HEADER HYDROLASE 15-JAN-05 1YJU TITLE SOLUTION STRUCTURE OF THE APO FORM OF THE SIXTH SOLUBLE DOMAIN OF TITLE 2 MENKES PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-TRANSPORTING ATPASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SIXTH SOLUBLE DOMAIN; COMPND 5 SYNONYM: COPPER PUMP 1, MENKES DISEASE-ASSOCIATED PROTEIN; COMPND 6 EC: 3.6.3.4; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ATP7A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET20B+ KEYWDS METALLOCHAPERONE, PROTEIN-PROTEIN INTERACTION, COPPER(I), METAL KEYWDS 2 HOMEOSTASIS, STRUCTURAL PROTEOMICS IN EUROPE, SPINE, STRUCTURAL KEYWDS 3 GENOMICS, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR L.BANCI,I.BERTINI,F.CANTINI,M.MIGLIARDI,A.ROSATO,S.WANG,STRUCTURAL AUTHOR 2 PROTEOMICS IN EUROPE (SPINE) REVDAT 3 02-MAR-22 1YJU 1 REMARK SEQADV REVDAT 2 24-FEB-09 1YJU 1 VERSN REVDAT 1 03-JAN-06 1YJU 0 JRNL AUTH L.BANCI,I.BERTINI,F.CANTINI,M.MIGLIARDI,A.ROSATO,S.WANG JRNL TITL AN ATOMIC-LEVEL INVESTIGATION OF THE DISEASE-CAUSING A629P JRNL TITL 2 MUTANT OF THE MENKES PROTEIN, ATP7A JRNL REF J.MOL.BIOL. V. 352 409 2005 JRNL REFN ISSN 0022-2836 JRNL PMID 16083905 JRNL DOI 10.1016/J.JMB.2005.07.034 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR, AMBER 5.0 REMARK 3 AUTHORS : REMARK 3 PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON,SEIBEL,SINGH, REMARK 3 WEINER,KOLLMAN (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES WERE BASED ON A TOTAL OF REMARK 3 1992 MEANINGFUL DISTANCE CONSTRAINTS, 81 DIHEDRAL ANGLE REMARK 3 RESTRAINTS REMARK 4 REMARK 4 1YJU COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031595. 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 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.8MM 15N LABELED SAMPLE; 5MM REMARK 210 DTT; 100MM PHOSPHATE BUFFER; REMARK 210 0.8MM 15N 13C LABELED SAMPLE; REMARK 210 5MM DTT; 100MM PHOSPHATE BUFFER; REMARK 210 1.0MM UNLABELED SAMPLE; 5MM DTT; REMARK 210 100MM PHOSPHATE BUFFER REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; CBCANH; REMARK 210 CBCACONH; HNCO; HNCACO; 2D NOESY; REMARK 210 2D TOCSY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CARA 1.2, DYANA 1.5 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS COUPLED REMARK 210 WITH SIMULATED ANNEALING REMARK 210 FOLLOWED BY RESTRAINED ENERGY REMARK 210 MINIMIZATION 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 : 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 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 6 82.92 -150.64 REMARK 500 1 MET A 13 173.67 62.63 REMARK 500 1 THR A 14 -81.03 -154.03 REMARK 500 1 CYS A 15 131.37 -172.13 REMARK 500 1 ALA A 16 -146.12 48.45 REMARK 500 1 SER A 17 -86.83 51.61 REMARK 500 1 VAL A 19 -72.18 -54.03 REMARK 500 1 ARG A 30 32.63 -72.56 REMARK 500 1 ASN A 42 56.66 34.59 REMARK 500 1 LEU A 71 72.22 -62.88 REMARK 500 1 LYS A 73 101.72 65.34 REMARK 500 1 ILE A 74 63.91 31.55 REMARK 500 2 THR A 14 17.72 -156.40 REMARK 500 2 VAL A 19 -73.04 -53.32 REMARK 500 2 ARG A 30 48.86 -75.76 REMARK 500 2 ASN A 42 38.73 37.71 REMARK 500 2 GLU A 51 -43.22 -168.07 REMARK 500 3 ASP A 3 -12.35 -48.70 REMARK 500 3 THR A 14 17.38 -154.03 REMARK 500 3 SER A 17 -71.74 -57.92 REMARK 500 3 VAL A 19 -73.57 -54.84 REMARK 500 3 LYS A 28 -23.61 -174.00 REMARK 500 3 ARG A 30 -3.85 67.84 REMARK 500 3 ILE A 53 -55.58 -155.72 REMARK 500 3 ARG A 56 -50.88 -29.23 REMARK 500 3 LEU A 65 -76.90 -64.27 REMARK 500 3 LYS A 73 92.90 55.87 REMARK 500 3 ILE A 74 52.97 75.72 REMARK 500 4 CYS A 15 152.53 68.46 REMARK 500 4 ALA A 16 72.99 -60.25 REMARK 500 4 SER A 17 -46.88 -178.80 REMARK 500 4 VAL A 19 -73.26 -42.70 REMARK 500 5 CYS A 15 176.88 69.73 REMARK 500 5 ALA A 16 -37.96 -37.18 REMARK 500 5 LYS A 28 -69.98 -148.98 REMARK 500 5 ARG A 30 47.08 -77.99 REMARK 500 5 GLU A 51 -47.92 -166.34 REMARK 500 5 LEU A 65 -73.41 -65.64 REMARK 500 5 LEU A 71 128.48 -39.22 REMARK 500 6 ASP A 3 -110.12 -84.56 REMARK 500 6 THR A 14 16.39 -143.73 REMARK 500 6 SER A 17 -75.56 -59.52 REMARK 500 6 VAL A 19 -80.27 -53.21 REMARK 500 6 LYS A 28 1.29 -67.02 REMARK 500 6 ARG A 30 -3.02 65.92 REMARK 500 6 ASN A 42 59.13 37.35 REMARK 500 6 LEU A 65 -92.71 -69.81 REMARK 500 7 ALA A 16 -37.43 -37.05 REMARK 500 7 SER A 17 -79.39 -52.46 REMARK 500 7 ARG A 30 -1.95 67.68 REMARK 500 REMARK 500 THIS ENTRY HAS 228 RAMACHANDRAN OUTLIERS. 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 GLY A 66 PHE A 67 1 -144.74 REMARK 500 ILE A 74 GLU A 75 1 133.96 REMARK 500 MET A 1 GLY A 2 2 138.35 REMARK 500 GLY A 66 PHE A 67 2 -137.84 REMARK 500 GLY A 66 PHE A 67 4 -133.96 REMARK 500 MET A 1 GLY A 2 6 -130.34 REMARK 500 MET A 1 GLY A 2 7 -129.34 REMARK 500 GLY A 66 PHE A 67 8 -148.76 REMARK 500 LEU A 8 VAL A 9 9 148.95 REMARK 500 GLY A 2 ASP A 3 10 149.36 REMARK 500 GLY A 66 PHE A 67 10 -133.12 REMARK 500 MET A 1 GLY A 2 11 -140.65 REMARK 500 GLY A 66 PHE A 67 11 -145.64 REMARK 500 MET A 1 GLY A 2 15 135.30 REMARK 500 GLY A 66 PHE A 67 15 -126.70 REMARK 500 MET A 1 GLY A 2 16 140.93 REMARK 500 GLY A 66 PHE A 67 17 -144.46 REMARK 500 PHE A 67 GLU A 68 17 145.88 REMARK 500 GLY A 66 PHE A 67 18 -142.58 REMARK 500 GLY A 66 PHE A 67 20 -135.86 REMARK 500 GLY A 66 PHE A 67 21 -128.15 REMARK 500 MET A 1 GLY A 2 22 -132.61 REMARK 500 CYS A 35 SER A 36 22 146.60 REMARK 500 MET A 1 GLY A 2 24 -142.23 REMARK 500 GLY A 66 PHE A 67 24 -131.65 REMARK 500 GLY A 66 PHE A 67 26 -135.93 REMARK 500 ASP A 3 GLY A 4 28 148.36 REMARK 500 GLY A 66 PHE A 67 28 -135.44 REMARK 500 MET A 1 GLY A 2 29 -133.43 REMARK 500 MET A 1 GLY A 2 30 138.19 REMARK 500 GLY A 66 PHE A 67 30 -135.12 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 HIS A 29 0.10 SIDE CHAIN REMARK 500 1 TYR A 34 0.18 SIDE CHAIN REMARK 500 1 PHE A 67 0.08 SIDE CHAIN REMARK 500 2 TYR A 34 0.09 SIDE CHAIN REMARK 500 3 TYR A 34 0.07 SIDE CHAIN REMARK 500 3 TYR A 48 0.08 SIDE CHAIN REMARK 500 3 PHE A 67 0.10 SIDE CHAIN REMARK 500 4 ARG A 56 0.12 SIDE CHAIN REMARK 500 6 TYR A 34 0.13 SIDE CHAIN REMARK 500 6 TYR A 48 0.07 SIDE CHAIN REMARK 500 7 ARG A 11 0.08 SIDE CHAIN REMARK 500 7 TYR A 34 0.10 SIDE CHAIN REMARK 500 7 PHE A 67 0.10 SIDE CHAIN REMARK 500 8 TYR A 34 0.15 SIDE CHAIN REMARK 500 8 ARG A 56 0.10 SIDE CHAIN REMARK 500 8 PHE A 67 0.11 SIDE CHAIN REMARK 500 9 HIS A 29 0.08 SIDE CHAIN REMARK 500 9 TYR A 34 0.11 SIDE CHAIN REMARK 500 9 PHE A 67 0.10 SIDE CHAIN REMARK 500 10 TYR A 34 0.11 SIDE CHAIN REMARK 500 11 ARG A 11 0.08 SIDE CHAIN REMARK 500 11 TYR A 48 0.07 SIDE CHAIN REMARK 500 11 PHE A 67 0.08 SIDE CHAIN REMARK 500 13 HIS A 29 0.09 SIDE CHAIN REMARK 500 14 TYR A 34 0.14 SIDE CHAIN REMARK 500 14 TYR A 48 0.08 SIDE CHAIN REMARK 500 14 PHE A 67 0.09 SIDE CHAIN REMARK 500 16 ARG A 56 0.12 SIDE CHAIN REMARK 500 17 TYR A 34 0.15 SIDE CHAIN REMARK 500 17 PHE A 67 0.09 SIDE CHAIN REMARK 500 18 HIS A 29 0.10 SIDE CHAIN REMARK 500 18 TYR A 48 0.09 SIDE CHAIN REMARK 500 18 ARG A 56 0.10 SIDE CHAIN REMARK 500 19 ARG A 30 0.15 SIDE CHAIN REMARK 500 19 TYR A 34 0.07 SIDE CHAIN REMARK 500 19 ARG A 56 0.11 SIDE CHAIN REMARK 500 20 TYR A 34 0.07 SIDE CHAIN REMARK 500 21 TYR A 34 0.08 SIDE CHAIN REMARK 500 22 TYR A 48 0.13 SIDE CHAIN REMARK 500 25 TYR A 34 0.08 SIDE CHAIN REMARK 500 25 TYR A 48 0.11 SIDE CHAIN REMARK 500 26 TYR A 34 0.13 SIDE CHAIN REMARK 500 26 ARG A 56 0.11 SIDE CHAIN REMARK 500 27 TYR A 34 0.18 SIDE CHAIN REMARK 500 27 PHE A 67 0.09 SIDE CHAIN REMARK 500 28 TYR A 34 0.08 SIDE CHAIN REMARK 500 28 HIS A 45 0.10 SIDE CHAIN REMARK 500 29 ARG A 56 0.12 SIDE CHAIN REMARK 500 30 HIS A 29 0.08 SIDE CHAIN REMARK 500 30 TYR A 48 0.08 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 51 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1YJR RELATED DB: PDB REMARK 900 THE APO FORM OF THE SAME PROTEIN, A69P MUTANT REMARK 900 RELATED ID: 1YJT RELATED DB: PDB REMARK 900 THE COPPER FORM OF THE SAME PROTEIN, A69P MUTANT REMARK 900 RELATED ID: 1YJV RELATED DB: PDB REMARK 900 THE CU(I) FORM OF THE SAME PROTEIN REMARK 900 RELATED ID: CIRMMP28 RELATED DB: TARGETDB DBREF 1YJU A 2 73 UNP Q04656 ATP7A_HUMAN 562 633 SEQADV 1YJU MET A 1 UNP Q04656 CLONING ARTIFACT SEQADV 1YJU ILE A 74 UNP Q04656 CLONING ARTIFACT SEQADV 1YJU GLU A 75 UNP Q04656 CLONING ARTIFACT SEQRES 1 A 75 MET GLY ASP GLY VAL LEU GLU LEU VAL VAL ARG GLY MET SEQRES 2 A 75 THR CYS ALA SER CYS VAL HIS LYS ILE GLU SER SER LEU SEQRES 3 A 75 THR LYS HIS ARG GLY ILE LEU TYR CYS SER VAL ALA LEU SEQRES 4 A 75 ALA THR ASN LYS ALA HIS ILE LYS TYR ASP PRO GLU ILE SEQRES 5 A 75 ILE GLY PRO ARG ASP ILE ILE HIS THR ILE GLU SER LEU SEQRES 6 A 75 GLY PHE GLU ALA SER LEU VAL LYS ILE GLU HELIX 1 1 SER A 17 LYS A 28 1 12 HELIX 2 2 LEU A 39 THR A 41 5 3 HELIX 3 3 GLY A 54 PHE A 67 1 14 SHEET 1 A 4 ILE A 32 ALA A 38 0 SHEET 2 A 4 LYS A 43 TYR A 48 -1 O HIS A 45 N SER A 36 SHEET 3 A 4 VAL A 5 ARG A 11 -1 N LEU A 8 O ALA A 44 SHEET 4 A 4 GLU A 68 LEU A 71 -1 O SER A 70 N VAL A 9 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