HEADER CHAPERONE 16-OCT-07 2RK6
TITLE STRUCTURE OF E163K DJ-1
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: PROTEIN DJ-1;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: ONCOGENE DJ1, PARKINSON DISEASE PROTEIN 7;
COMPND 5 ENGINEERED: YES;
COMPND 6 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: PARK7;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3);
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3);
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS PARKINSON'S DISEASE, THIJ, PFPI, CHAPERONE, CYTOPLASM,
KEYWDS 2 DISEASE MUTATION, NUCLEUS, ONCOGENE, OXIDATION, PARKINSON
KEYWDS 3 DISEASE, PHOSPHORYLATION, POLYMORPHISM, UBL CONJUGATION
EXPDTA X-RAY DIFFRACTION
AUTHOR M.LAKSHMINARASIMHAN,M.T.MALDONADO,W.ZHOU,A.L.FINK,M.A.WILSON
REVDAT 3 24-FEB-09 2RK6 1 VERSN
REVDAT 2 19-FEB-08 2RK6 1 JRNL
REVDAT 1 15-JAN-08 2RK6 0
JRNL AUTH M.LAKSHMINARASIMHAN,M.T.MALDONADO,W.ZHOU,A.L.FINK,
JRNL AUTH 2 M.A.WILSON
JRNL TITL STRUCTURAL IMPACT OF THREE PARKINSONISM-ASSOCIATED
JRNL TITL 2 MISSENSE MUTATIONS ON HUMAN DJ-1.
JRNL REF BIOCHEMISTRY V. 47 1381 2008
JRNL REFN ISSN 0006-2960
JRNL PMID 18181649
JRNL DOI 10.1021/BI701189C
REMARK 1
REMARK 2
REMARK 2 RESOLUTION. 1.15 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : SHELXL-97
REMARK 3 AUTHORS : G.M.SHELDRICK
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 3 CROSS-VALIDATION METHOD : FREE R
REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF).
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.150
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.149
REMARK 3 FREE R VALUE (NO CUTOFF) : 0.175
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4331
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 86744
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F).
REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.122
REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.121
REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.143
REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000
REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3317
REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 66376
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1453
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 190
REMARK 3
REMARK 3 MODEL REFINEMENT.
REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1556.80
REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 1385.00
REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 10
REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 14801
REMARK 3 NUMBER OF RESTRAINTS : 18983
REMARK 3
REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES.
REMARK 3 BOND LENGTHS (A) : 0.013
REMARK 3 ANGLE DISTANCES (A) : 0.029
REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000
REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.029
REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.075
REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.087
REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.029
REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005
REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.055
REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.106
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED: BABINET
REMARK 3
REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER
REMARK 3 SPECIAL CASE: NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2RK6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-07.
REMARK 100 THE RCSB ID CODE IS RCSB044958.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-MAR-06
REMARK 200 TEMPERATURE (KELVIN) : 110
REMARK 200 PH : 7.5
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 14-BM-C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.90
REMARK 200 MONOCHROMATOR : SINGLE CRYSTAL BENT GE(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000
REMARK 200 DATA SCALING SOFTWARE : HKL-2000
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 86963
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150
REMARK 200 RESOLUTION RANGE LOW (A) : 50.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0
REMARK 200 DATA REDUNDANCY : 10.700
REMARK 200 R MERGE (I) : 0.07900
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 34.1000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : 9.40
REMARK 200 R MERGE FOR SHELL (I) : 0.81900
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: SHELXL
REMARK 200 STARTING MODEL: 1P5F
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 59.70
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5 M SODIUM CITRATE, 20 MM HEPES,
REMARK 280 PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -Y,X-Y,Z+1/3
REMARK 290 3555 -X+Y,-X,Z+2/3
REMARK 290 4555 Y,X,-Z
REMARK 290 5555 X-Y,-Y,-Z+2/3
REMARK 290 6555 -X,-X+Y,-Z+1/3
REMARK 290
REMARK 290 WHERE NNN -> OPERATOR NUMBER
REMARK 290 MMM -> TRANSLATION VECTOR
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS
REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM
REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY
REMARK 290 RELATED MOLECULES.
REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 25.04900
REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 50.09800
REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000
REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 50.09800
REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000
REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 25.04900
REMARK 290
REMARK 290 REMARK: NULL
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: DIMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 2540 ANGSTROM**2
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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000
REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 25.04900
REMARK 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLY A -2
REMARK 465 SER A -1
REMARK 465 HIS A 0
REMARK 465 MET A 1
REMARK 465 LYS A 188
REMARK 465 ASP A 189
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 ARG A 5 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES
REMARK 500 ARG A 5 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES
REMARK 500 GLY A 65 C - N - CA ANGL. DEV. = -12.8 DEGREES
REMARK 500 ARG A 98 CD - NE - CZ ANGL. DEV. = 11.8 DEGREES
REMARK 500 ARG A 98 NE - CZ - NH1 ANGL. DEV. = 5.0 DEGREES
REMARK 500 ARG A 98 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES
REMARK 500 ARG A 145 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES
REMARK 500 ARG A 145 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES
REMARK 500 LEU A 151 CA - CB - CG ANGL. DEV. = 15.5 DEGREES
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 2RK3 RELATED DB: PDB
REMARK 900 STRUCTURE OF A104T DJ-1
REMARK 900 RELATED ID: 2RK4 RELATED DB: PDB
REMARK 900 STRUCTURE OF M26I DJ-1
DBREF 2RK6 A 1 189 UNP Q99497 PARK7_HUMAN 1 189
SEQADV 2RK6 GLY A -2 UNP Q99497 EXPRESSION TAG
SEQADV 2RK6 SER A -1 UNP Q99497 EXPRESSION TAG
SEQADV 2RK6 HIS A 0 UNP Q99497 EXPRESSION TAG
SEQADV 2RK6 LYS A 163 UNP Q99497 GLU 163 ENGINEERED
SEQRES 1 A 192 GLY SER HIS MET ALA SER LYS ARG ALA LEU VAL ILE LEU
SEQRES 2 A 192 ALA LYS GLY ALA GLU GLU MET GLU THR VAL ILE PRO VAL
SEQRES 3 A 192 ASP VAL MET ARG ARG ALA GLY ILE LYS VAL THR VAL ALA
SEQRES 4 A 192 GLY LEU ALA GLY LYS ASP PRO VAL GLN CYS SER ARG ASP
SEQRES 5 A 192 VAL VAL ILE CYS PRO ASP ALA SER LEU GLU ASP ALA LYS
SEQRES 6 A 192 LYS GLU GLY PRO TYR ASP VAL VAL VAL LEU PRO GLY GLY
SEQRES 7 A 192 ASN LEU GLY ALA GLN ASN LEU SER GLU SER ALA ALA VAL
SEQRES 8 A 192 LYS GLU ILE LEU LYS GLU GLN GLU ASN ARG LYS GLY LEU
SEQRES 9 A 192 ILE ALA ALA ILE CSW ALA GLY PRO THR ALA LEU LEU ALA
SEQRES 10 A 192 HIS GLU ILE GLY PHE GLY SER LYS VAL THR THR HIS PRO
SEQRES 11 A 192 LEU ALA LYS ASP LYS MET MET ASN GLY GLY HIS TYR THR
SEQRES 12 A 192 TYR SER GLU ASN ARG VAL GLU LYS ASP GLY LEU ILE LEU
SEQRES 13 A 192 THR SER ARG GLY PRO GLY THR SER PHE LYS PHE ALA LEU
SEQRES 14 A 192 ALA ILE VAL GLU ALA LEU ASN GLY LYS GLU VAL ALA ALA
SEQRES 15 A 192 GLN VAL LYS ALA PRO LEU VAL LEU LYS ASP
MODRES 2RK6 CSW A 106 CYS CYSTEINE-S-DIOXIDE
HET CSW A 106 8
HETNAM CSW CYSTEINE-S-DIOXIDE
HETSYN CSW CYSTEINE SULFINIC ACID
FORMUL 1 CSW C3 H7 N O4 S
FORMUL 2 HOH *190(H2 O)
HELIX 1 1 GLU A 15 ALA A 29 1 15
HELIX 2 2 LEU A 58 LYS A 63 1 6
HELIX 3 3 GLY A 75 SER A 85 1 11
HELIX 4 4 SER A 85 ARG A 98 1 14
HELIX 5 5 GLY A 108 HIS A 115 1 8
HELIX 6 6 HIS A 126 LEU A 128 5 3
HELIX 7 7 ALA A 129 MET A 134 1 6
HELIX 8 8 GLY A 157 GLY A 159 5 3
HELIX 9 9 THR A 160 GLY A 174 1 15
HELIX 10 10 GLY A 174 ALA A 183 1 10
HELIX 11 11 PRO A 184 VAL A 186 5 3
SHEET 1 A 7 ALA A 56 SER A 57 0
SHEET 2 A 7 LYS A 32 GLY A 37 1 N GLY A 37 O ALA A 56
SHEET 3 A 7 ARG A 5 LEU A 10 1 N LEU A 10 O ALA A 36
SHEET 4 A 7 VAL A 69 LEU A 72 1 O VAL A 71 N LEU A 7
SHEET 5 A 7 LEU A 101 ILE A 105 1 O ALA A 103 N VAL A 70
SHEET 6 A 7 ILE A 152 SER A 155 1 O LEU A 153 N ILE A 102
SHEET 7 A 7 VAL A 146 ASP A 149 -1 N GLU A 147 O THR A 154
SHEET 1 B 2 VAL A 44 GLN A 45 0
SHEET 2 B 2 VAL A 51 ILE A 52 -1 O ILE A 52 N VAL A 44
SHEET 1 C 2 LYS A 122 VAL A 123 0
SHEET 2 C 2 THR A 140 TYR A 141 1 O THR A 140 N VAL A 123
LINK C ILE A 105 N CSW A 106 1555 1555 1.36
LINK C CSW A 106 N ALA A 107 1555 1555 1.34
CISPEP 1 GLY A 65 PRO A 66 0 1.54
CRYST1 74.928 74.928 75.147 90.00 90.00 120.00 P 31 2 1 6
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 0.013346 0.007705 0.000000 0.00000
SCALE2 0.000000 0.015411 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013307 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
