PDB Short entry for 1JJD 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