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

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Basic information

Entry
Database: PDB / ID: 1doh
TitleSTRUCTURE OF TRIHYDROXYNAPHTHALENE REDUCTASE IN COMPLEX WITH NADPH AND 4-NITRO-INDEN-1-ONE
ComponentsTRIHYDROXYNAPHTHALENE REDUCTASE
KeywordsOXIDOREDUCTASE / PROTEIN-NADPH-ACTIVE SITE INHIBITOR COMPLEX / DINUCLEOTIDE BINDING FOLD
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
Chem-NDP / 4-NITRO-INDEN-1-ONE / Tetrahydroxynaphthalene reductase
Similarity search - Component
Biological speciesMagnaporthe grisea (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsLiao, D.I. / Basarab, G.S. / Gatenby, A.A. / Jordan, D.B.
CitationJournal: Structure / Year: 2001
Title: Structures of trihydroxynaphthalene reductase-fungicide complexes: implications for structure-based design and catalysis.
Authors: Liao, D. / Basarab, G.S. / Gatenby, A.A. / Valent, B. / Jordan, D.B.
History
DepositionDec 20, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Nov 3, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 7, 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)62,1966
Polymers60,3552
Non-polymers1,8414
Water7,512417
1
A: TRIHYDROXYNAPHTHALENE REDUCTASE
B: TRIHYDROXYNAPHTHALENE REDUCTASE
hetero molecules

A: TRIHYDROXYNAPHTHALENE REDUCTASE
B: TRIHYDROXYNAPHTHALENE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,39312
Polymers120,7114
Non-polymers3,6828
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area24050 Å2
ΔGint-112 kcal/mol
Surface area33630 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)142.800, 142.800, 72.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein TRIHYDROXYNAPHTHALENE REDUCTASE


Mass: 30177.682 Da / Num. of mol.: 2 / Mutation: S241V, A242Q, H247R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe grisea (fungus) / Plasmid: PTHNR2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PET11 (NOVAGEN)
References: UniProt: Q12634, tetrahydroxynaphthalene reductase
#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-NID / 4-NITRO-INDEN-1-ONE


Mass: 175.141 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H5NO3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 3.56 Å3/Da / Density % sol: 65.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG6000, GLYCEROL, HEPES, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 %PEG60001reservoir
210 %glycerol1reservoir
30.1 MMES-NaOH1reservoir
420-23 mg/mlprotein1drop
550 mMTris-HCl1drop
610 mMNADPH1drop
72 mMinhibitor1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 18, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 49907 / Num. obs: 47473 / % possible obs: 94.6 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 25.47 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 14.9
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 2.04 % / Rmerge(I) obs: 0.283 / % possible all: 76
Reflection
*PLUS
Num. measured all: 209443
Reflection shell
*PLUS
% possible obs: 76 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.1→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.257 4616 -
Rwork0.205 --
obs0.205 46163 97 %
all-46505 -
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4057 0 122 417 4596
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_deg1.451
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
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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