HEADER LIGASE 09-NOV-18 6IR0 TITLE ZINC FINGER DOMAIN OF THE HUMAN DTX PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE E3 UBIQUITIN-PROTEIN LIGASE DTX2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: ZINC FINGER DOMAIN; COMPND 5 SYNONYM: PROTEIN DELTEX-2,HDTX2,RING FINGER PROTEIN 58,RING-TYPE E3 COMPND 6 UBIQUITIN TRANSFERASE DTX2; COMPND 7 EC: 2.3.2.27; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606 KEYWDS RING FINGER, DTX, ZINC FINGER, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.MIYAMOTO REVDAT 4 15-MAY-24 6IR0 1 REMARK REVDAT 3 14-JUN-23 6IR0 1 LINK REVDAT 2 29-JAN-20 6IR0 1 JRNL REVDAT 1 13-NOV-19 6IR0 0 JRNL AUTH K.MIYAMOTO,Y.FUJIWARA,K.SAITO JRNL TITL ZINC FINGER DOMAIN OF THE HUMAN DTX PROTEIN ADOPTS A UNIQUE JRNL TITL 2 RING FOLD. JRNL REF PROTEIN SCI. V. 28 1151 2019 JRNL REFN ESSN 1469-896X JRNL PMID 30927328 JRNL DOI 10.1002/PRO.3610 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: VER. 2.1 REMARK 4 REMARK 4 6IR0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1300009755. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 6.9 REMARK 210 IONIC STRENGTH : 70 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM U-13C, 15N ZINC FINGER REMARK 210 DOMAIN OF THE HUMAN DTX PROTEIN, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 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 : NMRVIEW, NMRPIPE, CYANA 2.1 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 : 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 GLU A 4 92.79 -38.21 REMARK 500 1 LYS A 7 -28.26 -37.33 REMARK 500 1 PRO A 10 -163.84 -69.75 REMARK 500 1 ASP A 13 136.27 64.29 REMARK 500 1 CYS A 14 166.59 -49.88 REMARK 500 1 THR A 23 -93.53 -55.11 REMARK 500 1 ALA A 24 -176.78 178.91 REMARK 500 1 SER A 38 48.18 177.31 REMARK 500 1 LEU A 39 49.49 -177.69 REMARK 500 1 LEU A 44 125.57 -37.95 REMARK 500 1 SER A 48 71.52 82.75 REMARK 500 1 HIS A 49 -99.98 -117.86 REMARK 500 1 ALA A 50 133.00 158.99 REMARK 500 1 PHE A 51 148.62 -176.58 REMARK 500 1 HIS A 52 99.51 -48.55 REMARK 500 1 ASN A 64 53.95 35.81 REMARK 500 1 ASP A 66 -47.65 -157.01 REMARK 500 1 SER A 68 -95.55 -152.50 REMARK 500 1 LEU A 69 174.83 177.32 REMARK 500 1 SER A 73 -71.79 -57.95 REMARK 500 2 GLU A 5 133.47 -35.06 REMARK 500 2 LYS A 7 -28.34 -37.31 REMARK 500 2 ASP A 11 10.62 83.00 REMARK 500 2 GLU A 12 -93.24 -67.89 REMARK 500 2 ASP A 13 115.89 161.21 REMARK 500 2 CYS A 14 144.30 -39.44 REMARK 500 2 ILE A 16 -71.89 -84.71 REMARK 500 2 THR A 23 -90.43 -58.32 REMARK 500 2 SER A 28 -28.20 -38.31 REMARK 500 2 THR A 31 64.81 -115.99 REMARK 500 2 ALA A 35 -41.64 -134.47 REMARK 500 2 LEU A 36 -78.40 -90.95 REMARK 500 2 SER A 38 94.28 -40.11 REMARK 500 2 LEU A 39 -21.72 161.31 REMARK 500 2 SER A 48 39.12 83.42 REMARK 500 2 PHE A 51 173.84 169.88 REMARK 500 2 ASN A 64 45.87 34.43 REMARK 500 2 SER A 68 -73.14 -164.26 REMARK 500 2 LEU A 69 -178.30 -179.89 REMARK 500 2 PRO A 72 0.37 -69.75 REMARK 500 3 GLU A 5 145.39 -39.26 REMARK 500 3 PRO A 10 -163.83 -69.84 REMARK 500 3 ASP A 13 128.69 65.39 REMARK 500 3 CYS A 14 157.47 -40.60 REMARK 500 3 ALA A 24 170.78 75.27 REMARK 500 3 SER A 33 -92.37 42.01 REMARK 500 3 LYS A 34 -56.54 -176.70 REMARK 500 3 SER A 38 26.36 49.61 REMARK 500 3 SER A 48 31.28 83.13 REMARK 500 3 PHE A 51 -179.18 171.11 REMARK 500 REMARK 500 THIS ENTRY HAS 420 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 14 SG REMARK 620 2 CYS A 17 SG 117.1 REMARK 620 3 HIS A 52 ND1 85.8 97.9 REMARK 620 4 CYS A 55 SG 118.3 118.3 110.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 47 SG REMARK 620 2 HIS A 49 ND1 110.7 REMARK 620 3 CYS A 71 SG 93.7 100.9 REMARK 620 4 CYS A 74 SG 115.4 118.2 114.3 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 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 36217 RELATED DB: BMRB REMARK 900 ZINC FINGER DOMAIN OF THE HUMAN DTX PROTEIN DBREF 6IR0 A 1 76 UNP Q86UW9 DTX2_HUMAN 399 474 SEQADV 6IR0 LEU A 36 UNP Q86UW9 ILE 434 ENGINEERED MUTATION SEQRES 1 A 76 ASN TYR THR GLU GLU LEU LYS VAL PRO PRO ASP GLU ASP SEQRES 2 A 76 CYS ILE ILE CYS MET GLU LYS LEU SER THR ALA SER GLY SEQRES 3 A 76 TYR SER ASP VAL THR ASP SER LYS ALA LEU GLY SER LEU SEQRES 4 A 76 ALA VAL GLY HIS LEU THR LYS CYS SER HIS ALA PHE HIS SEQRES 5 A 76 LEU LEU CYS LEU LEU ALA MET TYR CYS ASN GLY ASN LYS SEQRES 6 A 76 ASP GLY SER LEU GLN CYS PRO SER CYS LYS THR HET ZN A 201 1 HET ZN A 202 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 AA1 SER A 25 VAL A 30 5 6 HELIX 2 AA2 LEU A 53 TYR A 60 1 8 SHEET 1 AA1 2 VAL A 41 LEU A 44 0 SHEET 2 AA1 2 HIS A 49 HIS A 52 -1 O HIS A 49 N LEU A 44 LINK SG CYS A 14 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 17 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 47 ZN ZN A 202 1555 1555 2.37 LINK ND1 HIS A 49 ZN ZN A 202 1555 1555 2.34 LINK ND1 HIS A 52 ZN ZN A 201 1555 1555 2.37 LINK SG CYS A 55 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 71 ZN ZN A 202 1555 1555 2.33 LINK SG CYS A 74 ZN ZN A 202 1555 1555 2.33 SITE 1 AC1 5 CYS A 14 CYS A 17 GLY A 26 HIS A 52 SITE 2 AC1 5 CYS A 55 SITE 1 AC2 5 CYS A 47 HIS A 49 CYS A 71 SER A 73 SITE 2 AC2 5 CYS A 74 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