HEADER DNA BINDING PROTEIN 03-JUN-08 2K4B TITLE COPR REPRESSOR STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOCOCCUS LACTIS SUBSP. LACTIS; SOURCE 3 ORGANISM_COMMON: STREPTOCOCCUS LACTIS; SOURCE 4 ORGANISM_TAXID: 1360; SOURCE 5 GENE: COPR, LL0832, L451, L45109; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) (STRATAGENE); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLLCOPYLT298 KEYWDS DNA BINDING PROTEIN, WINGED HELIX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.CANTINI,L.BANCI,D.MAGNANI,M.SOLIOZ REVDAT 3 29-MAY-24 2K4B 1 REMARK REVDAT 2 16-MAR-22 2K4B 1 REMARK SEQADV REVDAT 1 27-JAN-09 2K4B 0 JRNL AUTH F.CANTINI,L.BANCI,M.SOLIOZ JRNL TITL THE COPPER-RESPONSIVE REPRESSOR COPR OF LACTOCOCCUS LACTIS JRNL TITL 2 IS A 'WINGED HELIX' PROTEIN. JRNL REF BIOCHEM.J. V. 417 493 2009 JRNL REFN ISSN 0264-6021 JRNL PMID 18837698 JRNL DOI 10.1042/BJ20081713 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CARA 1.8.4, AMBER 9 REMARK 3 AUTHORS : CARA (CARA), CASE, D. ET AL. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2K4B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JUN-08. REMARK 100 THE DEPOSITION ID IS D_1000100658. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.5 REMARK 210 IONIC STRENGTH : 0.25 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.2 MM [U-99% 13C; U-99% 15N] REMARK 210 COPR-NTD, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCO; 3D HNCA; REMARK 210 3D HNCACB; 3D HN(CO)CA; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY; 3D REMARK 210 HCCH-TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 2.1, TOPSPIN REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 350 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 TYR A 3 REMARK 465 TYR A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 HIS A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 ASP A 11 REMARK 465 TYR A 12 REMARK 465 ASP A 13 REMARK 465 ILE A 14 REMARK 465 PRO A 15 REMARK 465 THR A 16 REMARK 465 THR A 17 REMARK 465 GLU A 18 REMARK 465 ASN A 19 REMARK 465 LEU A 20 REMARK 465 TYR A 21 REMARK 465 PHE A 22 REMARK 465 GLN A 23 REMARK 465 GLY A 24 REMARK 465 ALA A 25 REMARK 465 MET A 26 REMARK 465 ASN A 27 REMARK 465 GLU A 28 REMARK 465 VAL A 29 REMARK 465 GLU A 30 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 1 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 1 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 2 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 3 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 3 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 3 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 3 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 4 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 5 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 6 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 7 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 4.9 DEGREES REMARK 500 10 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 10 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 11 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 11 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 12 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 12 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 76 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 14 ARG A 95 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 15 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 16 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 17 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 18 ARG A 95 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 19 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 19 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 20 ARG A 51 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 20 ARG A 90 NE - CZ - NH1 ANGL. DEV. = 3.2 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 ARG A 90 16.04 52.97 REMARK 500 2 ASN A 35 -169.31 58.62 REMARK 500 2 GLU A 37 -178.64 -176.88 REMARK 500 2 GLU A 88 72.10 -112.06 REMARK 500 3 SER A 34 43.96 -75.29 REMARK 500 3 LEU A 38 -48.19 -141.83 REMARK 500 3 ILE A 39 -75.69 -77.12 REMARK 500 3 LEU A 47 -72.89 -70.12 REMARK 500 3 LYS A 80 -113.34 -80.14 REMARK 500 3 GLU A 81 -1.72 -153.03 REMARK 500 4 MET A 41 32.46 -80.94 REMARK 500 4 ARG A 42 -69.32 -134.45 REMARK 500 4 GLU A 64 -5.77 146.81 REMARK 500 4 ARG A 90 25.85 46.68 REMARK 500 5 GLU A 64 0.80 83.34 REMARK 500 5 GLU A 81 18.55 59.19 REMARK 500 5 PRO A 96 36.49 -88.23 REMARK 500 5 LEU A 97 104.87 -55.39 REMARK 500 6 ASN A 32 -65.15 -153.80 REMARK 500 6 ASN A 35 65.68 -158.02 REMARK 500 6 GLU A 37 41.68 -77.38 REMARK 500 6 LEU A 38 -60.99 -121.84 REMARK 500 6 GLU A 88 79.12 -117.67 REMARK 500 7 SER A 34 -177.62 -173.95 REMARK 500 7 ASN A 35 139.21 68.88 REMARK 500 7 LEU A 38 -104.33 -128.21 REMARK 500 7 GLN A 61 -20.33 -160.66 REMARK 500 8 GLU A 81 -42.78 176.14 REMARK 500 8 MET A 82 -64.58 -26.47 REMARK 500 8 MET A 98 -41.36 -145.82 REMARK 500 9 GLU A 64 -12.07 174.35 REMARK 500 9 LYS A 80 -97.47 -88.12 REMARK 500 9 GLU A 81 11.36 -158.57 REMARK 500 10 LEU A 38 -39.61 66.96 REMARK 500 10 ILE A 39 -72.08 -66.22 REMARK 500 10 MET A 41 0.38 -66.89 REMARK 500 10 LYS A 80 -90.07 -95.86 REMARK 500 10 GLU A 81 -11.71 -164.22 REMARK 500 11 GLU A 37 44.60 -71.04 REMARK 500 11 LEU A 38 -67.94 -146.40 REMARK 500 11 GLU A 64 -1.36 59.77 REMARK 500 11 LEU A 97 -169.22 -110.11 REMARK 500 12 ASN A 35 -60.04 -132.65 REMARK 500 12 GLU A 37 -158.15 -168.41 REMARK 500 12 GLN A 61 6.74 -64.62 REMARK 500 12 GLU A 64 22.33 80.54 REMARK 500 13 VAL A 33 -24.76 -149.17 REMARK 500 13 ASN A 35 123.89 140.70 REMARK 500 13 GLU A 37 -179.48 -177.05 REMARK 500 13 LEU A 38 -32.75 -131.91 REMARK 500 REMARK 500 THIS ENTRY HAS 94 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 95 0.12 SIDE CHAIN REMARK 500 2 TYR A 94 0.07 SIDE CHAIN REMARK 500 4 ARG A 95 0.09 SIDE CHAIN REMARK 500 5 ARG A 90 0.08 SIDE CHAIN REMARK 500 8 ARG A 95 0.08 SIDE CHAIN REMARK 500 9 ARG A 95 0.09 SIDE CHAIN REMARK 500 10 ARG A 42 0.11 SIDE CHAIN REMARK 500 12 TYR A 56 0.08 SIDE CHAIN REMARK 500 12 ARG A 95 0.09 SIDE CHAIN REMARK 500 14 ARG A 42 0.11 SIDE CHAIN REMARK 500 20 ARG A 51 0.11 SIDE CHAIN REMARK 500 20 ARG A 90 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2K4B A 26 99 UNP Q9CHA6 Q9CHA6_LACLA 1 74 SEQADV 2K4B MET A 1 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B SER A 2 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B TYR A 3 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B TYR A 4 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B HIS A 5 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B HIS A 6 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B HIS A 7 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B HIS A 8 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B HIS A 9 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B HIS A 10 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B ASP A 11 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B TYR A 12 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B ASP A 13 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B ILE A 14 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B PRO A 15 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B THR A 16 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B THR A 17 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B GLU A 18 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B ASN A 19 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B LEU A 20 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B TYR A 21 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B PHE A 22 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B GLN A 23 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B GLY A 24 UNP Q9CHA6 EXPRESSION TAG SEQADV 2K4B ALA A 25 UNP Q9CHA6 EXPRESSION TAG SEQRES 1 A 99 MET SER TYR TYR HIS HIS HIS HIS HIS HIS ASP TYR ASP SEQRES 2 A 99 ILE PRO THR THR GLU ASN LEU TYR PHE GLN GLY ALA MET SEQRES 3 A 99 ASN GLU VAL GLU PHE ASN VAL SER ASN ALA GLU LEU ILE SEQRES 4 A 99 VAL MET ARG VAL ILE TRP SER LEU GLY GLU ALA ARG VAL SEQRES 5 A 99 ASP GLU ILE TYR ALA GLN ILE PRO GLN GLU LEU GLU TRP SEQRES 6 A 99 SER LEU ALA THR VAL LYS THR LEU LEU GLY ARG LEU VAL SEQRES 7 A 99 LYS LYS GLU MET LEU SER THR GLU LYS GLU GLY ARG LYS SEQRES 8 A 99 PHE VAL TYR ARG PRO LEU MET GLU HELIX 1 1 LEU A 38 GLY A 48 1 11 HELIX 2 2 VAL A 52 GLN A 58 1 7 HELIX 3 3 PRO A 60 GLU A 64 5 5 HELIX 4 4 SER A 66 LYS A 80 1 15 SHEET 1 A 3 ALA A 50 ARG A 51 0 SHEET 2 A 3 LYS A 91 ARG A 95 -1 O TYR A 94 N ALA A 50 SHEET 3 A 3 SER A 84 GLU A 88 -1 N GLU A 86 O VAL A 93 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