PDB Short entry for 2DLQ HEADER TRANSCRIPTION 20-APR-06 2DLQ TITLE SOLUTION STRUCTURE OF THE TANDEM FOUR ZF-C2H2 DOMAIN REPEATS OF MURINE TITLE 2 GLI-KRUPPEL FAMILY MEMBER HKR3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLI-KRUPPEL FAMILY MEMBER HKR3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZF-C2H2 DOMAIN, RESIDUES 8-118; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: HKR3; SOURCE 6 EXPRESSION_SYSTEM: CELL FREE SYNTHESIS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: P050302-67; SOURCE 9 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS ZF-C2H2 DOMAIN, GLI-KRUPPEL FAMILY MEMBER HKR3, HKR3, STRUCTURAL KEYWDS 2 GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND KEYWDS 3 FUNCTIONAL ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS KEYWDS 4 INITIATIVE, RSGI, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.INOUE,F.HAYASHI,K.IZUMI,M.YOSHIDA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2DLQ 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2DLQ 1 VERSN REVDAT 1 20-OCT-06 2DLQ 0 JRNL AUTH K.INOUE,F.HAYASHI,K.IZUMI,M.YOSHIDA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE TANDEM FOUR ZF-C2H2 DOMAIN REPEATS JRNL TITL 2 OF MURINE GLI-KRUPPEL FAMILY MEMBER HKR3 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CYANA 2.0.17 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2DLQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000025561. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.20MM U-15N, 13C-LABELED REMARK 210 PROTEIN; 20MM D-TRIS-HCL; 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; REMARK 210 50UM ZNCL2+1MM IDA; 10% D2O, 90% REMARK 210 H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.93191, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION, STRUCTURES WITH REMARK 210 THE LOWEST ENERGY, STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: SPECTROMETER_ID 1 FOR 3D_15N_SEPARATED_NOESY; REMARK 210 SPECTROMETER_ID 2 FOR 3D_13C_SEPARATED_NOESY; 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: 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 PRO A 11 9.87 -69.79 REMARK 500 1 MET A 60 129.58 -34.23 REMARK 500 1 ASN A 61 116.79 -172.16 REMARK 500 1 ARG A 62 103.49 -34.53 REMARK 500 1 GLN A 65 107.95 -53.57 REMARK 500 1 CYS A 69 177.16 -57.77 REMARK 500 1 GLU A 74 -173.55 -62.50 REMARK 500 1 SER A 101 30.69 74.92 REMARK 500 1 GLN A 102 -174.51 -63.80 REMARK 500 1 SER A 123 42.25 -103.83 REMARK 500 2 PRO A 11 4.48 -69.78 REMARK 500 2 LYS A 34 98.82 -33.21 REMARK 500 2 PRO A 35 6.09 -69.74 REMARK 500 2 GLU A 37 130.18 -172.45 REMARK 500 2 PRO A 39 1.56 -69.74 REMARK 500 2 GLU A 64 -177.18 -64.74 REMARK 500 2 CYS A 69 172.67 -50.88 REMARK 500 2 VAL A 71 -45.56 -133.36 REMARK 500 2 GLU A 74 -173.59 -55.60 REMARK 500 2 GLN A 102 -174.84 -64.73 REMARK 500 2 HIS A 118 34.76 -89.91 REMARK 500 3 SER A 2 157.84 -48.78 REMARK 500 3 PRO A 11 11.68 -69.78 REMARK 500 3 LYS A 34 151.20 -42.62 REMARK 500 3 PRO A 39 0.92 -69.73 REMARK 500 3 TYR A 45 107.85 -167.72 REMARK 500 3 MET A 60 153.65 -42.99 REMARK 500 3 CYS A 69 172.25 -56.80 REMARK 500 3 GLU A 74 -174.87 -57.41 REMARK 500 3 GLN A 102 -174.29 -69.09 REMARK 500 3 HIS A 118 39.96 -90.44 REMARK 500 3 SER A 119 49.21 -75.98 REMARK 500 3 SER A 123 139.12 -170.86 REMARK 500 4 PRO A 11 5.05 -69.77 REMARK 500 4 GLU A 37 123.15 -170.91 REMARK 500 4 CYS A 38 105.74 -36.37 REMARK 500 4 PRO A 39 2.10 -69.74 REMARK 500 4 TYR A 45 114.62 -165.10 REMARK 500 4 ARG A 57 -70.26 -54.16 REMARK 500 4 GLN A 65 104.41 -45.56 REMARK 500 4 CYS A 69 172.39 -53.34 REMARK 500 4 VAL A 71 -44.56 -134.13 REMARK 500 4 GLU A 74 -173.60 -56.15 REMARK 500 4 GLN A 102 -173.69 -60.75 REMARK 500 4 HIS A 118 34.15 -90.69 REMARK 500 4 SER A 119 -71.19 -61.78 REMARK 500 5 PRO A 11 6.36 -69.76 REMARK 500 5 PRO A 39 0.68 -69.74 REMARK 500 5 GLN A 102 -175.14 -65.37 REMARK 500 5 HIS A 118 35.42 -87.42 REMARK 500 REMARK 500 THIS ENTRY HAS 217 RAMACHANDRAN OUTLIERS. 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 200 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 10 SG REMARK 620 2 CYS A 13 SG 109.4 REMARK 620 3 HIS A 26 NE2 107.0 104.2 REMARK 620 4 HIS A 30 NE2 104.7 114.2 117.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 300 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 38 SG REMARK 620 2 CYS A 41 SG 103.2 REMARK 620 3 HIS A 54 NE2 104.7 105.0 REMARK 620 4 CYS A 59 SG 114.7 111.3 116.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 400 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 69 SG REMARK 620 2 CYS A 72 SG 113.6 REMARK 620 3 HIS A 85 NE2 102.9 107.5 REMARK 620 4 HIS A 89 NE2 109.0 109.7 114.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 500 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 97 SG REMARK 620 2 CYS A 100 SG 108.8 REMARK 620 3 HIS A 113 NE2 104.7 106.0 REMARK 620 4 HIS A 118 NE2 104.6 115.4 116.7 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 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 500 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: MMI002017035.1 RELATED DB: TARGETDB DBREF 2DLQ A 8 118 UNP Q99K15 Q99K15_MOUSE 284 394 SEQADV 2DLQ GLY A 1 UNP Q99K15 CLONING ARTIFACT SEQADV 2DLQ SER A 2 UNP Q99K15 CLONING ARTIFACT SEQADV 2DLQ SER A 3 UNP Q99K15 CLONING ARTIFACT SEQADV 2DLQ GLY A 4 UNP Q99K15 CLONING ARTIFACT SEQADV 2DLQ SER A 5 UNP Q99K15 CLONING ARTIFACT SEQADV 2DLQ SER A 6 UNP Q99K15 CLONING ARTIFACT SEQADV 2DLQ GLY A 7 UNP Q99K15 CLONING ARTIFACT SEQADV 2DLQ SER A 119 UNP Q99K15 CLONING ARTIFACT SEQADV 2DLQ GLY A 120 UNP Q99K15 CLONING ARTIFACT SEQADV 2DLQ PRO A 121 UNP Q99K15 CLONING ARTIFACT SEQADV 2DLQ SER A 122 UNP Q99K15 CLONING ARTIFACT SEQADV 2DLQ SER A 123 UNP Q99K15 CLONING ARTIFACT SEQADV 2DLQ GLY A 124 UNP Q99K15 CLONING ARTIFACT SEQRES 1 A 124 GLY SER SER GLY SER SER GLY VAL GLU CYS PRO THR CYS SEQRES 2 A 124 HIS LYS LYS PHE LEU SER LYS TYR TYR LEU LYS VAL HIS SEQRES 3 A 124 ASN ARG LYS HIS THR GLY GLU LYS PRO PHE GLU CYS PRO SEQRES 4 A 124 LYS CYS GLY LYS CYS TYR PHE ARG LYS GLU ASN LEU LEU SEQRES 5 A 124 GLU HIS GLU ALA ARG ASN CYS MET ASN ARG SER GLU GLN SEQRES 6 A 124 VAL PHE THR CYS SER VAL CYS GLN GLU THR PHE ARG ARG SEQRES 7 A 124 ARG MET GLU LEU ARG LEU HIS MET VAL SER HIS THR GLY SEQRES 8 A 124 GLU MET PRO TYR LYS CYS SER SER CYS SER GLN GLN PHE SEQRES 9 A 124 MET GLN LYS LYS ASP LEU GLN SER HIS MET ILE LYS LEU SEQRES 10 A 124 HIS SER GLY PRO SER SER GLY HET ZN A 200 1 HET ZN A 300 1 HET ZN A 400 1 HET ZN A 500 1 HETNAM ZN ZINC ION FORMUL 2 ZN 4(ZN 2+) HELIX 1 1 SER A 19 THR A 31 1 13 HELIX 2 2 ARG A 47 ASN A 58 1 12 HELIX 3 3 ARG A 78 THR A 90 1 13 HELIX 4 4 GLN A 106 LEU A 117 1 12 SHEET 1 A 2 PHE A 67 THR A 68 0 SHEET 2 A 2 THR A 75 PHE A 76 -1 O PHE A 76 N PHE A 67 SHEET 1 B 2 TYR A 95 LYS A 96 0 SHEET 2 B 2 GLN A 103 PHE A 104 -1 O PHE A 104 N TYR A 95 LINK SG CYS A 10 ZN ZN A 200 1555 1555 2.36 LINK SG CYS A 13 ZN ZN A 200 1555 1555 2.36 LINK NE2 HIS A 26 ZN ZN A 200 1555 1555 2.05 LINK NE2 HIS A 30 ZN ZN A 200 1555 1555 2.05 LINK SG CYS A 38 ZN ZN A 300 1555 1555 2.36 LINK SG CYS A 41 ZN ZN A 300 1555 1555 2.36 LINK NE2 HIS A 54 ZN ZN A 300 1555 1555 2.06 LINK SG CYS A 59 ZN ZN A 300 1555 1555 2.06 LINK SG CYS A 69 ZN ZN A 400 1555 1555 2.37 LINK SG CYS A 72 ZN ZN A 400 1555 1555 2.23 LINK NE2 HIS A 85 ZN ZN A 400 1555 1555 2.08 LINK NE2 HIS A 89 ZN ZN A 400 1555 1555 2.06 LINK SG CYS A 97 ZN ZN A 500 1555 1555 2.36 LINK SG CYS A 100 ZN ZN A 500 1555 1555 2.32 LINK NE2 HIS A 113 ZN ZN A 500 1555 1555 2.06 LINK NE2 HIS A 118 ZN ZN A 500 1555 1555 2.06 SITE 1 AC1 4 CYS A 10 CYS A 13 HIS A 26 HIS A 30 SITE 1 AC2 4 CYS A 38 CYS A 41 HIS A 54 CYS A 59 SITE 1 AC3 4 CYS A 69 CYS A 72 HIS A 85 HIS A 89 SITE 1 AC4 4 CYS A 97 CYS A 100 HIS A 113 HIS A 118 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