HEADER METAL BINDING PROTEIN 13-MAY-09 2KIZ
TITLE SOLUTION STRUCTURE OF ARKADIA RING-H2 FINGER DOMAIN
CAVEAT 2KIZ CHIRALITY ERRORS AT CA CENTERS OF RESIDUES 1,2,3 AND 65 IN
CAVEAT 2 2KIZ CHAIN A OF MODEL 1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE ARKADIA;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: RING FINGER PROTEIN 111;
COMPND 5 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: RNF111;
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 ARKADIA, RING-H2 FINGER, E3 LIGASE, ZN BINDING DOMAIN, METAL-BINDING,
KEYWDS 2 ZINC-FINGER, METAL BINDING PROTEIN
EXPDTA SOLUTION NMR
NUMMDL 31
MDLTYP MINIMIZED AVERAGE
AUTHOR N.G.KANDIAS,C.T.CHASAPIS,D.BENTROP,V.EPISKOPOU,G.A.SPYROULIAS
REVDAT 2 20-MAR-13 2KIZ 1 JRNL VERSN
REVDAT 1 19-MAY-10 2KIZ 0
JRNL AUTH C.T.CHASAPIS,N.G.KANDIAS,V.EPISKOPOU,D.BENTROP,
JRNL AUTH 2 G.A.SPYROULIAS
JRNL TITL NMR-BASED INSIGHTS INTO THE CONFORMATIONAL AND INTERACTION
JRNL TITL 2 PROPERTIES OF ARKADIA RING-H2 E3 UB LIGASE.
JRNL REF PROTEINS V. 80 1484 2012
JRNL REFN ISSN 0887-3585
JRNL PMID 22411132
JRNL DOI 10.1002/PROT.24048
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH N.G.KANDIAS,C.T.CHASAPIS,D.BENTROP,V.EPISKOPOU,
REMARK 1 AUTH 2 G.A.SPYROULIAS
REMARK 1 TITL HIGH YIELD EXPRESSION AND NMR CHARACTERIZATION OF ARKADIA E3
REMARK 1 TITL 2 UBIQUITIN LIGASE RING-H2 FINGER DOMAIN.
REMARK 1 REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 378 498 2009
REMARK 1 REFN ISSN 0006-291X
REMARK 1 PMID 19032943
REMARK 1 DOI 10.1016/J.BBRC.2008.11.055
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : AMBER 4.1
REMARK 3 AUTHORS : EARLMAN,CASE,CALDWELL,ROSS,CHEATHAM, FERGUSON,
REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2KIZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-MAY-09.
REMARK 100 THE RCSB ID CODE IS RCSB101178.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.9
REMARK 210 IONIC STRENGTH : 50
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-98% 13C; U-98% 15N]
REMARK 210 RING FINGER MONOMER, 50 MM PI,
REMARK 210 90% H2O/10% D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC;
REMARK 210 3D HN(CO)CA; 3D HNCA; 3D CBCA(CO)
REMARK 210 NH; 3D HNCACB; 3D HNCO; 3D HCCH-
REMARK 210 TOCSY; 3D HBHA(CO)NH; 2D (HB)
REMARK 210 CB(CGCD)HDAROM; 2D 2J-EDITED 1H-
REMARK 210 15N HSQC; 3D 1H-15N NOESY; 3D 1H-
REMARK 210 13C NOESY
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ
REMARK 210 SPECTROMETER MODEL : AVANCE
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : CARA 1.8.4
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 31
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 31
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: COVALENT BOND ANGLES
REMARK 500
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)
REMARK 500
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996
REMARK 500
REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3
REMARK 500 1 LYS A 2 C - N - CA ANGL. DEV. = 16.8 DEGREES
REMARK 500 12 CYS A 57 CA - CB - SG ANGL. DEV. = 11.6 DEGREES
REMARK 500 17 CYS A 57 CA - CB - SG ANGL. DEV. = 11.6 DEGREES
REMARK 500 18 CYS A 57 CA - CB - SG ANGL. DEV. = 11.7 DEGREES
REMARK 500 28 CYS A 57 CA - CB - SG ANGL. DEV. = 13.8 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
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 LYS A 2 -119.68 -95.27
REMARK 500 1 GLN A 3 164.51 -34.82
REMARK 500 1 GLU A 6 109.15 -43.14
REMARK 500 1 GLU A 10 -120.55 -145.47
REMARK 500 1 LEU A 21 51.40 34.18
REMARK 500 1 PRO A 34 5.65 -66.61
REMARK 500 1 MET A 36 -51.26 164.26
REMARK 500 1 ASP A 45 -70.29 -68.55
REMARK 500 1 THR A 50 -76.99 -91.85
REMARK 500 1 ARG A 58 -0.76 84.41
REMARK 500 1 LEU A 65 20.19 136.06
REMARK 500 1 PRO A 66 -119.54 -79.95
REMARK 500 1 SER A 67 -80.33 -151.58
REMARK 500 2 GLU A 6 103.48 53.77
REMARK 500 2 GLU A 10 -64.10 -139.31
REMARK 500 2 LEU A 21 20.12 44.96
REMARK 500 2 MET A 36 -46.97 145.20
REMARK 500 2 THR A 50 -76.66 -88.27
REMARK 500 2 LYS A 52 35.86 -75.11
REMARK 500 2 ALA A 63 -147.44 41.89
REMARK 500 2 PRO A 66 41.48 -89.24
REMARK 500 2 SER A 67 158.52 74.36
REMARK 500 3 GLU A 6 -72.05 69.02
REMARK 500 3 GLU A 11 -137.48 50.77
REMARK 500 3 ASP A 12 75.15 56.97
REMARK 500 3 MET A 36 -53.58 156.69
REMARK 500 3 ASP A 45 -72.08 -70.59
REMARK 500 3 THR A 50 -74.41 -87.12
REMARK 500 3 LYS A 52 21.09 -77.69
REMARK 500 3 ILE A 56 -71.21 -88.20
REMARK 500 3 GLU A 62 84.02 56.33
REMARK 500 3 LEU A 65 88.91 53.92
REMARK 500 3 SER A 67 155.29 68.25
REMARK 500 3 GLU A 68 -65.53 -154.62
REMARK 500 4 GLN A 3 110.91 -163.67
REMARK 500 4 THR A 9 -63.45 -163.39
REMARK 500 4 GLU A 11 86.60 30.43
REMARK 500 4 ASP A 12 -66.05 -163.63
REMARK 500 4 THR A 13 51.00 33.30
REMARK 500 4 LEU A 21 36.81 39.48
REMARK 500 4 MET A 36 -54.72 147.15
REMARK 500 4 ASP A 45 -73.76 -69.16
REMARK 500 4 THR A 50 -76.50 -88.63
REMARK 500 4 ILE A 56 -72.95 -84.17
REMARK 500 4 GLU A 62 59.11 177.23
REMARK 500 4 ALA A 63 -136.00 46.64
REMARK 500 4 GLN A 64 150.85 145.98
REMARK 500 4 SER A 67 -67.42 -160.62
REMARK 500 4 GLU A 68 151.04 63.66
REMARK 500 5 GLU A 11 179.72 59.06
REMARK 500
REMARK 500 THIS ENTRY HAS 344 RAMACHANDRAN OUTLIERS.
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS
REMARK 500
REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH
REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED
REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND
REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES.
REMARK 500 MODEL OMEGA
REMARK 500 ASP A 4 GLY A 5 1 -136.80
REMARK 500 ASP A 12 THR A 13 1 136.84
REMARK 500 ASP A 12 THR A 13 13 142.55
REMARK 500 GLU A 11 ASP A 12 18 -148.14
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: PLANAR GROUPS
REMARK 500
REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL
REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE
REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN
REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS
REMARK 500 AN RMSD GREATER THAN THIS VALUE
REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).
REMARK 500
REMARK 500 M RES CSSEQI RMS TYPE
REMARK 500 2 HIS A 40 0.08 SIDE CHAIN
REMARK 500 5 HIS A 40 0.10 SIDE CHAIN
REMARK 500 8 HIS A 40 0.10 SIDE CHAIN
REMARK 500 9 HIS A 40 0.08 SIDE CHAIN
REMARK 500 11 HIS A 40 0.08 SIDE CHAIN
REMARK 500 13 HIS A 40 0.09 SIDE CHAIN
REMARK 500 16 HIS A 40 0.09 SIDE CHAIN
REMARK 500 17 HIS A 40 0.08 SIDE CHAIN
REMARK 500 23 HIS A 40 0.08 SIDE CHAIN
REMARK 500 24 HIS A 40 0.09 SIDE CHAIN
REMARK 500 27 ARG A 31 0.08 SIDE CHAIN
REMARK 500 29 HIS A 40 0.09 SIDE CHAIN
REMARK 500 30 HIS A 40 0.09 SIDE CHAIN
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CHIRAL CENTERS
REMARK 500
REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL
REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY
REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR
REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE
REMARK 500 M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE
REMARK 500
REMARK 500 STANDARD TABLE:
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,6X,F5.1,6X,A1,10X,A1,3X,A16)
REMARK 500
REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS
REMARK 500 1 MET A 1 -26.9 L D WRONG HAND
REMARK 500 1 LYS A 2 -29.6 L D WRONG HAND
REMARK 500 1 GLN A 3 -26.2 L D WRONG HAND
REMARK 500 1 LEU A 65 -29.5 L D WRONG HAND
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 70 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 17 SG
REMARK 620 2 CYS A 20 SG 110.3
REMARK 620 3 HIS A 40 ND1 112.5 111.6
REMARK 620 4 CYS A 43 SG 123.2 85.6 110.6
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 1 ZN A 71 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 35 SG
REMARK 620 2 HIS A 37 ND1 113.4
REMARK 620 3 CYS A 54 SG 129.2 115.4
REMARK 620 4 CYS A 57 SG 72.7 111.7 77.0
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 70
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 71
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 15948 RELATED DB: BMRB
REMARK 900 1H, 13C, AND 15N CHEMICAL SHIFT ASSIGNMENTS FOR THE RING
REMARK 900 FINGER OF THE E3 UBIQUITIN LIGASE ARKADIA
DBREF 2KIZ A 2 69 UNP Q6ZNA4 RN111_HUMAN 927 994
SEQADV 2KIZ MET A 1 UNP Q6ZNA4 INITIATING METHIONINE
SEQRES 1 A 69 MET LYS GLN ASP GLY GLU GLU GLY THR GLU GLU ASP THR
SEQRES 2 A 69 GLU GLU LYS CYS THR ILE CYS LEU SER ILE LEU GLU GLU
SEQRES 3 A 69 GLY GLU ASP VAL ARG ARG LEU PRO CYS MET HIS LEU PHE
SEQRES 4 A 69 HIS GLN VAL CYS VAL ASP GLN TRP LEU ILE THR ASN LYS
SEQRES 5 A 69 LYS CYS PRO ILE CYS ARG VAL ASP ILE GLU ALA GLN LEU
SEQRES 6 A 69 PRO SER GLU SER
HET ZN A 70 1
HET ZN A 71 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 2(ZN 2+)
HELIX 1 1 GLN A 41 ASN A 51 1 11
SHEET 1 A 2 VAL A 30 ARG A 32 0
SHEET 2 A 2 LEU A 38 HIS A 40 -1 O PHE A 39 N ARG A 31
SSBOND 1 CYS A 20 CYS A 43 1555 1555 2.83
SSBOND 2 CYS A 35 CYS A 57 1555 1555 2.51
SSBOND 3 CYS A 54 CYS A 57 1555 1555 2.66
LINK SG CYS A 17 ZN ZN A 70 1555 1555 2.13
LINK SG CYS A 20 ZN ZN A 70 1555 1555 2.08
LINK SG CYS A 35 ZN ZN A 71 1555 1555 2.07
LINK ND1 HIS A 37 ZN ZN A 71 1555 1555 2.12
LINK ND1 HIS A 40 ZN ZN A 70 1555 1555 2.11
LINK SG CYS A 43 ZN ZN A 70 1555 1555 2.08
LINK SG CYS A 54 ZN ZN A 71 1555 1555 2.12
LINK SG CYS A 57 ZN ZN A 71 1555 1555 2.16
CISPEP 1 MET A 1 LYS A 2 1 19.37
CISPEP 2 LYS A 2 GLN A 3 1 -7.52
CISPEP 3 GLU A 6 GLU A 7 1 -20.64
CISPEP 4 GLY A 8 THR A 9 1 -17.28
CISPEP 5 GLN A 64 LEU A 65 1 17.24
CISPEP 6 SER A 67 GLU A 68 1 -21.90
SITE 1 AC1 4 CYS A 17 CYS A 20 HIS A 40 CYS A 43
SITE 1 AC2 4 CYS A 35 HIS A 37 CYS A 54 CYS A 57
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
