HEADER TRANSCRIPTION REGULATION 17-FEB-96 1PYC TITLE CYP1 (HAP1) DNA-BINDING DOMAIN (RESIDUES 60-100), NMR, 15 STRUCTURES COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYP1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 56 - 126; COMPND 5 SYNONYM: HAP1 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932 KEYWDS TRANSCRIPTION REGULATION, ACTIVATOR, DNA-BINDING, NUCLEAR PROTEIN, KEYWDS 2 ZINC, METAL-BINDING, HEME EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR J.TIMMERMAN,A.-L.VUIDEPOT,F.BONTEMS,J.-Y.LALLEMAND,M.GERVAIS, AUTHOR 2 E.SHECHTER,B.GUIARD REVDAT 3 02-MAR-22 1PYC 1 REMARK LINK REVDAT 2 24-FEB-09 1PYC 1 VERSN REVDAT 1 01-AUG-96 1PYC 0 JRNL AUTH J.TIMMERMAN,A.L.VUIDEPOT,F.BONTEMS,J.Y.LALLEMAND,M.GERVAIS, JRNL AUTH 2 E.SHECHTER,B.GUIARD JRNL TITL 1H, 15N RESONANCE ASSIGNMENT AND THREE-DIMENSIONAL STRUCTURE JRNL TITL 2 OF CYP1 (HAP1) DNA-BINDING DOMAIN. JRNL REF J.MOL.BIOL. V. 259 792 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8683583 JRNL DOI 10.1006/JMBI.1996.0358 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.E.TIMMERMAN,B.GUIARD,E.SHECHTER,M.A.DELSUC,J.Y.LALLEMAND, REMARK 1 AUTH 2 M.GERVAIS REMARK 1 TITL THE DNA-BINDING DOMAIN OF THE YEAST SACCHAROMYCES CEREVISIAE REMARK 1 TITL 2 CYP1(HAP1) TRANSCRIPTION FACTOR POSSESSES TWO ZINC IONS REMARK 1 TITL 3 WHICH ARE COMPLEXED IN A ZINC CLUSTER REMARK 1 REF EUR.J.BIOCHEM. V. 225 593 1994 REMARK 1 REFN ISSN 0014-2956 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PYC COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000175876. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : NULL REMARK 210 PH : NULL REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : NULL REMARK 210 SPECTROMETER MODEL : NULL REMARK 210 SPECTROMETER MANUFACTURER : NULL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : NULL REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-15 REMARK 465 RES C SSSEQI REMARK 465 LYS A 56 REMARK 465 ARG A 57 REMARK 465 ASN A 58 REMARK 465 ARG A 59 REMARK 465 ALA A 101 REMARK 465 GLU A 102 REMARK 465 GLU A 103 REMARK 465 ALA A 104 REMARK 465 GLU A 105 REMARK 465 LYS A 106 REMARK 465 GLU A 107 REMARK 465 LEU A 108 REMARK 465 LEU A 109 REMARK 465 LYS A 110 REMARK 465 ASP A 111 REMARK 465 ASN A 112 REMARK 465 GLU A 113 REMARK 465 LEU A 114 REMARK 465 LYS A 115 REMARK 465 LYS A 116 REMARK 465 LEU A 117 REMARK 465 ARG A 118 REMARK 465 GLU A 119 REMARK 465 ARG A 120 REMARK 465 VAL A 121 REMARK 465 LYS A 122 REMARK 465 SER A 123 REMARK 465 LEU A 124 REMARK 465 GLU A 125 REMARK 465 LYS A 126 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 VAL A 89 CA - CB - CG2 ANGL. DEV. = 17.3 DEGREES REMARK 500 2 TYR A 95 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 3 TYR A 95 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 5 VAL A 89 CA - CB - CG1 ANGL. DEV. = -14.6 DEGREES REMARK 500 5 VAL A 89 CA - CB - CG2 ANGL. DEV. = 12.1 DEGREES REMARK 500 5 TYR A 95 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 6 VAL A 89 CA - CB - CG2 ANGL. DEV. = 16.8 DEGREES REMARK 500 7 VAL A 89 CA - CB - CG1 ANGL. DEV. = -11.3 DEGREES REMARK 500 8 VAL A 89 CG1 - CB - CG2 ANGL. DEV. = -10.5 DEGREES REMARK 500 8 VAL A 89 CA - CB - CG1 ANGL. DEV. = -12.9 DEGREES REMARK 500 8 VAL A 89 CA - CB - CG2 ANGL. DEV. = 17.1 DEGREES REMARK 500 11 VAL A 89 CA - CB - CG2 ANGL. DEV. = 18.1 DEGREES REMARK 500 11 TYR A 95 CB - CG - CD1 ANGL. DEV. = -3.7 DEGREES REMARK 500 12 VAL A 89 CA - CB - CG2 ANGL. DEV. = 16.1 DEGREES REMARK 500 13 VAL A 89 CG1 - CB - CG2 ANGL. DEV. = 13.0 DEGREES REMARK 500 14 VAL A 89 CA - CB - CG1 ANGL. DEV. = -13.7 DEGREES REMARK 500 14 VAL A 89 CA - CB - CG2 ANGL. DEV. = 13.0 DEGREES REMARK 500 15 VAL A 89 CA - CB - CG1 ANGL. DEV. = -11.2 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 LYS A 71 64.17 73.87 REMARK 500 2 LYS A 71 72.60 72.46 REMARK 500 2 LYS A 76 43.23 70.40 REMARK 500 2 GLU A 97 -52.13 -128.55 REMARK 500 2 THR A 99 -21.18 -142.87 REMARK 500 3 LYS A 71 55.90 75.66 REMARK 500 3 LYS A 76 31.22 75.55 REMARK 500 3 VAL A 89 42.36 -102.37 REMARK 500 3 GLU A 97 114.01 74.32 REMARK 500 4 LYS A 71 60.73 73.41 REMARK 500 4 VAL A 89 40.50 -100.58 REMARK 500 5 LEU A 62 156.65 72.51 REMARK 500 5 LYS A 71 78.59 74.85 REMARK 500 5 LYS A 76 70.05 69.11 REMARK 500 5 ARG A 78 129.00 59.90 REMARK 500 5 VAL A 89 42.14 -96.76 REMARK 500 6 LYS A 71 74.98 71.92 REMARK 500 7 LYS A 71 58.60 71.74 REMARK 500 7 LYS A 76 52.87 75.61 REMARK 500 7 ARG A 78 115.69 75.75 REMARK 500 7 VAL A 89 41.08 -109.22 REMARK 500 7 GLU A 97 -107.76 67.21 REMARK 500 8 LYS A 71 80.48 75.45 REMARK 500 8 VAL A 89 54.57 -115.61 REMARK 500 8 GLU A 97 86.47 69.69 REMARK 500 9 LYS A 71 55.95 71.18 REMARK 500 9 ASP A 75 -110.01 -133.95 REMARK 500 9 LYS A 76 22.32 177.39 REMARK 500 9 VAL A 89 48.80 -107.45 REMARK 500 10 LYS A 71 76.49 67.52 REMARK 500 10 VAL A 89 41.77 -102.04 REMARK 500 11 LYS A 71 58.65 74.52 REMARK 500 11 LYS A 76 37.33 73.16 REMARK 500 12 LYS A 71 78.35 73.36 REMARK 500 12 ARG A 78 128.23 93.96 REMARK 500 12 VAL A 89 31.83 -147.80 REMARK 500 13 LYS A 71 58.76 79.45 REMARK 500 13 LYS A 76 39.00 72.86 REMARK 500 14 LYS A 71 80.19 74.36 REMARK 500 14 ASP A 75 -47.63 -135.69 REMARK 500 14 LYS A 76 73.51 47.06 REMARK 500 14 ARG A 78 136.06 72.57 REMARK 500 14 VAL A 89 49.01 -109.42 REMARK 500 14 GLU A 97 117.91 60.12 REMARK 500 15 LEU A 62 162.67 70.66 REMARK 500 15 LYS A 71 56.78 73.11 REMARK 500 15 ASP A 75 -83.19 -150.01 REMARK 500 15 LYS A 76 -17.99 167.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 CYS A 74 ASP A 75 5 -140.36 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 95 0.08 SIDE CHAIN REMARK 500 8 TYR A 95 0.09 SIDE CHAIN REMARK 500 12 TYR A 95 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 127 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 64 SG REMARK 620 2 CYS A 67 SG 77.0 REMARK 620 3 CYS A 74 SG 104.2 119.6 REMARK 620 4 CYS A 81 SG 108.5 132.4 105.1 REMARK 620 5 ZN A 128 ZN 56.6 96.9 134.9 56.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 128 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 64 SG REMARK 620 2 CYS A 81 SG 108.4 REMARK 620 3 CYS A 84 SG 109.6 120.1 REMARK 620 4 CYS A 93 SG 115.7 93.0 109.7 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 127 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 128 DBREF 1PYC A 56 126 UNP P12351 CYP1_YEAST 56 126 SEQRES 1 A 71 LYS ARG ASN ARG ILE PRO LEU SER CYS THR ILE CYS ARG SEQRES 2 A 71 LYS ARG LYS VAL LYS CYS ASP LYS LEU ARG PRO HIS CYS SEQRES 3 A 71 GLN GLN CYS THR LYS THR GLY VAL ALA HIS LEU CYS HIS SEQRES 4 A 71 TYR MET GLU GLN THR TRP ALA GLU GLU ALA GLU LYS GLU SEQRES 5 A 71 LEU LEU LYS ASP ASN GLU LEU LYS LYS LEU ARG GLU ARG SEQRES 6 A 71 VAL LYS SER LEU GLU LYS HET ZN A 127 1 HET ZN A 128 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 THR A 65 ARG A 70 1 6 HELIX 2 2 GLN A 82 THR A 87 1 6 LINK SG CYS A 64 ZN ZN A 127 1555 1555 2.50 LINK SG CYS A 64 ZN ZN A 128 1555 1555 2.50 LINK SG CYS A 67 ZN ZN A 127 1555 1555 2.50 LINK SG CYS A 74 ZN ZN A 127 1555 1555 2.50 LINK SG CYS A 81 ZN ZN A 127 1555 1555 2.50 LINK SG CYS A 81 ZN ZN A 128 1555 1555 2.50 LINK SG CYS A 84 ZN ZN A 128 1555 1555 2.50 LINK SG CYS A 93 ZN ZN A 128 1555 1555 2.50 LINK ZN ZN A 127 ZN ZN A 128 1555 1555 2.76 CISPEP 1 ARG A 78 PRO A 79 1 4.75 CISPEP 2 ARG A 78 PRO A 79 2 -11.56 CISPEP 3 ARG A 78 PRO A 79 3 -8.83 CISPEP 4 ARG A 78 PRO A 79 4 -9.99 CISPEP 5 ARG A 78 PRO A 79 5 11.67 CISPEP 6 ARG A 78 PRO A 79 6 -15.05 CISPEP 7 ARG A 78 PRO A 79 7 10.16 CISPEP 8 ARG A 78 PRO A 79 8 -4.94 CISPEP 9 ARG A 78 PRO A 79 9 -11.67 CISPEP 10 ARG A 78 PRO A 79 10 -8.01 CISPEP 11 ARG A 78 PRO A 79 11 -3.14 CISPEP 12 ARG A 78 PRO A 79 12 -4.40 CISPEP 13 ARG A 78 PRO A 79 13 -2.02 CISPEP 14 ARG A 78 PRO A 79 14 4.02 CISPEP 15 ARG A 78 PRO A 79 15 -13.56 SITE 1 AC1 5 CYS A 64 CYS A 67 CYS A 74 CYS A 81 SITE 2 AC1 5 ZN A 128 SITE 1 AC2 5 CYS A 64 CYS A 81 CYS A 84 CYS A 93 SITE 2 AC2 5 ZN A 127 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 MODEL 1