Header list of 1yjt.pdb file
Complete list - v 10 2 Bytes
HEADER HYDROLASE 15-JAN-05 1YJT
TITLE SOLUTION STRUCTURE OF THE CU(I) FORM OF THE SIXTH SOLUBLE DOMAIN A69P
TITLE 2 MUTANT OF 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;
COMPND 8 MUTATION: 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, HYDROLASE
EXPDTA SOLUTION NMR
NUMMDL 30
AUTHOR L.BANCI,I.BERTINI,F.CANTINI,M.MIGLIARDI,A.ROSATO,S.WANG
REVDAT 3 10-NOV-21 1YJT 1 REMARK SEQADV LINK
REVDAT 2 24-FEB-09 1YJT 1 VERSN
REVDAT 1 03-JAN-06 1YJT 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 1901 MEANINGFUL DISTANCE CONSTRAINTS, 81 DIHEDRAL ANGLE
REMARK 3 RESTRAINTS
REMARK 4
REMARK 4 1YJT 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_1000031594.
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: 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 21 GLU A 75 CA - C - O ANGL. DEV. = -39.4 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 14 25.46 -157.84
REMARK 500 1 THR A 27 72.75 -68.06
REMARK 500 1 LYS A 28 -38.88 -171.83
REMARK 500 1 ASN A 42 54.99 35.06
REMARK 500 1 PRO A 50 48.70 -81.48
REMARK 500 1 GLU A 51 -63.09 -137.29
REMARK 500 1 VAL A 72 -52.97 -140.40
REMARK 500 1 LYS A 73 81.17 57.42
REMARK 500 1 ILE A 74 -84.62 -73.84
REMARK 500 2 ASP A 3 170.71 61.64
REMARK 500 2 THR A 14 22.30 -153.34
REMARK 500 2 THR A 27 72.12 -65.49
REMARK 500 2 LYS A 28 -43.58 -150.52
REMARK 500 2 ARG A 30 -82.12 131.36
REMARK 500 2 ASN A 42 54.99 33.73
REMARK 500 2 PRO A 50 41.26 -77.84
REMARK 500 2 ILE A 52 -54.46 -132.12
REMARK 500 2 PRO A 69 80.79 -68.82
REMARK 500 2 LEU A 71 64.16 -68.50
REMARK 500 2 LYS A 73 136.07 68.27
REMARK 500 3 ASP A 3 -143.20 52.78
REMARK 500 3 GLU A 51 -68.63 -135.16
REMARK 500 3 VAL A 72 57.73 -102.71
REMARK 500 3 LYS A 73 -137.33 45.55
REMARK 500 4 THR A 14 41.91 -152.81
REMARK 500 4 HIS A 29 87.08 -68.48
REMARK 500 4 ARG A 30 -66.21 23.27
REMARK 500 4 PRO A 50 47.56 -80.63
REMARK 500 4 GLU A 51 -63.90 -134.16
REMARK 500 4 VAL A 72 -76.70 -81.28
REMARK 500 4 LYS A 73 150.31 67.62
REMARK 500 5 ASP A 3 75.16 35.01
REMARK 500 5 THR A 14 11.62 -155.22
REMARK 500 5 LYS A 28 -38.03 -169.91
REMARK 500 5 ASN A 42 41.81 79.24
REMARK 500 5 GLU A 51 25.66 -159.99
REMARK 500 5 ILE A 52 -50.70 -167.17
REMARK 500 5 VAL A 72 -43.36 -141.81
REMARK 500 5 LYS A 73 -123.90 42.83
REMARK 500 5 ILE A 74 -71.20 -91.49
REMARK 500 6 ASP A 3 162.89 63.00
REMARK 500 6 VAL A 5 61.86 -153.98
REMARK 500 6 THR A 14 10.85 -155.10
REMARK 500 6 THR A 27 75.84 -66.81
REMARK 500 6 LYS A 28 -40.02 179.64
REMARK 500 6 ASN A 42 47.02 34.78
REMARK 500 6 LYS A 73 -160.43 57.67
REMARK 500 7 ASP A 3 173.73 174.80
REMARK 500 7 LYS A 28 -30.83 -162.69
REMARK 500 7 ARG A 30 -85.60 139.59
REMARK 500
REMARK 500 THIS ENTRY HAS 192 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 CYS A 35 SER A 36 1 140.33
REMARK 500 MET A 1 GLY A 2 2 -136.35
REMARK 500 CYS A 35 SER A 36 3 144.76
REMARK 500 HIS A 29 ARG A 30 4 145.39
REMARK 500 CYS A 35 SER A 36 5 142.04
REMARK 500 LYS A 43 ALA A 44 8 147.94
REMARK 500 ALA A 44 HIS A 45 8 148.79
REMARK 500 ILE A 74 GLU A 75 10 137.40
REMARK 500 CYS A 35 SER A 36 16 144.34
REMARK 500 MET A 1 GLY A 2 17 136.37
REMARK 500 CYS A 35 SER A 36 17 142.87
REMARK 500 CYS A 35 SER A 36 20 139.42
REMARK 500 MET A 1 GLY A 2 22 131.59
REMARK 500 MET A 1 GLY A 2 24 141.00
REMARK 500 ILE A 74 GLU A 75 26 135.79
REMARK 500 CYS A 35 SER A 36 29 141.83
REMARK 500 ALA A 44 HIS A 45 30 149.47
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 ARG A 11 0.11 SIDE CHAIN
REMARK 500 2 TYR A 34 0.15 SIDE CHAIN
REMARK 500 2 TYR A 48 0.10 SIDE CHAIN
REMARK 500 3 ARG A 11 0.08 SIDE CHAIN
REMARK 500 3 HIS A 29 0.09 SIDE CHAIN
REMARK 500 3 TYR A 48 0.10 SIDE CHAIN
REMARK 500 4 ARG A 30 0.12 SIDE CHAIN
REMARK 500 5 ARG A 11 0.14 SIDE CHAIN
REMARK 500 5 TYR A 48 0.08 SIDE CHAIN
REMARK 500 6 HIS A 45 0.08 SIDE CHAIN
REMARK 500 6 TYR A 48 0.07 SIDE CHAIN
REMARK 500 7 TYR A 48 0.13 SIDE CHAIN
REMARK 500 8 ARG A 11 0.10 SIDE CHAIN
REMARK 500 8 ARG A 56 0.10 SIDE CHAIN
REMARK 500 11 ARG A 56 0.09 SIDE CHAIN
REMARK 500 12 TYR A 34 0.07 SIDE CHAIN
REMARK 500 13 HIS A 29 0.09 SIDE CHAIN
REMARK 500 14 HIS A 45 0.10 SIDE CHAIN
REMARK 500 14 TYR A 48 0.12 SIDE CHAIN
REMARK 500 15 HIS A 45 0.11 SIDE CHAIN
REMARK 500 15 ARG A 56 0.12 SIDE CHAIN
REMARK 500 17 TYR A 48 0.17 SIDE CHAIN
REMARK 500 17 ARG A 56 0.13 SIDE CHAIN
REMARK 500 18 ARG A 11 0.10 SIDE CHAIN
REMARK 500 19 HIS A 45 0.09 SIDE CHAIN
REMARK 500 19 TYR A 48 0.10 SIDE CHAIN
REMARK 500 20 HIS A 45 0.10 SIDE CHAIN
REMARK 500 20 TYR A 48 0.07 SIDE CHAIN
REMARK 500 21 ARG A 11 0.08 SIDE CHAIN
REMARK 500 21 TYR A 48 0.09 SIDE CHAIN
REMARK 500 22 ARG A 56 0.15 SIDE CHAIN
REMARK 500 23 ARG A 30 0.08 SIDE CHAIN
REMARK 500 23 TYR A 48 0.20 SIDE CHAIN
REMARK 500 24 HIS A 29 0.09 SIDE CHAIN
REMARK 500 24 TYR A 34 0.12 SIDE CHAIN
REMARK 500 24 HIS A 45 0.10 SIDE CHAIN
REMARK 500 27 TYR A 48 0.08 SIDE CHAIN
REMARK 500 28 TYR A 48 0.09 SIDE CHAIN
REMARK 500 29 ARG A 56 0.10 SIDE CHAIN
REMARK 500 30 TYR A 34 0.08 SIDE CHAIN
REMARK 500 30 TYR A 48 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 76 CU
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 15 SG
REMARK 620 2 CYS A 18 SG 156.7
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 76
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: 1YJU RELATED DB: PDB
REMARK 900 THE APO FORM OF THE SAME PROTEIN
REMARK 900 RELATED ID: 1YJV RELATED DB: PDB
REMARK 900 THE CU(I) FORM OF THE SAME PROTEIN
DBREF 1YJT A 2 73 UNP Q04656 ATP7A_HUMAN 562 633
SEQADV 1YJT MET A 1 UNP Q04656 CLONING ARTIFACT
SEQADV 1YJT PRO A 69 UNP Q04656 ALA 629 ENGINEERED MUTATION
SEQADV 1YJT ILE A 74 UNP Q04656 CLONING ARTIFACT
SEQADV 1YJT 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 PRO SER LEU VAL LYS ILE GLU
HET CU1 A 76 1
HETNAM CU1 COPPER (I) ION
FORMUL 2 CU1 CU 1+
HELIX 1 1 CYS A 15 THR A 27 1 13
HELIX 2 2 GLY A 54 SER A 64 1 11
SHEET 1 A 4 ILE A 32 ALA A 38 0
SHEET 2 A 4 LYS A 43 TYR A 48 -1 O LYS A 47 N TYR A 34
SHEET 3 A 4 LEU A 6 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
LINK SG CYS A 15 CU CU1 A 76 1555 1555 2.15
LINK SG CYS A 18 CU CU1 A 76 1555 1555 2.15
SITE 1 AC1 2 CYS A 15 CYS A 18
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
Complete list - v 10 2 Bytes