HEADER HYDROLASE 07-JAN-02 1KQK TITLE SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF A POTENTIAL COPPER- TITLE 2 TRANSLOCATING P-TYPE ATPASE FROM BACILLUS SUBTILIS IN THE CU(I)LOADED TITLE 3 STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: POTENTIAL COPPER-TRANSPORTING ATPASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; COMPND 5 SYNONYM: P-TYPE ATPASE, COPA; COMPND 6 EC: 3.6.3.4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: YVGX; 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 COPA, FOLDING, P-TYPE ATPASE, COPPER TRANSPORTING PROTEIN, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR L.BANCI,I.BERTINI,S.CIOFI-BAFFONI,M.D'ONOFRIO,L.GONNELLI, AUTHOR 2 F.C.MARHUENDA-EGEA,F.J.RUIZ-DUENAS REVDAT 4 23-FEB-22 1KQK 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1KQK 1 VERSN REVDAT 2 01-APR-03 1KQK 1 JRNL REVDAT 1 17-APR-02 1KQK 0 JRNL AUTH L.BANCI,I.BERTINI,S.CIOFI-BAFFONI,M.D'ONOFRIO,L.GONNELLI, JRNL AUTH 2 F.C.MARHUENDA-EGEA,F.J.RUIZ-DUENAS JRNL TITL SOLUTION STRUCTURE OF THE N-TERMINAL DOMAIN OF A POTENTIAL JRNL TITL 2 COPPER-TRANSLOCATING P-TYPE ATPASE FROM BACILLUS SUBTILIS IN JRNL TITL 3 THE APO AND CU(I) LOADED STATES. JRNL REF J.MOL.BIOL. V. 317 415 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 11922674 JRNL DOI 10.1006/JMBI.2002.5430 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CORMA, AMBER 5.0 REMARK 3 AUTHORS : BORGIAS, B.; THOMAS, P.D.; JAMES, T.L. (CORMA), REMARK 3 PEARLMAN, D.A.; CASE, D.A.; CALDWELL, J.W.; ROSS, REMARK 3 W.S.; CHEATHAM, T.E.; FERGUSON, D.M.; SEIBEL, G.L.; REMARK 3 SINGH, U.C.; WEINER, P.K.; KOLLMAN, P.A. (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 1502 RESTRAINTS, 1415 ARE REMARK 3 NOE-DERIVED REMARK 3 DISTANCE CONSTRAINTS, 87 DIHEDRAL ANGLE RESTRAINTS REMARK 4 REMARK 4 1KQK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-JAN-02. REMARK 100 THE DEPOSITION ID IS D_1000015235. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : 100MM PHOSPHATE BUFFER NA REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 2MM CU(I)COPA 15N; 100MM REMARK 210 PHOSPHATE BUFFER NA; 90%H2O, 10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : HNHA; 3D 15N NOESY-HSQC; 2D REMARK 210 NOESY; 2D TOCSY 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 : DYANA 1.5, XEASY 3.2, XWINNMR REMARK 210 2.6 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR AND 3D HETERONUCLEAR TECHNIQUES 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 26 ARG A 80 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 THR A 2 -177.11 54.41 REMARK 500 1 ALA A 34 61.13 -179.23 REMARK 500 1 ALA A 39 -57.38 -159.64 REMARK 500 1 LYS A 50 -60.08 -144.94 REMARK 500 1 GLU A 73 31.94 -166.16 REMARK 500 1 GLN A 74 54.38 -159.11 REMARK 500 1 ILE A 77 -68.24 71.05 REMARK 500 1 GLU A 78 155.70 65.37 REMARK 500 2 MET A 12 73.23 32.80 REMARK 500 2 ALA A 34 59.94 -172.28 REMARK 500 2 ALA A 39 -55.93 -138.95 REMARK 500 2 LYS A 50 -56.65 -136.30 REMARK 500 2 LYS A 71 -146.92 -125.47 REMARK 500 2 GLN A 74 72.97 52.06 REMARK 500 2 ILE A 77 90.90 -161.40 REMARK 500 3 MET A 12 45.08 -82.63 REMARK 500 3 CYS A 14 -30.29 -156.10 REMARK 500 3 ALA A 15 -55.73 74.88 REMARK 500 3 ALA A 34 67.55 -178.79 REMARK 500 3 ALA A 39 -60.96 -160.57 REMARK 500 3 LYS A 50 -19.15 -154.67 REMARK 500 3 LYS A 71 -51.73 -127.10 REMARK 500 3 SER A 76 -73.40 -88.61 REMARK 500 3 ILE A 77 80.29 54.48 REMARK 500 4 MET A 12 59.37 21.56 REMARK 500 4 ALA A 34 55.09 -169.29 REMARK 500 4 ALA A 39 -49.95 -154.18 REMARK 500 4 GLU A 41 49.91 81.58 REMARK 500 4 LYS A 50 -55.63 -135.65 REMARK 500 4 LYS A 71 -51.55 -124.49 REMARK 500 4 GLU A 73 40.14 -165.53 REMARK 500 4 GLN A 74 54.11 -162.06 REMARK 500 5 ALA A 34 57.18 -175.62 REMARK 500 5 ALA A 39 -55.74 -167.62 REMARK 500 5 GLU A 51 -67.22 -141.25 REMARK 500 5 LYS A 71 -51.07 -131.08 REMARK 500 5 GLN A 74 -47.29 177.16 REMARK 500 5 ASP A 75 -59.88 77.91 REMARK 500 5 ILE A 77 -84.75 -131.45 REMARK 500 5 GLU A 78 -97.78 -168.93 REMARK 500 6 MET A 12 64.53 33.56 REMARK 500 6 ALA A 34 56.91 -169.65 REMARK 500 6 ALA A 39 -55.30 -159.16 REMARK 500 6 GLU A 51 -61.38 -137.09 REMARK 500 6 LYS A 63 10.11 -69.46 REMARK 500 6 LYS A 71 -53.90 -121.24 REMARK 500 6 GLN A 74 123.25 68.19 REMARK 500 6 ILE A 77 105.87 -45.73 REMARK 500 7 THR A 2 172.14 66.77 REMARK 500 7 MET A 12 57.56 30.71 REMARK 500 REMARK 500 THIS ENTRY HAS 253 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 20 0.11 SIDE CHAIN REMARK 500 4 TYR A 47 0.07 SIDE CHAIN REMARK 500 4 TYR A 66 0.10 SIDE CHAIN REMARK 500 5 TYR A 47 0.06 SIDE CHAIN REMARK 500 7 TYR A 66 0.11 SIDE CHAIN REMARK 500 9 TYR A 47 0.09 SIDE CHAIN REMARK 500 10 TYR A 47 0.10 SIDE CHAIN REMARK 500 12 TYR A 47 0.07 SIDE CHAIN REMARK 500 13 TYR A 47 0.08 SIDE CHAIN REMARK 500 14 TYR A 66 0.09 SIDE CHAIN REMARK 500 15 TYR A 66 0.09 SIDE CHAIN REMARK 500 15 ARG A 80 0.10 SIDE CHAIN REMARK 500 16 TYR A 47 0.09 SIDE CHAIN REMARK 500 18 ARG A 20 0.09 SIDE CHAIN REMARK 500 18 TYR A 47 0.11 SIDE CHAIN REMARK 500 18 TYR A 66 0.08 SIDE CHAIN REMARK 500 19 TYR A 47 0.07 SIDE CHAIN REMARK 500 19 TYR A 66 0.09 SIDE CHAIN REMARK 500 20 TYR A 47 0.06 SIDE CHAIN REMARK 500 22 TYR A 66 0.08 SIDE CHAIN REMARK 500 25 TYR A 47 0.09 SIDE CHAIN REMARK 500 25 TYR A 66 0.09 SIDE CHAIN REMARK 500 26 TYR A 47 0.07 SIDE CHAIN REMARK 500 26 ARG A 80 0.12 SIDE CHAIN REMARK 500 28 TYR A 47 0.07 SIDE CHAIN REMARK 500 29 TYR A 47 0.07 SIDE CHAIN REMARK 500 30 TYR A 47 0.07 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 CU1 A 81 CU REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 14 SG REMARK 620 2 CYS A 17 SG 117.9 REMARK 620 N 1 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 81 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1JWW RELATED DB: PDB REMARK 900 1JWW CONTAINS THE SAME PROTEIN IN THE APO FORM. DBREF 1KQK A 2 76 UNP O32220 COPA_BACSU 73 147 SEQADV 1KQK MET A 1 UNP O32220 INITIATING METHIONINE SEQADV 1KQK ILE A 77 UNP O32220 SEE REMARK 999 SEQADV 1KQK GLU A 78 UNP O32220 SEE REMARK 999 SEQADV 1KQK GLY A 79 UNP O32220 SEE REMARK 999 SEQADV 1KQK ARG A 80 UNP O32220 SEE REMARK 999 SEQRES 1 A 80 MET THR GLU LYS ALA GLU PHE ASP ILE GLU GLY MET THR SEQRES 2 A 80 CYS ALA ALA CYS ALA ASN ARG ILE GLU LYS ARG LEU ASN SEQRES 3 A 80 LYS ILE GLU GLY VAL ALA ASN ALA PRO VAL ASN PHE ALA SEQRES 4 A 80 LEU GLU THR VAL THR VAL GLU TYR ASN PRO LYS GLU ALA SEQRES 5 A 80 SER VAL SER ASP LEU LYS GLU ALA VAL ASP LYS LEU GLY SEQRES 6 A 80 TYR LYS LEU LYS LEU LYS GLY GLU GLN ASP SER ILE GLU SEQRES 7 A 80 GLY ARG HET CU1 A 81 1 HETNAM CU1 COPPER (I) ION FORMUL 2 CU1 CU 1+ HELIX 1 1 ALA A 15 LYS A 27 1 13 HELIX 2 2 SER A 53 LYS A 63 1 11 SHEET 1 A 1 GLU A 3 GLU A 10 0 SHEET 1 B 2 GLY A 30 ASN A 33 0 SHEET 2 B 2 VAL A 36 ASN A 37 -1 N ALA A 5 O VAL A 45 SHEET 1 C 1 GLU A 41 ASN A 48 0 SHEET 1 D 1 LYS A 67 GLU A 73 0 LINK SG CYS A 14 CU CU1 A 81 1555 1555 2.17 LINK SG CYS A 17 CU CU1 A 81 1555 1555 2.18 SITE 1 AC1 2 CYS A 14 CYS A 17 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