HEADER LIGASE 24-NOV-06 2JMO TITLE IBR DOMAIN OF HUMAN PARKIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PARKIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IBR-TYPE 1 DOMAIN, RESIDUES 308-384; COMPND 5 SYNONYM: UBIQUITIN E3 LIGASE PRKN, PARKINSON JUVENILE DISEASE PROTEIN COMPND 6 2, PARKINSON DISEASE PROTEIN 2; 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: PARK2, PRKN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) STAR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: P11 (MODIFIED PET15B) KEYWDS PARKIN, IBR, E3 LIGASE, ZINC BINDING DOMAIN, RBR, LIGASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.A.BEASLEY,V.A.HRISTOVA,G.S.SHAW REVDAT 4 09-MAR-22 2JMO 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 2JMO 1 VERSN REVDAT 2 13-MAR-07 2JMO 1 JRNL REVDAT 1 27-FEB-07 2JMO 0 JRNL AUTH S.A.BEASLEY,V.A.HRISTOVA,G.S.SHAW JRNL TITL STRUCTURE OF THE PARKIN IN-BETWEEN-RING DOMAIN PROVIDES JRNL TITL 2 INSIGHTS FOR E3-LIGASE DYSFUNCTION IN AUTOSOMAL RECESSIVE JRNL TITL 3 PARKINSON'S DISEASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 3095 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17360614 JRNL DOI 10.1073/PNAS.0610548104 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1B, CYANA 2.5.4 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT, MUMENTHALER AND WUTHRICH REMARK 3 (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE AUTHORS STATE THAT THEY USED A REMARK 3 CYANA RESIDUE LIBRARY WITH A MODIFIED CYSTEINE - ZINC LIGAND FOR REMARK 3 USE IN THE STRUCTURE CALCULATIONS. THESE WERE THE ANGLES AND REMARK 3 LENGTHS LISTED. REMARK 4 REMARK 4 2JMO COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-DEC-06. REMARK 100 THE DEPOSITION ID IS D_1000100024. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.95 REMARK 210 IONIC STRENGTH : 100 MM NACL, 25 MM NA2HPO4 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2 MM [U-100% 13C, U-100% 15N] REMARK 210 IBR, 25 MM SODIUM PHOSPHATE, 100 REMARK 210 MM SODIUM CHLORIDE, 1 MM DTT, REMARK 210 0.033 MM DSS, 100% D2O; 0.2 MM REMARK 210 [U-100% 13C, U-100% 15N] IBR, 25 REMARK 210 MM SODIUM PHOSPHATE, 100 MM REMARK 210 SODIUM CHLORIDE, 1 MM DTT, 0.033 REMARK 210 MM DSS, 90% H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 CBCA(CO)NH; 3D H(CCO)NH; 3D C(CO) REMARK 210 NH; 3D HCCH-TOCSY; 3D HBCBCHCDHD; REMARK 210 2D NOESY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY 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 : NMRVIEW 5.0.4.SOL7, NMRPIPE 2.3 REMARK 210 METHOD USED : SIMULATED ANNEALING, TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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 TYR A 8 105.17 -55.45 REMARK 500 1 PRO A 41 8.00 -69.73 REMARK 500 2 GLN A 22 -61.56 -94.17 REMARK 500 2 PRO A 31 89.23 -69.71 REMARK 500 2 PRO A 41 3.07 -69.72 REMARK 500 2 GLU A 72 148.18 176.95 REMARK 500 3 CYS A 33 104.69 -58.30 REMARK 500 3 PRO A 41 5.14 -69.82 REMARK 500 3 VAL A 76 178.80 -58.64 REMARK 500 4 PRO A 41 5.46 -69.70 REMARK 500 4 LEU A 54 177.06 -52.68 REMARK 500 4 TYR A 68 104.04 -52.06 REMARK 500 5 VAL A 20 31.92 36.98 REMARK 500 5 PRO A 41 2.39 -69.74 REMARK 500 5 TYR A 68 103.95 -53.50 REMARK 500 5 GLU A 72 154.68 179.35 REMARK 500 6 PRO A 41 6.57 -69.71 REMARK 500 6 TYR A 68 103.06 -52.15 REMARK 500 7 PRO A 31 96.55 -69.68 REMARK 500 7 PRO A 41 10.85 -69.79 REMARK 500 8 PRO A 39 -174.69 -69.87 REMARK 500 8 PRO A 41 4.68 -69.85 REMARK 500 8 TYR A 68 108.64 -51.87 REMARK 500 9 GLN A 22 -68.10 -94.83 REMARK 500 9 PRO A 29 0.32 -69.80 REMARK 500 9 PRO A 31 12.25 -69.74 REMARK 500 9 PRO A 41 11.14 -69.74 REMARK 500 10 ALA A 35 33.18 32.46 REMARK 500 10 LEU A 37 172.61 -52.05 REMARK 500 10 PRO A 41 12.97 -69.77 REMARK 500 10 GLU A 49 177.16 -58.55 REMARK 500 10 LYS A 65 32.01 39.43 REMARK 500 10 GLU A 72 140.54 177.93 REMARK 500 11 PRO A 29 3.28 -69.77 REMARK 500 11 PRO A 39 -166.32 -69.82 REMARK 500 11 PRO A 41 11.29 -69.82 REMARK 500 12 VAL A 20 32.03 33.93 REMARK 500 12 PRO A 41 12.39 -69.66 REMARK 500 12 TYR A 68 106.54 -52.17 REMARK 500 13 VAL A 20 32.03 34.08 REMARK 500 13 PRO A 39 -175.37 -69.82 REMARK 500 13 PRO A 41 6.50 -69.80 REMARK 500 13 TYR A 68 102.35 -52.04 REMARK 500 14 GLU A 5 31.92 35.80 REMARK 500 14 VAL A 20 33.22 32.80 REMARK 500 14 PRO A 39 -164.75 -69.72 REMARK 500 14 PRO A 41 15.45 -69.77 REMARK 500 14 TYR A 68 102.07 -52.10 REMARK 500 15 VAL A 20 -19.93 -44.23 REMARK 500 15 GLN A 22 -32.23 -39.95 REMARK 500 REMARK 500 THIS ENTRY HAS 76 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 28 SG REMARK 620 2 CYS A 33 SG 112.2 REMARK 620 3 CYS A 48 SG 104.7 112.2 REMARK 620 4 CYS A 56 SG 103.5 112.1 111.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 61 SG REMARK 620 2 CYS A 64 SG 103.3 REMARK 620 3 HIS A 69 NE2 118.3 104.6 REMARK 620 4 CYS A 73 SG 111.9 111.8 106.8 REMARK 620 N 1 2 3 REMARK 700 REMARK 700 SHEET REMARK 700 THE AUTHORS STATE THAT CD, NOE AND CHEMICAL SHIFT INDEX REMARK 700 DATA ARE NOT CONSISTENT WITH BETA SHEET CHARACTER IN THIS REMARK 700 PROTEIN. 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 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15074 RELATED DB: BMRB DBREF 2JMO A 4 80 UNP O60260 PRKN2_HUMAN 308 384 SEQADV 2JMO GLY A 1 UNP O60260 CLONING ARTIFACT SEQADV 2JMO HIS A 2 UNP O60260 CLONING ARTIFACT SEQADV 2JMO MET A 3 UNP O60260 CLONING ARTIFACT SEQRES 1 A 80 GLY HIS MET GLY GLU GLU GLN TYR ASN ARG TYR GLN GLN SEQRES 2 A 80 TYR GLY ALA GLU GLU CYS VAL LEU GLN MET GLY GLY VAL SEQRES 3 A 80 LEU CYS PRO ARG PRO GLY CYS GLY ALA GLY LEU LEU PRO SEQRES 4 A 80 GLU PRO ASP GLN ARG LYS VAL THR CYS GLU GLY GLY ASN SEQRES 5 A 80 GLY LEU GLY CYS GLY PHE ALA PHE CYS ARG GLU CYS LYS SEQRES 6 A 80 GLU ALA TYR HIS GLU GLY GLU CYS SER ALA VAL PHE GLU SEQRES 7 A 80 ALA SER HET ZN A 201 1 HET ZN A 401 1 HETNAM ZN ZINC ION FORMUL 2 ZN 2(ZN 2+) LINK SG CYS A 28 ZN ZN A 201 1555 1555 2.30 LINK SG CYS A 33 ZN ZN A 201 1555 1555 2.29 LINK SG CYS A 48 ZN ZN A 201 1555 1555 2.31 LINK SG CYS A 56 ZN ZN A 201 1555 1555 2.30 LINK SG CYS A 61 ZN ZN A 401 1555 1555 2.30 LINK SG CYS A 64 ZN ZN A 401 1555 1555 2.30 LINK NE2 HIS A 69 ZN ZN A 401 1555 1555 2.13 LINK SG CYS A 73 ZN ZN A 401 1555 1555 2.29 SITE 1 AC1 5 CYS A 28 CYS A 33 CYS A 48 LEU A 54 SITE 2 AC1 5 CYS A 56 SITE 1 AC2 4 CYS A 61 CYS A 64 HIS A 69 CYS A 73 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20