10 20 30 40 50 60 70 80 2KMV - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 05-AUG-09 2KMV
TITLE SOLUTION STRUCTURE OF THE NUCLEOTIDE BINDING DOMAIN OF THE TITLE 2 HUMAN MENKES PROTEIN IN THE ATP-FREE FORM
COMPND MOL_ID: 1; COMPND 2 MOLECULE: COPPER-TRANSPORTING ATPASE 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NUCLEOTIDE BINDING 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, MC1, MNK; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) ROSETTA2; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PETG-30A
KEYWDS ATP7A, MENKES, NMR, ATPASE, NUCLEOTIDE BINDING PROTEIN, KEYWDS 2 ALTERNATIVE SPLICING, ATP-BINDING, CELL MEMBRANE, COPPER, KEYWDS 3 COPPER TRANSPORT, CYTOPLASM, DISEASE MUTATION, ENDOPLASMIC KEYWDS 4 RETICULUM, GLYCOPROTEIN, GOLGI APPARATUS, HYDROLASE, ION KEYWDS 5 TRANSPORT, MAGNESIUM, MEMBRANE, METAL-BINDING, NUCLEOTIDE- KEYWDS 6 BINDING, PHOSPHOPROTEIN, POLYMORPHISM, TRANSMEMBRANE, KEYWDS 7 TRANSPORT
EXPDTA SOLUTION NMR
NUMMDL 20
AUTHOR L.BANCI,I.BERTINI,F.CANTINI,S.INAGAKI,M.MIGLIARDI,A.ROSATO
REVDAT 1 01-DEC-09 2KMV 0
JRNL AUTH L.BANCI,I.BERTINI,F.CANTINI,S.INAGAKI,M.MIGLIARDI, JRNL AUTH 2 A.ROSATO JRNL TITL THE BINDING MODE OF ATP REVEALED BY THE SOLUTION JRNL TITL 2 STRUCTURE OF THE N-DOMAIN OF HUMAN ATP7A. JRNL REF J.BIOL.CHEM. 2009 JRNL REFN ESSN 1083-351X JRNL PMID 19917612 JRNL DOI 10.1074/JBC.M109.054262
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 10 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, AND KOLLM REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 2KMV COMPLIES WITH FORMAT V. 3.20, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-AUG-09. REMARK 100 THE RCSB ID CODE IS RCSB101317.
REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7 REMARK 210 IONIC STRENGTH : PHOSPATE 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.5 MM [U-99% 15N] ATPFREE N- REMARK 210 MNK-1, 90% H2O/10% D2O; 0.8 MM REMARK 210 [U-95% 13C; U-95% 15N] ATPFREE REMARK 210 N-MNK-2, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C REMARK 210 HSQC; 2D 1H-1H TOCSY; 2D 1H-1H REMARK 210 NOESY; 3D HNCO; 3D HNCA; 3D REMARK 210 CBCA(CO)NH; 3D HNCACB; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 700 MHZ; 900 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CARA, XEASY, CYANA, REMARK 210 PSVS, PROCHECKNMR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 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 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 A1067 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 1 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 2 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 2 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 3 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 3 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 4 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 4 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 5 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 5 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 6 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 6 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 8 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 8 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 8 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 9 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 10 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 10 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 10 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 11 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 11 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 11 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 11 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 12 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 12 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 12 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 12 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 13 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 13 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 14 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 15 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 15 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 15 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 15 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 16 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 16 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 16 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 18 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 18 ARG A1190 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 19 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A1208 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 19 ARG A1211 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A1067 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 20 ARG A1185 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 51 ANGLE DEVIATIONS. 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 MET A1050 -24.65 -144.77 REMARK 500 1 SER A1065 2.87 -65.57 REMARK 500 1 ASN A1083 -162.81 -60.55 REMARK 500 1 GLU A1085 -80.06 -81.82 REMARK 500 1 CYS A1117 -55.39 -131.35 REMARK 500 1 LEU A1147 144.33 63.42 REMARK 500 1 ASN A1154 -168.79 57.41 REMARK 500 1 SER A1158 126.95 62.53 REMARK 500 1 SER A1162 160.63 65.52 REMARK 500 1 ILE A1164 49.61 -76.68 REMARK 500 1 ASP A1166 -14.01 60.26 REMARK 500 1 CYS A1223 -25.05 -142.05 REMARK 500 2 SER A1065 99.80 -56.38 REMARK 500 2 ASN A1066 -74.62 -141.04 REMARK 500 2 SER A1084 63.31 73.25 REMARK 500 2 PRO A1115 107.15 -55.51 REMARK 500 2 THR A1124 -145.51 -141.55 REMARK 500 2 ASN A1133 60.74 -154.71 REMARK 500 2 TRP A1135 -21.33 -144.20 REMARK 500 2 ASP A1139 30.27 -90.53 REMARK 500 2 LEU A1147 -127.32 -118.92 REMARK 500 2 ILE A1164 80.31 67.33 REMARK 500 2 CYS A1223 -34.27 -130.91 REMARK 500 3 HIS A1051 -154.02 55.26 REMARK 500 3 THR A1063 -169.99 -106.21 REMARK 500 3 ASN A1083 -176.16 -67.91 REMARK 500 3 PRO A1115 104.11 -50.22 REMARK 500 3 ILE A1137 47.58 -94.36 REMARK 500 3 LEU A1147 -169.11 -102.93 REMARK 500 3 GLN A1149 -42.82 -132.77 REMARK 500 3 ASP A1151 -36.09 -136.16 REMARK 500 3 SER A1162 -33.73 57.97 REMARK 500 3 ALA A1175 150.18 65.69 REMARK 500 3 THR A1212 135.34 -38.58 REMARK 500 4 GLU A1064 -61.16 -133.83 REMARK 500 4 SER A1065 -20.01 -159.40 REMARK 500 4 SER A1084 64.18 -162.91 REMARK 500 4 ASP A1101 17.36 59.38 REMARK 500 4 THR A1104 58.00 -93.98 REMARK 500 4 CYS A1117 -51.57 -135.48 REMARK 500 4 LYS A1132 -42.25 61.91 REMARK 500 4 ASN A1136 -16.20 52.97 REMARK 500 4 ASP A1139 -154.44 -78.91 REMARK 500 4 ASN A1140 3.32 58.54 REMARK 500 4 ILE A1150 105.21 56.21 REMARK 500 4 ASP A1151 -17.74 61.40 REMARK 500 4 ALA A1152 -147.83 48.46 REMARK 500 4 SER A1162 19.47 55.64 REMARK 500 4 MET A1163 -102.23 40.90 REMARK 500 4 ILE A1164 36.12 -141.57 REMARK 500 REMARK 500 THIS ENTRY HAS 272 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 2 TYR A1095 0.07 SIDE CHAIN REMARK 500 2 TYR A1178 0.08 SIDE CHAIN REMARK 500 3 ARG A1190 0.08 SIDE CHAIN REMARK 500 4 TYR A1178 0.10 SIDE CHAIN REMARK 500 8 TYR A1178 0.08 SIDE CHAIN REMARK 500 16 ARG A1185 0.11 SIDE CHAIN REMARK 500 17 PHE A1111 0.08 SIDE CHAIN REMARK 500 17 ARG A1211 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KMX RELATED DB: PDB REMARK 900 RELATED ID: 16440 RELATED DB: BMRB
DBREF 2KMV A 1051 1231 UNP Q04656 ATP7A_HUMAN 1051 1231
SEQADV 2KMV SER A 1047 UNP Q04656 EXPRESSION TAG SEQADV 2KMV PHE A 1048 UNP Q04656 EXPRESSION TAG SEQADV 2KMV THR A 1049 UNP Q04656 EXPRESSION TAG SEQADV 2KMV MET A 1050 UNP Q04656 EXPRESSION TAG
SEQRES 1 A 185 SER PHE THR MET HIS GLY THR PRO VAL VAL ASN GLN VAL SEQRES 2 A 185 LYS VAL LEU THR GLU SER ASN ARG ILE SER HIS HIS LYS SEQRES 3 A 185 ILE LEU ALA ILE VAL GLY THR ALA GLU SER ASN SER GLU SEQRES 4 A 185 HIS PRO LEU GLY THR ALA ILE THR LYS TYR CYS LYS GLN SEQRES 5 A 185 GLU LEU ASP THR GLU THR LEU GLY THR CYS ILE ASP PHE SEQRES 6 A 185 GLN VAL VAL PRO GLY CYS GLY ILE SER CYS LYS VAL THR SEQRES 7 A 185 ASN ILE GLU GLY LEU LEU HIS LYS ASN ASN TRP ASN ILE SEQRES 8 A 185 GLU ASP ASN ASN ILE LYS ASN ALA SER LEU VAL GLN ILE SEQRES 9 A 185 ASP ALA SER ASN GLU GLN SER SER THR SER SER SER MET SEQRES 10 A 185 ILE ILE ASP ALA GLN ILE SER ASN ALA LEU ASN ALA GLN SEQRES 11 A 185 GLN TYR LYS VAL LEU ILE GLY ASN ARG GLU TRP MET ILE SEQRES 12 A 185 ARG ASN GLY LEU VAL ILE ASN ASN ASP VAL ASN ASP PHE SEQRES 13 A 185 MET THR GLU HIS GLU ARG LYS GLY ARG THR ALA VAL LEU SEQRES 14 A 185 VAL ALA VAL ASP ASP GLU LEU CYS GLY LEU ILE ALA ILE SEQRES 15 A 185 ALA ASP THR
HELIX 1 1 SER A 1069 ALA A 1080 1 12 HELIX 2 2 GLU A 1081 ASN A 1083 5 3 HELIX 3 3 HIS A 1086 ASP A 1101 1 16 HELIX 4 4 ILE A 1126 LEU A 1130 5 5 HELIX 5 5 ASN A 1171 ALA A 1175 5 5 HELIX 6 6 ASN A 1184 GLY A 1192 1 9 HELIX 7 7 ASN A 1196 LYS A 1209 1 14
SHEET 1 A 6 VAL A1055 VAL A1061 0 SHEET 2 A 6 GLU A1221 ALA A1229 -1 O ALA A1227 N GLN A1058 SHEET 3 A 6 THR A1212 VAL A1218 -1 N VAL A1214 O ILE A1226 SHEET 4 A 6 TYR A1178 GLY A1183 -1 N GLY A1183 O LEU A1215 SHEET 5 A 6 GLY A1118 VAL A1123 -1 N VAL A1123 O TYR A1178 SHEET 6 A 6 GLN A1112 VAL A1114 -1 N GLN A1112 O SER A1120
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