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
COMPND 6 DISEASE PROTEIN 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
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR S.A.BEASLEY,V.A.HRISTOVA,G.S.SHAW
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
JRNL TITL 2 PROVIDES INSIGHTS FOR E3-LIGASE DYSFUNCTION IN
JRNL TITL 3 AUTOSOMAL RECESSIVE 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 1
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CYANA 2.5.4
REMARK 3 AUTHORS : GUNTERT, MUMENTHALER AND WUTHRICH
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
REMARK 3 FOR USE IN THE STRUCTURE CALCULATIONS. THESE WERE THE ANGLES
REMARK 3 AND 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 RCSB ID CODE IS RCSB100024.
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%
REMARK 210 15N] IBR, 25 MM SODIUM
REMARK 210 PHOSPHATE, 100 MM SODIUM
REMARK 210 CHLORIDE, 1 MM DTT, 0.033 MM
REMARK 210 DSS, 100% D2O; 0.2 MM [U-100%
REMARK 210 13C, U-100% 15N] IBR, 25 MM
REMARK 210 SODIUM PHOSPHATE, 100 MM
REMARK 210 SODIUM CHLORIDE, 1 MM DTT,
REMARK 210 0.033 MM DSS, 90% H2O, 10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC, 2D 1H-13C
REMARK 210 HSQC, 3D HNCO, 3D HNCA, 3D
REMARK 210 HNCACB, 3D CBCA(CO)NH, 3D
REMARK 210 HC(CO)NH, 3D C(CO)NH, 3D HCCH-
REMARK 210 TOCSY, 3D HBCBCHCDHD, 2D
REMARK 210 NOESY, 3D 1H-15N NOESY, 3D 1H-
REMARK 210 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 : VNMR 6.1B, NMRVIEW
REMARK 210 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 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 15 MET A 23 -31.01 -37.06
REMARK 500 15 PRO A 41 7.64 -69.83
REMARK 500 15 ARG A 44 -38.96 -35.96
REMARK 500 15 ASN A 52 -66.32 -95.14
REMARK 500 16 PRO A 41 9.15 -69.75
REMARK 500 16 GLU A 72 106.94 158.25
REMARK 500 17 VAL A 20 32.00 34.98
REMARK 500 17 PRO A 31 82.39 -69.76
REMARK 500 17 ALA A 35 43.81 28.98
REMARK 500 17 PRO A 41 0.80 -69.87
REMARK 500 17 TYR A 68 102.44 -52.01
REMARK 500 17 GLU A 72 137.13 177.91
REMARK 500 17 VAL A 76 178.90 -56.85
REMARK 500 18 CYS A 33 103.77 -54.95
REMARK 500 18 ALA A 35 178.74 -54.64
REMARK 500 18 PRO A 41 11.50 -69.70
REMARK 500 18 ALA A 79 102.50 -56.72
REMARK 500 19 GLN A 13 173.32 -52.22
REMARK 500 19 PRO A 41 3.65 -69.71
REMARK 500 19 LEU A 54 177.49 -52.44
REMARK 500 19 TYR A 68 107.80 -52.09
REMARK 500 20 ASN A 9 177.11 -54.25
REMARK 500 20 PRO A 39 -171.53 -69.78
REMARK 500 20 PRO A 41 5.34 -69.76
REMARK 500 20 ARG A 44 -39.49 -32.19
REMARK 500 20 TYR A 68 104.62 -51.95
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 1 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 1 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 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 ZN ZN A 201 SG CYS A 28 1555 1555 2.30
LINK ZN ZN A 201 SG CYS A 33 1555 1555 2.29
LINK ZN ZN A 201 SG CYS A 48 1555 1555 2.31
LINK ZN ZN A 201 SG CYS A 56 1555 1555 2.30
LINK ZN ZN A 401 SG CYS A 61 1555 1555 2.30
LINK ZN ZN A 401 SG CYS A 64 1555 1555 2.30
LINK ZN ZN A 401 NE2 HIS A 69 1555 1555 2.13
LINK ZN ZN A 401 SG CYS A 73 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
(ATOM LINES ARE NOT SHOWN.)
END
