HEADER TRANSFERASE 15-JUN-04 1TOT
TITLE ZZ DOMAIN OF CBP- A NOVEL FOLD FOR A PROTEIN INTERACTION MODULE
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: CREB-BINDING PROTEIN;
COMPND 3 CHAIN: A;
COMPND 4 FRAGMENT: ZZ DOMAIN OF MURINE CBP (RESIDUES 1700-1751);
COMPND 5 EC: 2.3.1.48;
COMPND 6 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS;
SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE;
SOURCE 4 ORGANISM_TAXID: 10090;
SOURCE 5 GENE: CREBBP, CBP;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) [DNAY];
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A
KEYWDS ZINC BINDING, CBP, TAZ2, TRANSFERASE
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR G.B.LEGGE,M.A.MARTINEZ-YAMOUT,D.M.HAMBLY,T.TRINH,H.J.DYSON,P.E.WRIGHT
REVDAT 3 02-MAR-22 1TOT 1 REMARK LINK
REVDAT 2 24-FEB-09 1TOT 1 VERSN
REVDAT 1 18-JAN-05 1TOT 0
JRNL AUTH G.B.LEGGE,M.A.MARTINEZ-YAMOUT,D.M.HAMBLY,T.TRINH,B.M.LEE,
JRNL AUTH 2 H.J.DYSON,P.E.WRIGHT
JRNL TITL ZZ DOMAIN OF CBP: AN UNUSUAL ZINC FINGER FOLD IN A PROTEIN
JRNL TITL 2 INTERACTION MODULE
JRNL REF J.MOL.BIOL. V. 343 1081 2004
JRNL REFN ISSN 0022-2836
JRNL PMID 15476823
JRNL DOI 10.1016/J.JMB.2004.08.087
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : DYANA 1.0, AMBER 8.0
REMARK 3 AUTHORS : GUNTERT (DYANA), CASE (AMBER)
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE CALCULATED STRUCTURES ARE BASED ON A TOTAL OF 1846 NOES, AND
REMARK 3 INCLUDE DUPLICATE NOES.
REMARK 3 441 INTRARESIDUE,
REMARK 3 328 SEQUENTIAL,
REMARK 3 157 MEDIUM RANGE,
REMARK 3 386 LONG RANGE,
REMARK 3 534 AMBIGOUS,
REMARK 3 5 DEFINED HYDROGEN BONDS FROM H/D EXCHANGE AND
REMARK 3 29 PHI AND 29 PSI CONSTRAINTS AND 22 CHI1 CONSTRAINTS.
REMARK 4
REMARK 4 1TOT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUL-04.
REMARK 100 THE DEPOSITION ID IS D_1000022801.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 298
REMARK 210 PH : 6.8
REMARK 210 IONIC STRENGTH : 10 MM
REMARK 210 PRESSURE : AMBIENT
REMARK 210 SAMPLE CONTENTS : 2.3 MM SOLUTIONS IN DEGASSED 10
REMARK 210 MM TRIS-D11 PH 6.8, 200 M ZNCL2,
REMARK 210 10 MM DTT-D10, 0.05% W/V SODIUM
REMARK 210 AZIDE, 94 % H2O, 6 % D2O
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N
REMARK 210 -SEPARATED_NOESY; HBHA(CCCO)NH
REMARK 210 TOSCY; CCONH TOCSY; HCCH TOSCSY;
REMARK 210 HCCH COSY; HNCO; HN(CA)CO;
REMARK 210 CBCACONH; HNCACB
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ
REMARK 210 SPECTROMETER MODEL : DRX; AMX
REMARK 210 SPECTROMETER MANUFACTURER : BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : SANE 1.0, AMBER 8.0, NMRPIPE
REMARK 210 1.0, NMRVIEW 5.04
REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS AND
REMARK 210 SIMULATED ANNEALING
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: THIS STRUCTURE WAS DETERMINED USING STANDARD 3D
REMARK 210 HOMONUCLEAR TECHNIQUES, AND BY CD113 NMR OF A CADMIUM
REMARK 210 SUBSTITUTED SAMPLE TO CONFIRM METAL COORDINATING LIGANDS AND
REMARK 210 COORDINATING ATOMS.
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: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE
REMARK 500
REMARK 500 REMARK: NULL
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 7 TYR A 7 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES
REMARK 500 8 ARG A 19 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES
REMARK 500 8 ARG A 19 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES
REMARK 500 10 ARG A 19 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES
REMARK 500 17 ARG A 19 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 19 ARG A 19 NE - CZ - NH2 ANGL. DEV. = -3.7 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 PHE A 5 10.79 -147.01
REMARK 500 1 VAL A 24 -65.32 -101.27
REMARK 500 1 THR A 37 -45.70 -130.93
REMARK 500 2 ASN A 10 0.44 -67.80
REMARK 500 2 VAL A 24 -63.66 -103.42
REMARK 500 3 PHE A 5 16.30 -147.16
REMARK 500 3 ASN A 10 0.57 -66.92
REMARK 500 3 VAL A 24 -61.30 -103.26
REMARK 500 3 LYS A 38 0.49 -68.63
REMARK 500 3 SER A 39 47.39 39.44
REMARK 500 3 LEU A 49 8.61 84.11
REMARK 500 4 PHE A 5 23.13 -154.17
REMARK 500 4 ASN A 10 1.19 -67.22
REMARK 500 5 PHE A 5 25.95 -159.95
REMARK 500 6 ASN A 10 0.48 -68.69
REMARK 500 6 VAL A 24 -60.14 -104.50
REMARK 500 7 PHE A 5 17.96 -151.47
REMARK 500 7 VAL A 24 -62.02 -102.41
REMARK 500 7 SER A 39 46.02 33.98
REMARK 500 7 LEU A 51 54.07 -148.98
REMARK 500 8 PHE A 5 25.64 -162.29
REMARK 500 8 VAL A 24 -62.09 -101.04
REMARK 500 8 THR A 37 -52.53 -128.04
REMARK 500 8 LYS A 43 97.86 -68.38
REMARK 500 8 LEU A 49 -1.21 76.84
REMARK 500 8 LEU A 51 34.66 -145.63
REMARK 500 9 PHE A 5 13.27 -152.27
REMARK 500 9 ASN A 10 1.27 -66.46
REMARK 500 9 VAL A 24 -65.38 -120.17
REMARK 500 10 ASP A 3 -133.79 -137.33
REMARK 500 11 ASN A 10 0.51 -68.23
REMARK 500 11 VAL A 24 -61.09 -102.63
REMARK 500 11 SER A 39 52.42 31.61
REMARK 500 11 LEU A 49 -6.12 -144.91
REMARK 500 12 PHE A 5 21.94 -149.72
REMARK 500 12 LYS A 38 0.94 -68.39
REMARK 500 12 SER A 39 47.64 35.91
REMARK 500 13 PHE A 5 12.20 -154.27
REMARK 500 13 ASN A 10 0.88 -67.69
REMARK 500 13 LYS A 13 18.53 59.75
REMARK 500 13 THR A 37 -53.48 -128.62
REMARK 500 13 THR A 41 25.66 -66.83
REMARK 500 13 LEU A 49 -1.59 -151.84
REMARK 500 14 VAL A 24 -60.23 -107.84
REMARK 500 14 ASP A 27 38.10 38.96
REMARK 500 14 LEU A 49 -16.86 -140.12
REMARK 500 14 LEU A 51 74.36 -119.59
REMARK 500 15 PHE A 5 10.64 -147.80
REMARK 500 15 ASN A 10 0.22 -68.70
REMARK 500 15 VAL A 24 -61.88 -99.75
REMARK 500
REMARK 500 THIS ENTRY HAS 71 RAMACHANDRAN OUTLIERS.
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 1 ARG A 4 0.08 SIDE CHAIN
REMARK 500 4 TYR A 7 0.13 SIDE CHAIN
REMARK 500 4 ARG A 19 0.12 SIDE CHAIN
REMARK 500 5 TYR A 7 0.11 SIDE CHAIN
REMARK 500 5 ARG A 19 0.08 SIDE CHAIN
REMARK 500 6 ARG A 19 0.10 SIDE CHAIN
REMARK 500 7 TYR A 7 0.15 SIDE CHAIN
REMARK 500 7 ARG A 19 0.10 SIDE CHAIN
REMARK 500 9 ARG A 4 0.08 SIDE CHAIN
REMARK 500 9 TYR A 7 0.10 SIDE CHAIN
REMARK 500 9 ARG A 19 0.10 SIDE CHAIN
REMARK 500 11 TYR A 7 0.10 SIDE CHAIN
REMARK 500 11 ARG A 19 0.09 SIDE CHAIN
REMARK 500 12 TYR A 7 0.10 SIDE CHAIN
REMARK 500 13 HIS A 14 0.08 SIDE CHAIN
REMARK 500 15 ARG A 19 0.08 SIDE CHAIN
REMARK 500 16 ARG A 19 0.09 SIDE CHAIN
REMARK 500 19 TYR A 7 0.08 SIDE CHAIN
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 54 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 9 SG
REMARK 620 2 CYS A 12 SG 103.6
REMARK 620 3 CYS A 31 SG 105.9 117.2
REMARK 620 4 CYS A 34 SG 112.3 114.4 103.5
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 53 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 22 SG
REMARK 620 2 CYS A 25 SG 107.3
REMARK 620 3 HIS A 40 NE2 104.7 121.0
REMARK 620 4 HIS A 42 ND1 111.0 111.1 101.5
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 53
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 54
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1F81 RELATED DB: PDB
REMARK 900 NEIGHBORING DOMAIN IN MURINE CBP
DBREF 1TOT A 1 52 UNP P45481 CBP_MOUSE 1700 1751
SEQRES 1 A 52 GLY GLN ASP ARG PHE VAL TYR THR CYS ASN GLU CYS LYS
SEQRES 2 A 52 HIS HIS VAL GLU THR ARG TRP HIS CYS THR VAL CYS GLU
SEQRES 3 A 52 ASP TYR ASP LEU CYS ILE ASN CYS TYR ASN THR LYS SER
SEQRES 4 A 52 HIS THR HIS LYS MET VAL LYS TRP GLY LEU GLY LEU ASP
HET ZN A 53 1
HET ZN A 54 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 2(ZN 2+)
HELIX 1 1 CYS A 31 SER A 39 1 9
SHEET 1 A 2 TYR A 7 THR A 8 0
SHEET 2 A 2 HIS A 15 VAL A 16 -1 O VAL A 16 N TYR A 7
SHEET 1 B 3 ASP A 29 LEU A 30 0
SHEET 2 B 3 ARG A 19 CYS A 22 -1 N TRP A 20 O LEU A 30
SHEET 3 B 3 MET A 44 TRP A 47 -1 O TRP A 47 N ARG A 19
LINK SG CYS A 9 ZN ZN A 54 1555 1555 2.27
LINK SG CYS A 12 ZN ZN A 54 1555 1555 2.30
LINK SG CYS A 22 ZN ZN A 53 1555 1555 2.30
LINK SG CYS A 25 ZN ZN A 53 1555 1555 2.32
LINK SG CYS A 31 ZN ZN A 54 1555 1555 2.29
LINK SG CYS A 34 ZN ZN A 54 1555 1555 2.30
LINK NE2 HIS A 40 ZN ZN A 53 1555 1555 2.09
LINK ND1 HIS A 42 ZN ZN A 53 1555 1555 2.10
SITE 1 AC1 5 CYS A 22 VAL A 24 CYS A 25 HIS A 40
SITE 2 AC1 5 HIS A 42
SITE 1 AC2 4 CYS A 9 CYS A 12 CYS A 31 CYS A 34
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
