HEADER METAL TRANSPORT 20-JUN-09 2KKH TITLE STRUCTURE OF THE ZINC BINDING DOMAIN OF THE ATPASE HMA4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE HEAVY METAL TRANSPORTER; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-96; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VARIANT: DE3 KEYWDS ZINC TRANSPORT, METAL BINDING, METAL SELECTIVITY, ARABIDOPSIS KEYWDS 2 THALIANA, FERREDOXIN FOLD, ATP-BINDING, HYDROLASE, NUCLEOTIDE- KEYWDS 3 BINDING, PHOSPHOPROTEIN, TRANSMEMBRANE, METAL TRANSPORT EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.ZIMMERMAN,O.CLARKE,J.M.GULBIS,D.W.KEIZER,R.S.JARVIS,C.S.COBBETT, AUTHOR 2 M.G.HINDS,Z.XIAO,A.G.WEDD REVDAT 3 29-MAY-24 2KKH 1 REMARK REVDAT 2 16-MAR-22 2KKH 1 REMARK LINK REVDAT 1 26-JAN-10 2KKH 0 JRNL AUTH M.ZIMMERMANN,O.CLARKE,J.M.GULBIS,D.W.KEIZER,R.S.JARVIS, JRNL AUTH 2 C.S.COBBETT,M.G.HINDS,Z.XIAO,A.G.WEDD JRNL TITL METAL BINDING AFFINITIES OF ARABIDOPSIS ZINC AND COPPER JRNL TITL 2 TRANSPORTERS: SELECTIVITIES MATCH THE RELATIVE, BUT NOT THE JRNL TITL 3 ABSOLUTE, AFFINITIES OF THEIR AMINO-TERMINAL DOMAINS JRNL REF BIOCHEMISTRY V. 48 11640 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19883117 JRNL DOI 10.1021/BI901573B REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.0, X-PLOR NIH 22 REMARK 3 AUTHORS : BRUKER AG (TOPSPIN), SCHWIETERS, KUSZEWSKI, REMARK 3 TJANDRA AND CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KKH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000101232. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.3 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-99% 13C; U-99% 15N] REMARK 210 PROTEIN-1, 50 MM POTASSIUM REMARK 210 PHOSPHATE-2, 0.02 % SODIUM AZIDE- REMARK 210 3, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCA; 3D REMARK 210 HNCACB; 3D HCCH-TOCSY; 3D HN(CO) REMARK 210 CA; 3D 1H-13C NOESY; 3D 1H-15N REMARK 210 NOESY; 3D C(CO)NH REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.0, XEASY 3.13, CYANA REMARK 210 2.1 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 256 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: HETERONUCLEAR SPECTRA WERE RECORDED ON SPECTROMETERS REMARK 210 EQUIPPED WITH CRYOGENICALLY COOLED PROBES. 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: 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 LEU A 3 169.10 58.08 REMARK 500 1 LYS A 6 -9.79 -55.47 REMARK 500 1 LYS A 14 70.41 -177.93 REMARK 500 1 LEU A 16 -172.30 59.29 REMARK 500 1 CYS A 28 -171.69 44.92 REMARK 500 1 GLU A 81 105.35 54.87 REMARK 500 1 ARG A 85 91.47 38.64 REMARK 500 1 GLU A 89 -13.95 -160.39 REMARK 500 1 THR A 90 79.61 43.47 REMARK 500 1 LYS A 93 -21.40 -156.02 REMARK 500 2 LYS A 12 108.27 56.44 REMARK 500 2 LYS A 14 -73.19 -92.58 REMARK 500 2 LYS A 15 -83.65 51.57 REMARK 500 2 CYS A 28 -156.89 39.77 REMARK 500 2 GLU A 89 172.56 54.57 REMARK 500 2 SER A 91 90.94 -171.43 REMARK 500 2 LYS A 93 -91.42 -86.67 REMARK 500 3 LEU A 3 6.02 55.06 REMARK 500 3 GLN A 4 -85.02 -133.20 REMARK 500 3 LYS A 10 172.30 54.64 REMARK 500 3 LYS A 12 -80.62 53.39 REMARK 500 3 LYS A 15 -71.34 -52.16 REMARK 500 3 LEU A 16 -168.42 43.20 REMARK 500 3 CYS A 28 -163.54 40.56 REMARK 500 3 GLU A 81 100.19 46.97 REMARK 500 3 ARG A 85 -90.00 36.43 REMARK 500 3 PHE A 92 -81.28 54.06 REMARK 500 4 LYS A 15 -159.02 -56.70 REMARK 500 4 CYS A 28 -155.69 36.59 REMARK 500 4 ARG A 55 27.74 43.88 REMARK 500 4 ALA A 78 38.31 -80.55 REMARK 500 4 ARG A 79 18.21 50.35 REMARK 500 4 GLU A 89 146.07 58.46 REMARK 500 4 THR A 90 -135.94 -157.67 REMARK 500 4 SER A 91 -170.90 54.75 REMARK 500 4 PHE A 92 115.54 55.43 REMARK 500 4 ASN A 94 -167.52 43.12 REMARK 500 5 LYS A 12 147.99 58.35 REMARK 500 5 LEU A 16 -157.61 -68.52 REMARK 500 5 CYS A 28 -160.95 39.36 REMARK 500 5 ALA A 78 34.52 -85.74 REMARK 500 5 ARG A 85 155.91 56.32 REMARK 500 6 LYS A 15 146.18 -172.36 REMARK 500 6 LEU A 16 -171.81 51.85 REMARK 500 6 CYS A 28 -167.53 43.67 REMARK 500 6 GLU A 81 107.81 55.85 REMARK 500 6 PHE A 92 -164.59 40.57 REMARK 500 7 LYS A 6 7.34 54.33 REMARK 500 7 LYS A 14 115.75 57.15 REMARK 500 7 LYS A 15 170.04 52.66 REMARK 500 REMARK 500 THIS ENTRY HAS 184 RAMACHANDRAN OUTLIERS. 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 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 27 SG REMARK 620 2 CYS A 28 SG 109.7 REMARK 620 3 GLU A 31 OE2 109.4 109.5 REMARK 620 4 HOH A 301 O 109.2 109.5 109.6 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 201 DBREF 2KKH A 2 96 UNP Q8RVG7 Q8RVG7_ARATH 2 96 SEQRES 1 A 95 ALA LEU GLN ASN LYS GLU GLU GLU LYS LYS LYS VAL LYS SEQRES 2 A 95 LYS LEU GLN LYS SER TYR PHE ASP VAL LEU GLY ILE CYS SEQRES 3 A 95 CYS THR SER GLU VAL PRO ILE ILE GLU ASN ILE LEU LYS SEQRES 4 A 95 SER LEU ASP GLY VAL LYS GLU TYR SER VAL ILE VAL PRO SEQRES 5 A 95 SER ARG THR VAL ILE VAL VAL HIS ASP SER LEU LEU ILE SEQRES 6 A 95 SER PRO PHE GLN ILE ALA LYS ALA LEU ASN GLU ALA ARG SEQRES 7 A 95 LEU GLU ALA ASN VAL ARG VAL ASN GLY GLU THR SER PHE SEQRES 8 A 95 LYS ASN LYS TRP HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *(H2 O) HELIX 1 1 ASN A 5 GLU A 9 5 5 HELIX 2 2 GLU A 31 LEU A 42 1 12 HELIX 3 3 SER A 67 ARG A 79 1 13 SHEET 1 A 4 VAL A 45 ILE A 51 0 SHEET 2 A 4 THR A 56 HIS A 61 -1 O VAL A 60 N LYS A 46 SHEET 3 A 4 GLN A 17 VAL A 23 -1 N GLN A 17 O HIS A 61 SHEET 4 A 4 ALA A 82 VAL A 84 -1 O ASN A 83 N ASP A 22 LINK SG CYS A 27 ZN ZN A 201 1555 1555 2.30 LINK SG CYS A 28 ZN ZN A 201 1555 1555 2.30 LINK OE2 GLU A 31 ZN ZN A 201 1555 1555 1.97 LINK ZN ZN A 201 O HOH A 301 1555 1555 2.20 SITE 1 AC1 4 CYS A 27 CYS A 28 GLU A 31 HOH A 301 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