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- PDB-1g0n: STRUCTURE OF TRIHYDROXYNAPHTHALENE REDUCTASE IN COMPLEX WITH NADP... -

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Basic information

Entry
Database: PDB / ID: 1g0n
TitleSTRUCTURE OF TRIHYDROXYNAPHTHALENE REDUCTASE IN COMPLEX WITH NADPH AND 4,5,6,7-TETRACHLORO-PHTHALIDE
ComponentsTRIHYDROXYNAPHTHALENE REDUCTASE
KeywordsOXIDOREDUCTASE / Protein-NADPH-active site inhibitor complex / diuncleotide binding fold / short chain dehydrogenase
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 / 4,5,6,7-TETRACHLORO-PHTHALIDE / Tetrahydroxynaphthalene reductase
Similarity search - Component
Biological speciesMagnaporthe grisea (fungus)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsLiao, D. / Basarab, G.S. / Gatenby, A.A. / Valent, B. / 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
DepositionOct 6, 2000Deposition 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

Downloads & links

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Assembly

Deposited unit
A: TRIHYDROXYNAPHTHALENE REDUCTASE
B: TRIHYDROXYNAPHTHALENE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,1185
Polymers60,3552
Non-polymers1,7633
Water6,954386
1
A: TRIHYDROXYNAPHTHALENE REDUCTASE
B: TRIHYDROXYNAPHTHALENE REDUCTASE
hetero molecules

A: TRIHYDROXYNAPHTHALENE REDUCTASE
B: TRIHYDROXYNAPHTHALENE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,23610
Polymers120,7114
Non-polymers3,5266
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_765-x+2,-x+y+1,-z+1/31
Buried area23030 Å2
ΔGint-171 kcal/mol
Surface area31450 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)140.5, 140.5, 72.7
Angle α, β, γ (deg.)90., 90., 120.
Int Tables number152
Space group name H-MP3121
DetailsThe biological assembly is a homo tetramer. The two molecules in the asymmetric unit represent half of the biological assembly. The tetramer has a 222 symmetry / The following transformation should be applied to both chain A and chain B to generate the tetramer. Rotation matrix: -0.500 -0.866 0.00 -0.866 0.500 0.00 0.00 0.00 -1.00 Translation vector: 214.21, 123.66, 24.31

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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)
References: UniProt: Q12634, tetrahydroxynaphthalene reductase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-PHH / 4,5,6,7-TETRACHLORO-PHTHALIDE / 4,5,6,7-TETRACHLORO-3H-ISOBENZOFURAN-1-ONE


Mass: 271.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H2Cl4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 3.43 Å3/Da / Density % sol: 64.15 %
Crystal growTemperature: 274 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 6K, glycerol, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 274K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %PEG60001reservoir
214 %glycerol1reservoir
30.1 MHEPES1reservoir
420-23 mg/mlprotein1drop
550 mMTris-HCl1drop
610 mMNADPH1drop
72 mMinhibitor1drop

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Data collection

DiffractionMean temperature: 102 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 26, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 54812 / Num. obs: 208682 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.351 / Num. unique all: 2189 / % possible all: 76.4
Reflection
*PLUS
Num. obs: 54812 / Num. measured all: 208682
Reflection shell
*PLUS
% possible obs: 76.4 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: Only one monomer of the dimer in the asymmetric unit has the electron density for the inhibitor.
RfactorNum. reflection
Rfree0.244 5314
Rwork0.195 -
all-53601
obs-53145
Refinement stepCycle: LAST / Resolution: 2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3921 0 110 386 4417
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg1.47
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

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