Header list of 1jjd.pdb file
Complete list - 25 201 Bytes
HEADER METAL BINDING PROTEIN 04-JUL-01 1JJD
TITLE NMR STRUCTURE OF THE CYANOBACTERIAL METALLOTHIONEIN SMTA
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: METALLOTHIONEIN;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: SMTA;
COMPND 5 ENGINEERED: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS ELONGATUS;
SOURCE 3 ORGANISM_TAXID: 1140;
SOURCE 4 STRAIN: PCC 7942;
SOURCE 5 GENE: SMTA;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET29A
KEYWDS ZINC FINGER, ZINC CLUSTER, METALLOTHIONEIN, METAL BINDING PROTEIN
EXPDTA SOLUTION NMR
MDLTYP MINIMIZED AVERAGE
AUTHOR P.J.SADLER,N.J.ROBINSON
REVDAT 3 13-JUL-11 1JJD 1 VERSN
REVDAT 2 24-FEB-09 1JJD 1 VERSN
REVDAT 1 22-AUG-01 1JJD 0
JRNL AUTH C.A.BLINDAUER,M.D.HARRISON,J.A.PARKINSON,A.K.ROBINSON,
JRNL AUTH 2 J.S.CAVET,N.J.ROBINSON,P.J.SADLER
JRNL TITL A METALLOTHIONEIN CONTAINING A ZINC FINGER WITHIN A
JRNL TITL 2 FOUR-METAL CLUSTER PROTECTS A BACTERIUM FROM ZINC TOXICITY.
JRNL REF PROC.NATL.ACAD.SCI.USA V. 98 9593 2001
JRNL REFN ISSN 0027-8424
JRNL PMID 11493688
JRNL DOI 10.1073/PNAS.171120098
REMARK 2
REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SYBYL 6.3
REMARK 3 AUTHORS : TRIPOS, INC.
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE STRUCTURE IS BASED ON A TOTAL OF 380 RESTRAINTS,
REMARK 3 291 ARE NOE-DERIVED DISTANCE RESTRAINTS, 37 ARE DIHEDRAL ANGLE
REMARK 3 RESTRAINTS,
REMARK 3 AND 52 ARE ZINC-LIGAND DISTANCE RESTRAINTS.
REMARK 4
REMARK 4 1JJD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-JUL-01.
REMARK 100 THE RCSB ID CODE IS RCSB013840.
REMARK 210
REMARK 210 EXPERIMENTAL DETAILS
REMARK 210 EXPERIMENT TYPE : NMR
REMARK 210 TEMPERATURE (KELVIN) : 308; 308; 308
REMARK 210 PH : 7.0; 7.0; 7.0
REMARK 210 IONIC STRENGTH : 50MM NACL; 50MM NACL; 50MM NACL
REMARK 210 PRESSURE : AMBIENT; AMBIENT; AMBIENT
REMARK 210 SAMPLE CONTENTS : 3MM ZN4SMTA; 50 MM [D-11]TRIS/
REMARK 210 HCL BUFFER; 50MM NACL;; 0.4MM 15N
REMARK 210 LABELLED ZN-SMTA; 50 MM [D-11]
REMARK 210 TRIS/HCL BUFFER; 50MM NACL;; 3MM
REMARK 210 CD4SMTA; 50 MM [D-11]TRIS/HCL
REMARK 210 BUFFER; 50MM NACL;
REMARK 210
REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; HNHA; 2D [1H,111CD]
REMARK 210 HSQC
REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 360 MHZ
REMARK 210 SPECTROMETER MODEL : UNITY; DMX
REMARK 210 SPECTROMETER MANUFACTURER : VARIAN; BRUKER
REMARK 210
REMARK 210 STRUCTURE DETERMINATION.
REMARK 210 SOFTWARE USED : VNMR 6.1C, XWINNMR 2.1, SYBYL
REMARK 210 6.3, DIANA 2.2.1
REMARK 210 METHOD USED : DISTANCE GEOMETRY, TORSION
REMARK 210 ANGLE DYNAMICS
REMARK 210
REMARK 210 CONFORMERS, NUMBER CALCULATED : 500
REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1
REMARK 210 CONFORMERS, SELECTION CRITERIA : DIANA TARGET FUNCTION
REMARK 210
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK 210
REMARK 210 REMARK: THE AVERAGE STRUCTURE WAS CALCULATED FROM THE BEST 20
REMARK 210 CONFORMERS.
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER;
REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465 RES C SSSEQI
REMARK 465 THR A 2
REMARK 465 SER A 3
REMARK 465 THR A 4
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS
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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)
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 RES CSSEQI ATM2 DEVIATION
REMARK 500 HIS A 40 CE1 HIS A 40 NE2 -0.067
REMARK 500 HIS A 49 CE1 HIS A 49 NE2 -0.067
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 ARG A 26 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES
REMARK 500 CYS A 47 CB - CA - C ANGL. DEV. = 7.4 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 ASN A 27 59.09 -146.75
REMARK 500 CYS A 32 -70.44 -61.35
REMARK 500 SER A 44 -87.03 -75.73
REMARK 500 ASN A 53 48.24 -91.10
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 LYS A 45 GLY A 46 124.67
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 TYR A 30 0.07 SIDE CHAIN
REMARK 500 TYR A 31 0.10 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 101 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 9 SG
REMARK 620 2 CYS A 14 SG 111.5
REMARK 620 3 CYS A 32 SG 115.3 105.4
REMARK 620 4 CYS A 36 SG 111.9 119.6 91.6
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 102 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 11 SG
REMARK 620 2 CYS A 36 SG 114.1
REMARK 620 3 HIS A 40 NE2 109.0 109.5
REMARK 620 4 CYS A 54 SG 123.2 105.6 93.1
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 103 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 16 SG
REMARK 620 2 CYS A 32 SG 126.0
REMARK 620 3 CYS A 47 SG 102.2 103.9
REMARK 620 4 HIS A 49 NE2 108.8 114.1 96.3
REMARK 620 N 1 2 3
REMARK 620
REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL
REMARK 620 ZN A 104 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 14 SG
REMARK 620 2 CYS A 47 SG 109.5
REMARK 620 3 CYS A 52 SG 105.3 105.6
REMARK 620 4 CYS A 54 SG 116.3 115.6 103.2
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 101
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 102
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC3
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 103
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC4
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 104
DBREF 1JJD A 2 56 UNP P30331 MT_SYNP7 1 55
SEQRES 1 A 55 THR SER THR THR LEU VAL LYS CYS ALA CYS GLU PRO CYS
SEQRES 2 A 55 LEU CYS ASN VAL ASP PRO SER LYS ALA ILE ASP ARG ASN
SEQRES 3 A 55 GLY LEU TYR TYR CYS SER GLU ALA CYS ALA ASP GLY HIS
SEQRES 4 A 55 THR GLY GLY SER LYS GLY CYS GLY HIS THR GLY CYS ASN
SEQRES 5 A 55 CYS HIS GLY
HET ZN A 101 1
HET ZN A 102 1
HET ZN A 103 1
HET ZN A 104 1
HETNAM ZN ZINC ION
FORMUL 2 ZN 4(ZN 2+)
HELIX 1 1 SER A 33 GLY A 39 1 7
SHEET 1 A 2 ILE A 24 ASP A 25 0
SHEET 2 A 2 TYR A 30 TYR A 31 -1 O TYR A 31 N ILE A 24
LINK SG CYS A 9 ZN ZN A 101 1555 1555 2.38
LINK SG CYS A 14 ZN ZN A 101 1555 1555 2.38
LINK SG CYS A 32 ZN ZN A 101 1555 1555 2.37
LINK SG CYS A 36 ZN ZN A 101 1555 1555 2.38
LINK SG CYS A 11 ZN ZN A 102 1555 1555 2.39
LINK SG CYS A 36 ZN ZN A 102 1555 1555 2.36
LINK NE2 HIS A 40 ZN ZN A 102 1555 1555 1.94
LINK SG CYS A 54 ZN ZN A 102 1555 1555 2.38
LINK SG CYS A 16 ZN ZN A 103 1555 1555 2.36
LINK SG CYS A 32 ZN ZN A 103 1555 1555 2.37
LINK SG CYS A 47 ZN ZN A 103 1555 1555 2.35
LINK NE2 HIS A 49 ZN ZN A 103 1555 1555 1.91
LINK SG CYS A 14 ZN ZN A 104 1555 1555 2.37
LINK SG CYS A 47 ZN ZN A 104 1555 1555 2.38
LINK SG CYS A 52 ZN ZN A 104 1555 1555 2.37
LINK SG CYS A 54 ZN ZN A 104 1555 1555 2.38
SITE 1 AC1 6 CYS A 9 CYS A 14 CYS A 32 CYS A 36
SITE 2 AC1 6 ZN A 103 ZN A 104
SITE 1 AC2 4 CYS A 11 CYS A 36 HIS A 40 CYS A 54
SITE 1 AC3 7 CYS A 14 CYS A 16 CYS A 32 CYS A 47
SITE 2 AC3 7 HIS A 49 ZN A 101 ZN A 104
SITE 1 AC4 6 CYS A 14 CYS A 47 CYS A 52 CYS A 54
SITE 2 AC4 6 ZN A 101 ZN A 103
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
Complete list - 25 201 Bytes