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- PDB-1std: CRYSTAL STRUCTURE OF SCYTALONE DEHYDRATASE: A DISEASE DETERMINANT... -

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Basic information

Entry
Database: PDB / ID: 1std
TitleCRYSTAL STRUCTURE OF SCYTALONE DEHYDRATASE: A DISEASE DETERMINANT OF THE RICE PATHOGEN, MAGNAPORTHE GRISEA
ComponentsSCYTALONE DEHYDRATASE
KeywordsLYASE (CARBON-OXYGEN)
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
N-[1-(4-BROMOPHENYL)ETHYL]-5-FLUORO SALICYLAMIDE / Scytalone dehydratase
Similarity search - Component
Biological speciesMagnaporthe grisea (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsLundqvist, T. / Lindqvist, Y.
Citation
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.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Preliminary Crystallographic Studies on Scytalone Dehydratase from Magnaporthe Grisea
Authors: Lundqvist, T. / Weber, P.C. / Hodge, C.N. / Braswell, E.H. / Rice, J. / Pierce, J.
History
DepositionAug 19, 1994Processing site: BNL
Revision 1.0Aug 19, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SCYTALONE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,7153
Polymers20,2811
Non-polymers4342
Water724
1
A: SCYTALONE DEHYDRATASE
hetero molecules

A: SCYTALONE DEHYDRATASE
hetero molecules

A: SCYTALONE DEHYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1459
Polymers60,8433
Non-polymers1,3036
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 area8410 Å2
ΔGint-75 kcal/mol
Surface area20360 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)75.500, 75.500, 73.800
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) / 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-BFS / N-[1-(4-BROMOPHENYL)ETHYL]-5-FLUORO SALICYLAMIDE


Mass: 338.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13BrFNO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.91 %
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Lundqvist, T., (1993) J.Mol.Biol., 232, 999.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.2 Macetate1reservoir
20.28 Mammonium sulfate1reservoir
310-15 %PEG40001reservoir
48 mg/mlprotein1drop

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Data collection

Reflection
*PLUS
Highest resolution: 2.9 Å / Num. obs: 5646 / % possible obs: 99.5 % / Num. measured all: 41844 / Rmerge(I) obs: 0.085

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.179 / Rfactor obs: 0.179 / Highest resolution: 2.9 Å
Refinement stepCycle: LAST / Highest resolution: 2.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 25 4 1383
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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
Refinement
*PLUS
Lowest resolution: 6 Å / Rfactor obs: 0.191 / Rfactor Rwork: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS

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