HEADER LIGASE 20-MAY-06 2DQ5 TITLE SOLUTION STRUCTURE OF THE MID1 B BOX2 CHC(D/C)C2H2 ZINC-BINDING TITLE 2 DOMAIN: INSIGHTS INTO AN EVOLUTIONARY CONSERVED RING FOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: MIDLINE-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: BBOX2 DOMAIN; COMPND 5 SYNONYM: TRIPARTITE MOTIF PROTEIN 18, PUTATIVE TRANSCRIPTION FACTOR COMPND 6 XPRF, MIDIN, RING FINGER PROTEIN 59, MIDLINE 1 RING FINGER PROTEIN; COMPND 7 EC: 6.3.2.-; COMPND 8 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: MID1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T2 KEYWDS E3 LIGASE, RING LIKE, ZINC COORDINATION, LIGASE EXPDTA SOLUTION NMR NUMMDL 16 AUTHOR M.A.MASSIAH,J.A.B.MATTS,K.M.SHORT,B.N.SIMMONS,S.SINGIREDDY,J.ZOU, AUTHOR 2 T.C.COX REVDAT 5 09-MAR-22 2DQ5 1 REMARK LINK REVDAT 4 24-FEB-09 2DQ5 1 VERSN REVDAT 3 29-MAY-07 2DQ5 3 ATOM REVDAT 2 29-MAY-07 2DQ5 1 JRNL REVDAT 1 03-APR-07 2DQ5 0 JRNL AUTH M.A.MASSIAH,J.A.B.MATTS,K.M.SHORT,B.N.SIMMONS,S.SINGIREDDY, JRNL AUTH 2 Z.YI,T.C.COX JRNL TITL SOLUTION STRUCTURE OF THE MID1 B-BOX2 CHC(D/C)C(2)H(2) JRNL TITL 2 ZINC-BINDING DOMAIN: INSIGHTS INTO AN EVOLUTIONARILY JRNL TITL 3 CONSERVED RING FOLD JRNL REF J.MOL.BIOL. V. 369 1 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17428496 JRNL DOI 10.1016/J.JMB.2007.03.017 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, CYANA 2.1 REMARK 3 AUTHORS : DELAGLIO, F., GRZESIEK, S., VUISTER, G.W., ZHU, G. REMARK 3 PFEIFER, J., BAX, A. (NMRPIPE), GUENTERT, P. REMARK 3 (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A TOTAL OF 200 RANDOM STRUCTURES WERE REMARK 3 CALCULATED WITH CYANA2.1 USING A FAST TORSION ANGLE DYNAMICS REMARK 3 ALGORITHM AND THE BEST STRUCTURES WERE SELECTED BASED ON THEIR REMARK 3 LOW TARGET FUNCTION (LESS 1), NO NOE VIOLATION LESS THAN 0.2 ANG, REMARK 3 VDW < 0.25, DIHEDRAL <3O. REMARK 4 REMARK 4 2DQ5 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000025710. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 294 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 50MM TRIS-HCL; 100MM NACL; 5MM REMARK 210 ZNCL2, 10MM BETA-MERCAPTOETHANOL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.75-1.0MM 15N & 15N/13C LABELED REMARK 210 BBOX2; 50MM TRIS-HCL, 100MM NACL, REMARK 210 1MM ZNCL2, 10MM BETA- REMARK 210 MERCAPTOETHANOL; 2% SODIUM AZIDE; REMARK 210 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 15N-H1 HSQC; HNCA AND HNCACB; 3D REMARK 210 -1H-15N-15N-HSQC-NOESY-HSQC; 1H- REMARK 210 15N-NOESY-HSQC AND 1H-13C-NOESY- REMARK 210 HSQC; 15N-1H HSQC; 1H-13C-HCCH- REMARK 210 TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3.110, TALOS REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, LOW REMARK 210 TARGET FUNCTION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 16 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: 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 HIS A 169 65.47 -168.34 REMARK 500 1 LEU A 173 56.96 -119.09 REMARK 500 1 ASP A 180 34.71 -94.95 REMARK 500 1 VAL A 183 174.52 -53.59 REMARK 500 1 ASN A 184 -40.86 -132.83 REMARK 500 1 HIS A 204 37.35 -95.65 REMARK 500 1 LEU A 212 105.29 63.37 REMARK 500 2 LEU A 173 74.32 -108.25 REMARK 500 2 MET A 174 -169.82 -110.14 REMARK 500 2 ASN A 184 -51.19 -133.05 REMARK 500 2 HIS A 204 38.68 -95.99 REMARK 500 2 SER A 213 -172.02 63.19 REMARK 500 3 ASP A 180 34.41 -97.93 REMARK 500 3 VAL A 183 175.17 -53.59 REMARK 500 3 ASN A 184 -40.05 -131.04 REMARK 500 3 HIS A 204 43.99 -92.36 REMARK 500 4 ASP A 180 34.59 -95.88 REMARK 500 4 VAL A 183 171.11 -51.86 REMARK 500 4 ASN A 184 -39.39 -132.45 REMARK 500 4 MET A 185 -169.95 -164.07 REMARK 500 4 HIS A 204 38.27 -94.59 REMARK 500 5 ARG A 171 179.36 62.75 REMARK 500 5 ASP A 180 34.57 -95.40 REMARK 500 5 ASN A 184 -43.09 -130.39 REMARK 500 5 HIS A 204 38.64 -96.95 REMARK 500 6 LEU A 173 106.22 63.53 REMARK 500 6 ASP A 180 34.71 -95.54 REMARK 500 6 HIS A 204 47.94 -90.04 REMARK 500 6 SER A 213 114.39 -175.88 REMARK 500 7 ASP A 180 34.78 -95.23 REMARK 500 7 HIS A 204 39.91 -94.12 REMARK 500 7 LEU A 212 177.98 63.07 REMARK 500 8 ARG A 171 38.10 -97.10 REMARK 500 8 ASP A 180 34.62 -95.44 REMARK 500 8 GLU A 181 112.98 -160.75 REMARK 500 8 VAL A 183 171.25 -51.94 REMARK 500 8 ASN A 184 -38.72 -132.33 REMARK 500 8 HIS A 204 38.36 -94.55 REMARK 500 9 ARG A 171 90.26 54.46 REMARK 500 9 LEU A 173 46.56 -143.61 REMARK 500 9 ASP A 180 34.72 -94.31 REMARK 500 9 VAL A 183 170.56 -51.51 REMARK 500 9 ASN A 184 -38.71 -131.85 REMARK 500 9 HIS A 204 37.95 -94.78 REMARK 500 10 LEU A 173 106.40 63.54 REMARK 500 10 MET A 174 -169.93 -110.04 REMARK 500 10 ASP A 180 34.60 -95.55 REMARK 500 10 ASN A 184 -50.87 -134.05 REMARK 500 10 HIS A 204 38.84 -95.47 REMARK 500 11 ASP A 180 34.60 -95.45 REMARK 500 REMARK 500 THIS ENTRY HAS 78 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 A1175 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 175 SG REMARK 620 2 HIS A 178 ND1 116.6 REMARK 620 3 CYS A 195 SG 106.8 111.4 REMARK 620 4 CYS A 198 SG 106.7 111.6 102.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1187 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 187 SG REMARK 620 2 ASP A 190 OD1 112.5 REMARK 620 3 HIS A 204 ND1 122.4 114.7 REMARK 620 4 HIS A 207 ND1 122.0 84.4 93.9 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 1175 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1187 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FRE RELATED DB: PDB REMARK 900 XNF-7; FIRST DESCRIBED BBOX2 DOMAIN DBREF 2DQ5 A 168 214 UNP O15344 TRI18_HUMAN 168 214 SEQRES 1 A 47 SER HIS ILE ARG GLY LEU MET CYS LEU GLU HIS GLU ASP SEQRES 2 A 47 GLU LYS VAL ASN MET TYR CYS VAL THR ASP ASP GLN LEU SEQRES 3 A 47 ILE CYS ALA LEU CYS LYS LEU VAL GLY ARG HIS ARG ASP SEQRES 4 A 47 HIS GLN VAL ALA ALA LEU SER GLU HET ZN A1175 1 HET ZN A1187 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 CYS A 195 VAL A 201 1 7 SHEET 1 A 2 MET A 185 CYS A 187 0 SHEET 2 A 2 GLN A 192 ILE A 194 -1 O ILE A 194 N MET A 185 LINK SG CYS A 175 ZN ZN A1175 1555 1555 2.30 LINK ND1 HIS A 178 ZN ZN A1175 1555 1555 2.16 LINK SG CYS A 187 ZN ZN A1187 1555 1555 2.30 LINK OD1 ASP A 190 ZN ZN A1187 1555 1555 2.34 LINK SG CYS A 195 ZN ZN A1175 1555 1555 2.44 LINK SG CYS A 198 ZN ZN A1175 1555 1555 2.45 LINK ND1 HIS A 204 ZN ZN A1187 1555 1555 2.08 LINK ND1 HIS A 207 ZN ZN A1187 1555 1555 2.07 SITE 1 AC1 4 CYS A 175 HIS A 178 CYS A 195 CYS A 198 SITE 1 AC2 4 CYS A 187 ASP A 190 HIS A 204 HIS A 207 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