PDB Short entry for 2CQF HEADER TRANSCRIPTION 19-MAY-05 2CQF TITLE SOLUTION STRUCTURE OF THE ZINC-FINGER DOMAIN IN LIN-28 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA-BINDING PROTEIN LIN-28; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC-FINGER (130-192); COMPND 5 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: LIN28; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P041101-01; SOURCE 8 OTHER_DETAILS: CELL-FREE PROTEIN SYNTHESIS KEYWDS CCHC ZINC-FINGER, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON KEYWDS 2 PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, TRANSCRIPTION EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.SOMEYA,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA,M.SHIROUZU,S.YOKOYAMA,RIKEN AUTHOR 2 STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2CQF 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 2CQF 1 VERSN REVDAT 1 19-NOV-05 2CQF 0 JRNL AUTH T.SOMEYA,Y.MUTO,M.INOUE,T.KIGAWA,T.TERADA,M.SHIROUZU, JRNL AUTH 2 S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE ZINC-FINGER DOMAIN IN LIN-28 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 3.5, CYANA 2.0.17 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CQF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAY-05. REMARK 100 THE DEPOSITION ID IS D_1000024506. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.13MM PROTEIN U-15N,13C; 20MM D REMARK 210 -TRIS-HCL(PH7.0); 100MM NACL; REMARK 210 1MM D-DTT; 0.02% NAN3; 0.25MM REMARK 210 ZNCL2+1MM IDA; 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20030801, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.9295, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 RESTRAINTED MOLECULAR 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: 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: 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 CYS A 139 109.40 -53.49 REMARK 500 1 TYR A 140 42.27 -80.06 REMARK 500 1 ASN A 141 -56.60 -133.53 REMARK 500 1 CYS A 152 148.13 -33.66 REMARK 500 1 LEU A 154 153.02 -37.74 REMARK 500 1 GLN A 157 157.92 -41.31 REMARK 500 1 PRO A 158 6.27 -69.83 REMARK 500 1 LYS A 159 -174.82 -53.56 REMARK 500 1 HIS A 162 34.89 -90.28 REMARK 500 1 PHE A 163 -53.45 -130.34 REMARK 500 1 SER A 168 -75.17 -65.59 REMARK 500 1 CYS A 174 118.64 -35.32 REMARK 500 1 ALA A 178 37.81 -95.35 REMARK 500 2 CYS A 139 116.85 -39.45 REMARK 500 2 TYR A 140 39.72 -83.25 REMARK 500 2 ASN A 141 -61.20 -131.33 REMARK 500 2 CYS A 152 152.49 -35.33 REMARK 500 2 LEU A 154 156.11 -38.07 REMARK 500 2 GLN A 157 155.93 -46.95 REMARK 500 2 PRO A 158 9.98 -69.80 REMARK 500 2 HIS A 162 30.23 -86.78 REMARK 500 2 PHE A 163 -51.01 -123.61 REMARK 500 2 ILE A 167 -19.41 -48.14 REMARK 500 2 SER A 168 -71.92 -62.78 REMARK 500 2 CYS A 174 122.51 -34.60 REMARK 500 2 PRO A 189 3.02 -69.80 REMARK 500 3 TYR A 140 37.82 -91.34 REMARK 500 3 ASN A 141 -60.25 -128.77 REMARK 500 3 CYS A 152 153.19 -35.79 REMARK 500 3 LEU A 154 156.62 -39.24 REMARK 500 3 GLN A 157 157.63 -43.45 REMARK 500 3 PRO A 158 12.05 -69.83 REMARK 500 3 LYS A 159 170.40 -44.89 REMARK 500 3 HIS A 162 32.95 -85.73 REMARK 500 3 PHE A 163 -55.53 -129.07 REMARK 500 3 CYS A 174 113.09 -38.36 REMARK 500 4 TYR A 140 38.87 -90.93 REMARK 500 4 ASN A 141 -55.90 -130.15 REMARK 500 4 CYS A 152 145.51 -33.93 REMARK 500 4 LEU A 154 157.93 -38.30 REMARK 500 4 PRO A 158 7.55 -69.76 REMARK 500 4 LYS A 159 -175.65 -51.06 REMARK 500 4 CYS A 161 126.63 -36.09 REMARK 500 4 HIS A 162 37.23 -92.22 REMARK 500 4 PHE A 163 -52.59 -132.10 REMARK 500 4 SER A 168 -71.91 -52.14 REMARK 500 4 CYS A 174 113.96 -37.74 REMARK 500 4 GLN A 179 47.57 -79.70 REMARK 500 5 SER A 131 85.59 -65.25 REMARK 500 5 TYR A 140 37.99 -87.06 REMARK 500 REMARK 500 THIS ENTRY HAS 274 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 330 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 139 SG REMARK 620 2 CYS A 142 SG 112.1 REMARK 620 3 HIS A 147 NE2 116.5 99.6 REMARK 620 4 CYS A 152 SG 118.2 118.5 88.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 530 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 161 SG REMARK 620 2 CYS A 164 SG 119.2 REMARK 620 3 HIS A 169 NE2 105.9 92.4 REMARK 620 4 CYS A 174 SG 118.9 119.0 88.4 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 330 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 530 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HSI002013570.1 RELATED DB: TARGETDB DBREF 2CQF A 137 186 UNP Q9H9Z2 Q9H9Z2_HUMAN 137 186 SEQADV 2CQF GLY A 130 UNP Q9H9Z2 CLONING ARTIFACT SEQADV 2CQF SER A 131 UNP Q9H9Z2 CLONING ARTIFACT SEQADV 2CQF SER A 132 UNP Q9H9Z2 CLONING ARTIFACT SEQADV 2CQF GLY A 133 UNP Q9H9Z2 CLONING ARTIFACT SEQADV 2CQF SER A 134 UNP Q9H9Z2 CLONING ARTIFACT SEQADV 2CQF SER A 135 UNP Q9H9Z2 CLONING ARTIFACT SEQADV 2CQF GLY A 136 UNP Q9H9Z2 CLONING ARTIFACT SEQADV 2CQF SER A 187 UNP Q9H9Z2 CLONING ARTIFACT SEQADV 2CQF GLY A 188 UNP Q9H9Z2 CLONING ARTIFACT SEQADV 2CQF PRO A 189 UNP Q9H9Z2 CLONING ARTIFACT SEQADV 2CQF SER A 190 UNP Q9H9Z2 CLONING ARTIFACT SEQADV 2CQF SER A 191 UNP Q9H9Z2 CLONING ARTIFACT SEQADV 2CQF GLY A 192 UNP Q9H9Z2 CLONING ARTIFACT SEQRES 1 A 63 GLY SER SER GLY SER SER GLY ASP ARG CYS TYR ASN CYS SEQRES 2 A 63 GLY GLY LEU ASP HIS HIS ALA LYS GLU CYS LYS LEU PRO SEQRES 3 A 63 PRO GLN PRO LYS LYS CYS HIS PHE CYS GLN SER ILE SER SEQRES 4 A 63 HIS MET VAL ALA SER CYS PRO LEU LYS ALA GLN GLN GLY SEQRES 5 A 63 PRO SER ALA GLN GLY SER GLY PRO SER SER GLY HET ZN A 330 1 HET ZN A 530 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) LINK SG CYS A 139 ZN ZN A 330 1555 1555 2.33 LINK SG CYS A 142 ZN ZN A 330 1555 1555 2.33 LINK NE2 HIS A 147 ZN ZN A 330 1555 1555 2.37 LINK SG CYS A 152 ZN ZN A 330 1555 1555 2.33 LINK SG CYS A 161 ZN ZN A 530 1555 1555 2.32 LINK SG CYS A 164 ZN ZN A 530 1555 1555 2.32 LINK NE2 HIS A 169 ZN ZN A 530 1555 1555 2.33 LINK SG CYS A 174 ZN ZN A 530 1555 1555 2.32 SITE 1 AC1 4 CYS A 139 CYS A 142 HIS A 147 CYS A 152 SITE 1 AC2 4 CYS A 161 CYS A 164 HIS A 169 CYS A 174 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