HEADER METAL TRANSPORT 21-SEP-01 1K0V TITLE COPPER TRAFFICKING: THE SOLUTION STRUCTURE OF BACILLUS SUBTILIS COPZ COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPZ; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PROBABLE MERCURIC ION-BINDING PROTEIN YVGY; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: COPZ IS INVOLVED IN THE COPPER TRAFFICKING OF BACILLUS COMPND 7 SUBTILIS AND IT DOES BIND COPPER(I) UNDER REDUCING CONDITIONS SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: BSCOPZ; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS BETA-ALPHA-BETA-BETA-ALPHA-BETA, METAL TRANSPORT EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR L.BANCI,I.BERTINI,R.DEL CONTE,J.MARKEY,F.J.RUIZ-DUENAS REVDAT 5 23-FEB-22 1K0V 1 REMARK REVDAT 4 24-FEB-09 1K0V 1 VERSN REVDAT 3 16-OCT-07 1K0V 1 HET REVDAT 2 13-MAR-02 1K0V 1 JRNL REMARK REVDAT 1 19-DEC-01 1K0V 0 JRNL AUTH L.BANCI,I.BERTINI,R.DEL CONTE,J.MARKEY,F.J.RUIZ-DUENAS JRNL TITL COPPER TRAFFICKING: THE SOLUTION STRUCTURE OF BACILLUS JRNL TITL 2 SUBTILIS COPZ. JRNL REF BIOCHEMISTRY V. 40 15660 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11747441 JRNL DOI 10.1021/BI0112715 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : DYANA 1.5, AMBER 5.0 REMARK 3 AUTHORS : GUENTER ET AL. 1997 (DYANA), PEARLMAN ET AL. 1997 REMARK 3 (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1K0V COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-01. REMARK 100 THE DEPOSITION ID IS D_1000014419. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 300 REMARK 210 PH : 7.0; 7.0 REMARK 210 IONIC STRENGTH : NULL; NULL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : SAMPLE 1: 2MM COPPER (I) LOADED REMARK 210 -BACILLUS SUBTILIS COPZ, 15N REMARK 210 LABELLED. DTT WAS USED AS REMARK 210 REDUCTANT. SAMPLE 2: 2MM COPPER REMARK 210 (I) LOADED-BACILLUS SUBTILIS REMARK 210 COPZ, NOT LABELLED. DTT WAS USED REMARK 210 AS REDUCTANT.; 2MM COPPER (I) REMARK 210 LOADED BACILLUS SUBTILIS COPZ, REMARK 210 NOT LABELLED. DTT WAS USED AS REMARK 210 REDUCTANT. REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D TOSCY-HSQC; 3D NOESY-HSQC; 3D REMARK 210 HNHA; 2D TOSCY; 2D NOESY; 2D HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.6, XEASY 1.3.13, REMARK 210 MOLMOL 2.4, CORMA REMARK 210 METHOD USED : SIMULATED ANNEALING TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : NULL REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING HETERONUCLEAR TECHNIQUE 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 7 ARG A 73 NE - CZ - NH2 ANGL. DEV. = -3.1 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 SER A 12 42.94 -156.17 REMARK 500 1 CYS A 16 -71.41 -54.66 REMARK 500 1 LEU A 27 95.37 -68.09 REMARK 500 1 ASP A 28 -51.73 -21.03 REMARK 500 1 HIS A 34 78.18 -116.66 REMARK 500 1 ASN A 36 48.78 -144.92 REMARK 500 1 SER A 45 66.36 -105.12 REMARK 500 1 ASP A 55 -72.14 -52.37 REMARK 500 1 TYR A 65 110.65 64.66 REMARK 500 1 ASP A 66 -32.25 163.47 REMARK 500 1 GLU A 71 -112.00 -110.14 REMARK 500 2 MET A 11 -179.35 -66.61 REMARK 500 2 SER A 12 65.23 -163.70 REMARK 500 2 GLN A 14 -3.24 -55.86 REMARK 500 2 LEU A 27 95.14 -68.08 REMARK 500 2 ASP A 28 -50.53 -19.02 REMARK 500 2 HIS A 34 88.83 -150.68 REMARK 500 2 ASN A 36 48.97 -145.48 REMARK 500 2 LYS A 50 -56.18 -121.19 REMARK 500 2 TYR A 65 102.25 62.64 REMARK 500 2 ASP A 66 -40.07 172.57 REMARK 500 2 VAL A 67 98.96 -69.06 REMARK 500 2 LYS A 69 146.28 -170.47 REMARK 500 3 GLN A 14 -4.20 -57.63 REMARK 500 3 CYS A 16 -74.45 -63.35 REMARK 500 3 ASN A 36 49.45 -156.79 REMARK 500 3 LYS A 50 -53.25 -130.52 REMARK 500 3 ASP A 55 -70.79 -68.90 REMARK 500 3 TYR A 65 112.96 64.00 REMARK 500 3 ASP A 66 -41.85 168.34 REMARK 500 3 GLU A 71 -82.49 -81.62 REMARK 500 4 SER A 12 21.28 -143.31 REMARK 500 4 GLN A 14 2.36 -66.80 REMARK 500 4 ASP A 43 71.39 -114.96 REMARK 500 4 SER A 45 71.32 -110.15 REMARK 500 4 LYS A 54 -54.47 -29.60 REMARK 500 4 TYR A 65 108.90 64.33 REMARK 500 4 ASP A 66 -36.58 171.75 REMARK 500 4 GLU A 71 -103.47 -106.39 REMARK 500 5 SER A 12 40.73 -156.07 REMARK 500 5 CYS A 16 -71.24 -57.53 REMARK 500 5 SER A 45 68.89 -103.80 REMARK 500 5 LYS A 50 -56.13 -121.48 REMARK 500 5 VAL A 51 -169.81 -128.41 REMARK 500 5 GLN A 63 46.57 -145.00 REMARK 500 5 TYR A 65 110.64 66.02 REMARK 500 5 ASP A 66 -38.55 169.78 REMARK 500 6 SER A 12 15.16 -155.53 REMARK 500 6 GLN A 14 2.56 -64.20 REMARK 500 6 CYS A 16 -70.16 -48.21 REMARK 500 REMARK 500 THIS ENTRY HAS 248 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 73 0.08 SIDE CHAIN REMARK 500 6 ARG A 73 0.10 SIDE CHAIN REMARK 500 10 PHE A 46 0.09 SIDE CHAIN REMARK 500 10 ARG A 73 0.10 SIDE CHAIN REMARK 500 14 TYR A 65 0.09 SIDE CHAIN REMARK 500 15 HIS A 15 0.10 SIDE CHAIN REMARK 500 18 TYR A 65 0.06 SIDE CHAIN REMARK 500 21 PHE A 46 0.09 SIDE CHAIN REMARK 500 22 PHE A 46 0.08 SIDE CHAIN REMARK 500 23 PHE A 46 0.08 SIDE CHAIN REMARK 500 25 HIS A 15 0.08 SIDE CHAIN REMARK 500 28 TYR A 65 0.08 SIDE CHAIN REMARK 500 29 PHE A 46 0.12 SIDE CHAIN REMARK 500 29 TYR A 65 0.07 SIDE CHAIN REMARK 500 30 TYR A 65 0.16 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 COPPER (I) IS COORDINATED BY REMARK 600 CYS 13 AND CYS 16. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CU1 A 74 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CPZ RELATED DB: PDB REMARK 900 COPPER(I)-LOADED COPZ FROM BACILLUS SUBTILIS. COPZ PROTEIN IS REMARK 900 INVOLVED IN THE COPPER TRAFFICKING OF BACILLUS SUBTILIS. COPZ FROM REMARK 900 BACILLUS SUBTILIS HAS HIGH HOMOLOGY WITH THAT OF COPZ PROTEIN FROM REMARK 900 ENTEROCOCCUS HIRAE. REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE LAST FOUR AMINO ACID SEGMENT IEGR, REMARK 999 CORRESPONDING TO THE FACTORXA RECOGNITION REMARK 999 SITE USED TO REMOVE THE HISTIDINE REMARK 999 TAG, WAS ENGINEERED AT THE C-TERMINUS REMARK 999 OF THE CONSTRUCT. DBREF 1K0V A 1 69 UNP O32221 COPZ_BACSU 1 69 SEQADV 1K0V ILE A 70 UNP O32221 SEE REMARK 999 SEQADV 1K0V GLU A 71 UNP O32221 SEE REMARK 999 SEQADV 1K0V GLY A 72 UNP O32221 SEE REMARK 999 SEQADV 1K0V ARG A 73 UNP O32221 SEE REMARK 999 SEQRES 1 A 73 MET GLU GLN LYS THR LEU GLN VAL GLU GLY MET SER CYS SEQRES 2 A 73 GLN HIS CYS VAL LYS ALA VAL GLU THR SER VAL GLY GLU SEQRES 3 A 73 LEU ASP GLY VAL SER ALA VAL HIS VAL ASN LEU GLU ALA SEQRES 4 A 73 GLY LYS VAL ASP VAL SER PHE ASP ALA ASP LYS VAL SER SEQRES 5 A 73 VAL LYS ASP ILE ALA ASP ALA ILE GLU ASP GLN GLY TYR SEQRES 6 A 73 ASP VAL ALA LYS ILE GLU GLY ARG HET CU1 A 74 1 HETNAM CU1 COPPER (I) ION FORMUL 2 CU1 CU 1+ HELIX 1 1 CYS A 13 GLY A 25 1 13 HELIX 2 2 SER A 52 GLY A 64 1 13 SHEET 1 A 4 VAL A 33 HIS A 34 0 SHEET 2 A 4 LYS A 41 VAL A 44 -1 O ASP A 43 N HIS A 34 SHEET 3 A 4 LYS A 4 VAL A 8 -1 N LEU A 6 O VAL A 42 SHEET 4 A 4 VAL A 67 ILE A 70 -1 O ALA A 68 N GLN A 7 SITE 1 AC1 2 CYS A 13 CYS A 16 CRYST1 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