDE-4, 90% H2O/10% D2O; 0.7 MM REMARK 210 [U-13C; U-15N] DDEF1 SH3-5, 20 REMARK 210 MM SODIUM PHOSPHATE-6, 50 MM REMARK 210 SODIUM CHLORIDE-7, 0.02 % SODIUM REMARK 210 AZIDE-8, 90% H2O/10% D2O; 0.7 MM REMARK 210 [U-13C; U-15N] DDEF1 SH3-9, 20 REMARK 210 MM SODIUM PHOSPHATE-10, 50 MM REMARK 210 SODIUM CHLORIDE-11, 0.02 % REMARK 210 SODIUM AZIDE-12, 100% D2O; 0.7 REMARK 210 MM [U-15% 13C; U-15N] DDEF1 SH3- REMARK 210 13, 20 MM SODIUM PHOSPHATE-14, REMARK 210 50 MM SODIUM CHLORIDE-15, 0.02 % REMARK 210 SODIUM AZIDE-16, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D HNCO; 3D HN(CA)CO; REMARK 210 3D H(CCO)NH; 3D HCCH-TOCSY; 3D REMARK 210 15N-EDITED NOESY; 3D 13C-EDITED REMARK 210 NOESY; 2D 1H-13C HSQC; 2D 1H-13C REMARK 210 CT-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY 3.115, CYANA 2.1 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 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: 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 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 GLN A1112 78.52 -154.32 REMARK 500 1 SER A1128 45.11 -80.80 REMARK 500 3 GLN A1112 79.66 -150.36 REMARK 500 6 SER A1128 45.37 -99.14 REMARK 500 7 ASP A1101 -158.39 -145.26 REMARK 500 9 ARG A1070 111.39 -169.41 REMARK 500 9 GLU A1100 -55.57 -121.86 REMARK 500 11 GLN A1112 72.50 -150.97 REMARK 500 13 ASP A1101 -166.15 -129.35 REMARK 500 13 SER A1128 42.00 -88.69 REMARK 500 15 GLN A1112 90.17 -162.31 REMARK 500 15 SER A1128 39.58 -90.25 REMARK 500 19 SER A1128 47.08 -90.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RQU RELATED DB: PDB DBREF 2RQT A 1069 1129 UNP Q9ULH1 ASAP1_HUMAN 1069 1129 SEQRES 1 A 61 VAL ARG ARG VAL LYS THR ILE TYR ASP CYS GLN ALA ASP SEQRES 2 A 61 ASN ASP ASP GLU LEU THR PHE ILE GLU GLY GLU VAL ILE SEQRES 3 A 61 ILE VAL THR GLY GLU GLU ASP GLN GLU TRP TRP ILE GLY SEQRES 4 A 61 HIS ILE GLU GLY GLN PRO GLU ARG LYS GLY VAL PHE PRO SEQRES 5 A 61 VAL SER PHE VAL HIS ILE LEU SER ASP SHEET 1 A 5 GLN A1112 PRO A1120 0 SHEET 2 A 5 TRP A1104 ILE A1109 -1 N ILE A1109 O ARG A1115 SHEET 3 A 5 VAL A1093 GLU A1099 -1 N ILE A1095 O HIS A1108 SHEET 4 A 5 ARG A1071 THR A1074 -1 N VAL A1072 O ILE A1094 SHEET 5 A 5 VAL A1124 LEU A1127 -1 O LEU A1127 N ARG A1071 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