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- PDB-2std: SCYTALONE DEHYDRATASE COMPLEXED WITH TIGHT-BINDING INHIBITOR CARP... -

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Basic information

Entry
Database: PDB / ID: 2std
TitleSCYTALONE DEHYDRATASE COMPLEXED WITH TIGHT-BINDING INHIBITOR CARPROPAMID
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
Chem-CRP / Scytalone dehydratase
Similarity search - Component
Biological speciesMagnaporthe grisea (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsNakasako, M. / Motoyama, T. / Kurahashi, Y. / Yamaguchi, I.
CitationJournal: 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.
History
DepositionDec 21, 1997Processing site: BNL
Revision 1.0Feb 16, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SCYTALONE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7123
Polymers20,2811
Non-polymers4312
Water3,135174
1
A: SCYTALONE DEHYDRATASE
hetero molecules

A: SCYTALONE DEHYDRATASE
hetero molecules

A: SCYTALONE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1359
Polymers60,8433
Non-polymers1,2926
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7670 Å2
ΔGint-116 kcal/mol
Surface area19850 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)74.540, 74.540, 71.200
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein SCYTALONE DEHYDRATASE


Mass: 20280.902 Da / Num. of mol.: 1
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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CRP / ((1RS,3SR)-2,2-DICHLORO-N-[(R)-1-(4-CHLOROPHENYL)ETHYL]-1-ETHYL-3-METHYLCYCLOPROPANECARBOXAMIDE / CARPROPAMID


Mass: 334.669 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H18Cl3NO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 65 %
Description: THE CRYSTAL IS NEARLY ISOMORPHOUS WITH THAT OF 1STD
Crystal growpH: 5.2 / Details: pH 5.2
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 mg/mlprotein1drop
214.5 %(w/v)PEG33501reservoir
3280 mMammonium sulfate1reservoir
4200 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 18, 1996 / Details: DOUBLE MIRROR FOCUSING
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→71.1 Å / Num. obs: 12014 / % possible obs: 85.6 % / Observed criterion σ(I): 1 / Redundancy: 4.18 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 14.5
Reflection shellResolution: 2.1→2.25 Å / Redundancy: 2.51 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3 / % possible all: 74.6
Reflection
*PLUS
Num. measured all: 50287
Reflection shell
*PLUS
Lowest resolution: 2.2 Å / % possible obs: 74.6 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
PROCESSdata reduction
PROCESSdata scaling
X-PLORphasing
RefinementStarting model: 1STD

1std


Resolution: 2.1→8 Å / Data cutoff high absF: 1000 / Data cutoff low absF: 1 / Isotropic thermal model: GAUSS / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.259 -10 %
Rwork0.179 --
obs0.179 11759 83.4 %
Displacement parametersBiso mean: 28.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 25 174 1542
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.264
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.72
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.653
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.1→2.19 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.248 -10.5 %
Rwork0.252 1104 -
obs--74.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.72
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.72
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.653
LS refinement shell
*PLUS
Rfactor obs: 0.252

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