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- PDB-1idp: Crystal structure of scytalone dehydratase F162A mutant in the un... -

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Basic information

Entry
Database: PDB / ID: 1idp
TitleCrystal structure of scytalone dehydratase F162A mutant in the unligated state
ComponentsSCYTALONE DEHYDRATASE
KeywordsLYASE / MELANINE BIOSYNTHESIS
Function / homology
Function and homology information


scytalone dehydratase / scytalone dehydratase activity / melanin biosynthetic process / endosome / metal ion binding
Similarity search - Function
Scytalone dehydratase / : / Scytalone dehydratase / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Scytalone dehydratase
Similarity search - Component
Biological speciesMagnaporthe grisea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsNakasako, M. / Motoyama, T. / Yamaguchi, I.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization of scytalone dehydratase F162A mutant in the unligated state and a preliminary X-ray diffraction study at 37 K
Authors: Motoyama, T. / Nakasako, M. / Yamaguchi, I.
#1: Journal: Biochemistry / Year: 1998
Title: Cryogenic X-ray crystal structure analysis for the complex of scytalone dehydratase of a rice blast fungus and its tight-binding inhibitor, carpropamid: the structural basis of tight-binding inhibition
Authors: Nakasako, M. / Motoyama, T. / Kurahashi, Y. / Yamaguchi, I.
#2: Journal: Proteins / Year: 1999
Title: High-resolution structures of scytalone dehydratase-inhibitor complexes crystallized at physiological pH
Authors: Wawrzak, Z. / Sandalova, T. / Steffens, J.J. / Basarab, G.S. / Lundqvist, T. / Lindqvist, Y. / Jordan, D.B.
#3: Journal: Structure / Year: 1994
Title: Crystal structure of scytalone dehydratase--a disease determinant of the rice pathogen, Magnaporthe grisea
Authors: Lundqvist, T. / Rice, J. / Hodge, C.N. / Basarab, G.S. / Pierce, J. / Lindqvist, Y.
#4: Journal: Biochemistry / Year: 1998
Title: Structure-based design of potent inhibitors of scytalone dehydratase: displacement of a water molecule from the active site
Authors: Chen, J.M. / Xu, S.L. / Wawrzak, Z. / Basarab, G.S. / Jordan, D.B.
#5: Journal: Biosci.Biotechnol.Biochem. / Year: 1998
Title: cDNA cloning, expression, and mutagenesis of scytalone dehydratase needed for pathogenicity of the rice blast fungus, Pyricularia oryzae
Authors: Motoyama, T. / Imanishi, K. / Yamaguchi, I.
History
DepositionApr 4, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 8, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_sheet
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_sheet.number_strands
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SCYTALONE DEHYDRATASE
B: SCYTALONE DEHYDRATASE
C: SCYTALONE DEHYDRATASE


Theoretical massNumber of molelcules
Total (without water)60,6143
Polymers60,6143
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-26 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.64, 61.31, 72.62
Angle α, β, γ (deg.)90.00, 120.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SCYTALONE DEHYDRATASE


Mass: 20204.807 Da / Num. of mol.: 3 / Mutation: F162A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe grisea (fungus) / Production host: Escherichia coli (E. coli) / References: UniProt: P56221, scytalone dehydratase

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG4000, sodium acetate, Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
230 %(w/v)PEG40001reservoir
30.2 Msodium acetate1reservoir
40.1 MTris1reservoirpH8.0

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1371
21121
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL41XU10.71
SYNCHROTRONSPring-8 BL44B220.7
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDDec 16, 2000K-B MIRROR
MARRESEARCH2CCDFeb 12, 2000CYLINDRICAL BENT MIRROR
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SISINGLE WAVELENGTHMx-ray1
2SISINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.711
20.71
ReflectionResolution: 1.45→100 Å / Num. all: 355404 / Num. obs: 96126 / % possible obs: 97.5 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 23.8
Reflection shellResolution: 1.45→1.47 Å / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 4.2 / % possible all: 100
Reflection
*PLUS
Num. obs: 98206 / % possible obs: 99.7 % / Num. measured all: 365877
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2STD

2std


Resolution: 1.45→8 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 1 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 -9.7 %RANDOM
Rwork0.199 ---
obs-92461 10 %-
Refinement stepCycle: LAST / Resolution: 1.45→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3692 0 0 0 3692
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.595
X-RAY DIFFRACTIONx_improper_angle_d1.818
LS refinement shellResolution: 1.45→1.52 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.266 1077 -
Rwork0.257 10507 -
obs-9430 93.5 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.818

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