PDB Short entry for 2JRJ HEADER LIGASE 27-JUN-07 2JRJ TITLE SOLUTION STRUCTURE OF THE HUMAN PIRH2 RING-H2 DOMAIN. NORTHEAST TITLE 2 STRUCTURAL GENOMICS CONSORTIUM TARGET HT2B COMPND MOL_ID: 1; COMPND 2 MOLECULE: RING FINGER AND CHY ZINC FINGER DOMAIN CONTAINING PROTEIN COMPND 3 1; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: PIRH2 RING-H2 DOMAIN: RESIDUES 138-189; COMPND 6 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: RCHY1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PGEX KEYWDS UBIQUITIN E3 LIGASE, RING DOMAIN, STRUCTURAL GENOMICS, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, PSI-2, NORTHEAST STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, NESG, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR Y.SHENG,A.LEMAK,R.C.LAISTER,B.WU,C.H.ARROWSMITH,NORTHEAST STRUCTURAL AUTHOR 2 GENOMICS CONSORTIUM (NESG) REVDAT 5 09-MAR-22 2JRJ 1 REMARK LINK REVDAT 4 28-APR-09 2JRJ 1 JRNL REVDAT 3 24-FEB-09 2JRJ 1 VERSN REVDAT 2 06-MAY-08 2JRJ 1 SOURCE REVDAT 1 10-JUL-07 2JRJ 0 JRNL AUTH Y.SHENG,R.C.LAISTER,A.LEMAK,B.WU,E.TAI,S.DUAN,J.LUKIN, JRNL AUTH 2 M.SUNNERHAGEN,S.SRISAILAM,M.KARRA,S.BENCHIMOL,C.H.ARROWSMITH JRNL TITL MOLECULAR BASIS OF PIRH2-MEDIATED P53 UBIQUITYLATION. JRNL REF NAT.STRUCT.MOL.BIOL. V. 15 1334 2008 JRNL REFN ISSN 1545-9993 JRNL PMID 19043414 JRNL DOI 10.1038/NSMB.1521 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, CNS REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), BRUNGER, ADAMS, CLORE, GROS, NILGES AND REMARK 3 READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2JRJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUL-07. REMARK 100 THE DEPOSITION ID IS D_1000100199. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 150 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.7 MM [U-13C; U-15N] PIRH2 RING REMARK 210 DOMAIN, 25 MM SODIUM PHOSPHATE, REMARK 210 150 MM POTASSIUM CHLORIDE, 10 UM REMARK 210 ZNCL2, 2 MM [U-99% 2H] DTT, 90% REMARK 210 H2O/10% D2O; 0.7 MM [U-13C; U- REMARK 210 15N] PIRH2 RING DOMAIN, 25 MM REMARK 210 SODIUM PHOSPHATE, 150 MM REMARK 210 POTASSIUM CHLORIDE, 10 UM ZNCL2, REMARK 210 2 MM [U-99% 2H] DTT, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D C(CO)NH; 3D HNCACB; 3D REMARK 210 H(CCO)NH; 3D HNCO; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 3D HCCH- REMARK 210 TOCSY; 3D 1H-13C_AROMATIC NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY, CYANA REMARK 210 METHOD USED : MOLECULAR 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 CYS A 20 18.15 -161.69 REMARK 500 2 ASN A 11 91.76 60.53 REMARK 500 2 SER A 13 83.53 -68.47 REMARK 500 2 GLN A 14 93.83 -165.86 REMARK 500 2 CYS A 20 12.12 -157.10 REMARK 500 2 CYS A 55 108.24 -54.59 REMARK 500 3 LEU A 21 72.28 52.41 REMARK 500 3 SER A 27 106.42 -52.35 REMARK 500 3 CYS A 55 109.62 -54.26 REMARK 500 4 CYS A 20 18.40 -156.70 REMARK 500 4 SER A 27 99.45 -57.54 REMARK 500 5 CYS A 20 17.49 -164.12 REMARK 500 6 CYS A 20 22.77 -165.21 REMARK 500 6 SER A 27 104.89 -59.63 REMARK 500 7 ASN A 11 66.70 -160.16 REMARK 500 7 CYS A 20 20.41 -165.15 REMARK 500 7 LEU A 21 89.65 55.73 REMARK 500 7 SER A 27 97.21 -66.30 REMARK 500 8 CYS A 20 19.36 -171.68 REMARK 500 8 CYS A 55 109.72 -54.14 REMARK 500 9 ASN A 11 126.58 -177.26 REMARK 500 9 SER A 13 118.71 -168.21 REMARK 500 9 CYS A 20 25.41 -166.42 REMARK 500 9 SER A 27 106.81 -58.23 REMARK 500 9 CYS A 55 107.83 -55.63 REMARK 500 10 CYS A 20 22.49 -173.55 REMARK 500 11 VAL A 12 79.15 -115.49 REMARK 500 11 CYS A 20 16.96 -157.57 REMARK 500 11 CYS A 55 108.28 -53.91 REMARK 500 12 ASN A 11 89.20 69.44 REMARK 500 12 CYS A 20 18.22 -164.81 REMARK 500 12 LEU A 21 83.68 49.91 REMARK 500 12 SER A 27 108.52 -45.47 REMARK 500 12 CYS A 55 108.80 -55.68 REMARK 500 13 CYS A 20 14.76 -158.08 REMARK 500 14 CYS A 20 10.81 -161.16 REMARK 500 14 LEU A 21 94.12 54.76 REMARK 500 14 SER A 27 86.79 -48.73 REMARK 500 15 VAL A 12 -77.13 -73.75 REMARK 500 15 CYS A 20 22.62 -163.09 REMARK 500 15 SER A 27 93.88 -61.65 REMARK 500 15 VAL A 30 -63.14 -99.09 REMARK 500 16 CYS A 20 12.63 -162.18 REMARK 500 16 LEU A 21 91.02 54.97 REMARK 500 16 SER A 27 89.91 -57.52 REMARK 500 17 CYS A 20 17.69 -163.61 REMARK 500 17 LEU A 21 80.00 49.08 REMARK 500 17 SER A 27 94.52 -60.12 REMARK 500 18 GLN A 15 87.69 -69.04 REMARK 500 18 CYS A 20 21.95 -167.87 REMARK 500 REMARK 500 THIS ENTRY HAS 60 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 62 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 17 SG REMARK 620 2 CYS A 20 SG 111.7 REMARK 620 3 HIS A 41 NE2 107.2 109.1 REMARK 620 4 CYS A 44 SG 109.2 112.5 107.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 63 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 36 SG REMARK 620 2 HIS A 38 NE2 106.0 REMARK 620 3 CYS A 55 SG 112.6 105.6 REMARK 620 4 CYS A 58 SG 114.5 106.4 111.0 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 62 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 63 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HT2B RELATED DB: TARGETDB DBREF 2JRJ A 10 61 UNP Q86X26 Q86X26_HUMAN 138 189 SEQRES 1 A 52 GLU ASN VAL SER GLN GLN ASN CYS PRO ILE CYS LEU GLU SEQRES 2 A 52 ASP ILE HIS THR SER ARG VAL VAL ALA HIS VAL LEU PRO SEQRES 3 A 52 CYS GLY HIS LEU LEU HIS ARG THR CYS TYR GLU GLU MET SEQRES 4 A 52 LEU LYS GLU GLY TYR ARG CYS PRO LEU CYS MET HIS SER HET ZN A 62 1 HET ZN A 63 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) HELIX 1 1 ARG A 42 GLY A 52 1 11 HELIX 2 2 CYS A 55 HIS A 60 5 6 SHEET 1 A 2 ASN A 16 CYS A 17 0 SHEET 2 A 2 GLU A 22 ASP A 23 -1 O GLU A 22 N CYS A 17 SHEET 1 B 2 ALA A 31 VAL A 33 0 SHEET 2 B 2 LEU A 39 HIS A 41 -1 O LEU A 40 N HIS A 32 LINK SG CYS A 17 ZN ZN A 62 1555 1555 2.34 LINK SG CYS A 20 ZN ZN A 62 1555 1555 2.34 LINK SG CYS A 36 ZN ZN A 63 1555 1555 2.35 LINK NE2 HIS A 38 ZN ZN A 63 1555 1555 2.06 LINK NE2 HIS A 41 ZN ZN A 62 1555 1555 2.08 LINK SG CYS A 44 ZN ZN A 62 1555 1555 2.33 LINK SG CYS A 55 ZN ZN A 63 1555 1555 2.34 LINK SG CYS A 58 ZN ZN A 63 1555 1555 2.33 SITE 1 AC1 4 CYS A 17 CYS A 20 HIS A 41 CYS A 44 SITE 1 AC2 4 CYS A 36 HIS A 38 CYS A 55 CYS A 58 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