PDB Short entry for 1RYU HEADER DNA BINDING PROTEIN 22-DEC-03 1RYU TITLE SOLUTION STRUCTURE OF THE SWI1 ARID COMPND MOL_ID: 1; COMPND 2 MOLECULE: SWI/SNF-RELATED, MATRIX-ASSOCIATED, ACTIN-DEPENDENT COMPND 3 REGULATOR OF CHROMATIN SUBFAMILY F MEMBER 1; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: SWI1 ARID (RESIDUES 617-736); COMPND 6 SYNONYM: SWI-SNF COMPLEX PROTEIN P270, B120; COMPND 7 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: BL21DE3; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS ARID, SWI1, STRUCTURAL GENOMICS, PROTEIN-DNA INTERACTION, DNA BINDING KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 8 MDLTYP MINIMIZED AVERAGE AUTHOR S.KIM,Z.ZHANG,S.UPCHURCH,N.ISERN,Y.CHEN REVDAT 3 02-MAR-22 1RYU 1 REMARK REVDAT 2 24-FEB-09 1RYU 1 VERSN REVDAT 1 25-MAY-04 1RYU 0 JRNL AUTH S.KIM,Z.ZHANG,S.UPCHURCH,N.ISERN,Y.CHEN JRNL TITL STRUCTURE AND DNA-BINDING SITES OF THE SWI1 AT-RICH JRNL TITL 2 INTERACTION DOMAIN (ARID) SUGGEST DETERMINANTS FOR JRNL TITL 3 SEQUENCE-SPECIFIC DNA RECOGNITION. JRNL REF J.BIOL.CHEM. V. 279 16670 2004 JRNL REFN ISSN 0021-9258 JRNL PMID 14722072 JRNL DOI 10.1074/JBC.M312115200 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 1.2 REMARK 3 AUTHORS : JENS LINGE, SEAN O'DONOGHUE, MICHAEL NILGES REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1RYU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-DEC-03. REMARK 100 THE DEPOSITION ID IS D_1000021160. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 100MM PHOSPHATE BUFFER REMARK 210 PRESSURE : 1 ATMOSPHERE REMARK 210 SAMPLE CONTENTS : APPROXIMATELY 1MM N15/C13 REMARK 210 LABELED PROTEIN IN 100MM REMARK 210 PHOSPHATE BUFFER, PH 6.0 AND 5MM REMARK 210 DTT, 100% D2O; APPROXIMATELY 1MM REMARK 210 N15/C13 LABELED PROTEIN IN 100MM REMARK 210 PHOSPHATE BUFFER, PH 6.0 AND 5MM REMARK 210 DTT, 90%H2O/10%D2O; REMARK 210 APPROXIMATELY 1MM N15 LABELED REMARK 210 PROTEIN IN 100MM PHOSPHATE REMARK 210 BUFFER, PH 6.0 AND 5MM DTT, 90% REMARK 210 H2O/10%D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; HCCH REMARK 210 -TOCSY; HNCACB, C(CO)NH, HNCO, REMARK 210 HN(CA)CO, H(CCO)NH; 3D_15N- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS; INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : VNMR 6.1, FELIX 98,2000, DYANA REMARK 210 1.5 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 8 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 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 3 TYR A 56 CE1 TYR A 56 CZ 0.097 REMARK 500 3 TYR A 56 CZ TYR A 56 CE2 -0.102 REMARK 500 7 TYR A 56 CE1 TYR A 56 CZ 0.107 REMARK 500 7 TYR A 56 CZ TYR A 56 CE2 -0.113 REMARK 500 8 TYR A 56 CE1 TYR A 56 CZ 0.114 REMARK 500 8 TYR A 56 CZ TYR A 56 CE2 -0.118 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 SER A 2 -77.83 -54.96 REMARK 500 1 THR A 3 -172.95 56.42 REMARK 500 1 ASN A 6 3.49 -67.11 REMARK 500 1 THR A 10 -24.78 -158.44 REMARK 500 1 GLU A 14 98.99 -162.46 REMARK 500 1 LEU A 42 -52.67 -140.27 REMARK 500 1 PRO A 43 29.81 -79.10 REMARK 500 1 ARG A 47 -94.66 -80.32 REMARK 500 1 PRO A 49 -127.59 -66.86 REMARK 500 1 LYS A 70 5.78 -152.29 REMARK 500 1 ASN A 82 93.94 54.01 REMARK 500 1 SER A 86 -78.41 -69.49 REMARK 500 1 SER A 87 -57.39 -156.19 REMARK 500 1 LEU A 101 -123.44 -91.72 REMARK 500 1 TYR A 102 -88.41 56.64 REMARK 500 1 ILE A 108 -22.61 -140.75 REMARK 500 1 PRO A 114 102.39 -23.46 REMARK 500 1 PRO A 115 96.46 -29.85 REMARK 500 1 PRO A 116 64.44 -68.95 REMARK 500 1 ASP A 117 18.75 51.58 REMARK 500 1 ILE A 118 83.99 -55.09 REMARK 500 1 PHE A 119 18.62 57.86 REMARK 500 2 SER A 2 -44.31 -137.87 REMARK 500 2 THR A 3 91.18 49.90 REMARK 500 2 THR A 10 -3.90 -169.31 REMARK 500 2 GLU A 14 -74.22 -116.50 REMARK 500 2 LEU A 15 -80.97 63.32 REMARK 500 2 THR A 40 -162.61 -100.48 REMARK 500 2 LEU A 42 -56.48 -133.72 REMARK 500 2 PRO A 43 32.62 -69.67 REMARK 500 2 ARG A 47 -123.53 -70.91 REMARK 500 2 PRO A 49 -101.74 -54.15 REMARK 500 2 ASP A 51 46.83 -76.66 REMARK 500 2 THR A 85 -73.15 68.18 REMARK 500 2 SER A 86 -94.84 20.61 REMARK 500 2 SER A 87 -47.04 -159.78 REMARK 500 2 LEU A 101 38.35 -164.45 REMARK 500 2 ASP A 113 -54.70 -133.60 REMARK 500 2 ASP A 117 -63.07 -176.32 REMARK 500 2 ILE A 118 -167.90 45.13 REMARK 500 3 THR A 10 5.77 -169.29 REMARK 500 3 LEU A 15 -75.87 -114.12 REMARK 500 3 ALA A 36 17.66 59.72 REMARK 500 3 THR A 40 -157.55 -97.86 REMARK 500 3 ARG A 47 -92.09 -110.46 REMARK 500 3 PRO A 49 -102.13 -57.12 REMARK 500 3 THR A 85 -148.25 -135.69 REMARK 500 3 SER A 86 91.93 -45.30 REMARK 500 3 SER A 87 -158.75 179.18 REMARK 500 3 ASP A 113 94.82 59.30 REMARK 500 REMARK 500 THIS ENTRY HAS 123 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 6 TYR A 13 0.06 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1RYU A 1 120 UNP O14497 ARI1A_HUMAN 617 736 SEQRES 1 A 120 SER SER THR THR THR ASN GLU LYS ILE THR LYS LEU TYR SEQRES 2 A 120 GLU LEU GLY GLY GLU PRO GLU ARG LYS MET TRP VAL ASP SEQRES 3 A 120 ARG TYR LEU ALA PHE THR GLU GLU LYS ALA MET GLY MET SEQRES 4 A 120 THR ASN LEU PRO ALA VAL GLY ARG LYS PRO LEU ASP LEU SEQRES 5 A 120 TYR ARG LEU TYR VAL SER VAL LYS GLU ILE GLY GLY LEU SEQRES 6 A 120 THR GLN VAL ASN LYS ASN LYS LYS TRP ARG GLU LEU ALA SEQRES 7 A 120 THR ASN LEU ASN VAL GLY THR SER SER SER ALA ALA SER SEQRES 8 A 120 SER LEU LYS LYS GLN TYR ILE GLN CYS LEU TYR ALA PHE SEQRES 9 A 120 GLU CYS LYS ILE GLU ARG GLY GLU ASP PRO PRO PRO ASP SEQRES 10 A 120 ILE PHE ALA HELIX 1 1 THR A 10 GLU A 14 5 5 HELIX 2 2 GLU A 18 LYS A 35 1 18 HELIX 3 3 ASP A 51 GLY A 63 1 13 HELIX 4 4 THR A 66 LYS A 70 5 5 HELIX 5 5 LYS A 72 LEU A 81 1 10 HELIX 6 6 SER A 87 LEU A 101 1 15 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