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- PDB-1ybv: STRUCTURE OF TRIHYDROXYNAPHTHALENE REDUCTASE IN COMPLEX WITH NADP... -

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Basic information

Entry
Database: PDB / ID: 1ybv
TitleSTRUCTURE OF TRIHYDROXYNAPHTHALENE REDUCTASE IN COMPLEX WITH NADPH AND AN ACTIVE SITE INHIBITOR
ComponentsTRIHYDROXYNAPHTHALENE REDUCTASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


tetrahydroxynaphthalene reductase / tetrahydroxynaphthalene reductase activity / melanin biosynthetic process
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-METHYL-1,2,4-TRIAZOLO[3,4-B]BENZOTHIAZOLE / Chem-NDP / Tetrahydroxynaphthalene reductase
Similarity search - Component
Biological speciesMagnaporthe grisea (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsAndersson, A. / Schneider, G. / Lindqvist, Y.
Citation
Journal: Structure / Year: 1996
Title: Crystal structure of the ternary complex of 1,3,8-trihydroxynaphthalene reductase from Magnaporthe grisea with NADPH and an active-site inhibitor.
Authors: Andersson, A. / Jordan, D. / Schneider, G. / Lindqvist, Y.
#1: Journal: Proteins / Year: 1996
Title: Crystallisation and Preliminary X-Ray Diffraction Study of 1,3,8-Trihydroxynaphthalene Reductase from Magnaporthe Grisea
Authors: Andersson, A. / Jordan, D. / Schneider, G. / Valent, B. / Lindqvist, Y.
History
DepositionSep 23, 1996Processing site: BNL
Revision 1.0Oct 15, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 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: TRIHYDROXYNAPHTHALENE REDUCTASE
B: TRIHYDROXYNAPHTHALENE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1756
Polymers60,3032
Non-polymers1,8714
Water0
1
A: TRIHYDROXYNAPHTHALENE REDUCTASE
B: TRIHYDROXYNAPHTHALENE REDUCTASE
hetero molecules

A: TRIHYDROXYNAPHTHALENE REDUCTASE
B: TRIHYDROXYNAPHTHALENE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,34912
Polymers120,6074
Non-polymers3,7438
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+2/31
Buried area22940 Å2
ΔGint-112 kcal/mol
Surface area33700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)142.600, 142.600, 72.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999978, -0.004005, 0.005347), (0.002301, 0.544827, 0.838545), (-0.006271, 0.838539, -0.544806)
Vector: 142.6044, -20.4747, 37.9884)

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Components

#1: Protein TRIHYDROXYNAPHTHALENE REDUCTASE / NAPHTHOL REDUCTASE


Mass: 30151.643 Da / Num. of mol.: 2 / Mutation: P2A, S241V, A242Q, H247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe grisea (fungus) / Strain: 409158 / Cell line: BL21 / Gene: BUF+ / Plasmid: PTHNR2 / Gene (production host): BUF+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PET11 (NOVAGEN) / References: UniProt: Q12634, EC: 1.3.1.50
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-BEA / 5-METHYL-1,2,4-TRIAZOLO[3,4-B]BENZOTHIAZOLE / TRICYCLAZOLE


Mass: 190.245 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H8N3S

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.55 Å3/Da / Density % sol: 58.5 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Andersson, A., (1996) Proteins: Struct.,Funct., Genet., 24, 525.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
22.5 mMHEPES1drop
32.5 mM1dropNaCl
49 %PEG60001drop
518 %PEG60001reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Dec 16, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 19294 / % possible obs: 91.4 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.086
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. measured all: 111124

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
RefinementResolution: 2.8→8 Å / σ(F): 2 / Details: STRICT TWO-FOLD NON-CRYSTALLOGRAPHIC SYMMETRY
RfactorNum. reflection
Rfree0.254 -
Rwork0.223 -
obs0.223 17495
Displacement parametersBiso mean: 26.3 Å2
Refinement stepCycle: LAST / Resolution: 2.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 122 0 4140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.5
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

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