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- PDB-1ja9: Crystal structure of 1,3,6,8-tetrahydroxynaphthalene reductase in... -

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Basic information

Entry
Database: PDB / ID: 1ja9
TitleCrystal structure of 1,3,6,8-tetrahydroxynaphthalene reductase in complex with NADPH and pyroquilon
Components1,3,6,8-tetrahydroxynaphthalene reductase
KeywordsOXIDOREDUCTASE / protein-NADPH-active site inhibitor complex / short chain dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
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 / PYROQUILON / 1,3,6,8-tetrahydroxynaphthalene reductase
Similarity search - Component
Biological speciesMagnaporthe grisea (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLiao, D.-I. / Thompson, J.E. / Fahnestock, S. / Valent, B. / Jordan, D.B.
CitationJournal: Biochemistry / Year: 2001
Title: A structural account of substrate and inhibitor specificity differences between two naphthol reductases.
Authors: Liao, D.I. / Thompson, J.E. / Fahnestock, S. / Valent, B. / Jordan, D.B.
History
DepositionMay 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1,3,6,8-tetrahydroxynaphthalene reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5893
Polymers28,6711
Non-polymers9192
Water3,927218
1
A: 1,3,6,8-tetrahydroxynaphthalene reductase
hetero molecules

A: 1,3,6,8-tetrahydroxynaphthalene reductase
hetero molecules

A: 1,3,6,8-tetrahydroxynaphthalene reductase
hetero molecules

A: 1,3,6,8-tetrahydroxynaphthalene reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,35712
Polymers114,6834
Non-polymers3,6758
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
crystal symmetry operation7_645y+1,x-1,-z1
crystal symmetry operation8_665-y+1,-x+1,-z1
Buried area18520 Å2
ΔGint-101 kcal/mol
Surface area32390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)94.800, 94.800, 71.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein 1,3,6,8-tetrahydroxynaphthalene reductase / 4HNR


Mass: 28670.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnaporthe grisea (fungus) / Gene: RICE BLAST FUNGUS / Plasmid: pFA168 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HFV6
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-PYQ / PYROQUILON / 1,2,5,6-TETRAHYDRO-4H-PYRROLO(3,2,1-IJ)QUINOLIN-4-ONE


Mass: 173.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H11NO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / 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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Li2SO4, HEPES, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.5 M1reservoirLi2SO4
20.1 MHEPES-NaOH1reservoir
320 mg/mlprotein1drop
410 mMNADPH1drop
52 mMpyroquilon1drop
650 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 0.963 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.963 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 51109 / Num. obs: 487876 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 9.5 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 22.8
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.9 / % possible all: 71.6
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 51109 / Num. measured all: 487876
Reflection shell
*PLUS
Highest resolution: 1.5 Å / % possible obs: 71.6 % / Rmerge(I) obs: 0.381

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G0O with NADPH and pyroquilon removed from the model.

1g0o


Resolution: 1.5→30 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.221 4911 -
Rwork0.189 --
all-50204 -
obs-49111 10 %
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1912 0 61 218 2191
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.53
X-RAY DIFFRACTIONx_bond_d0.012
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.5 Å / Lowest resolution: 30 Å / σ(F): 2 / Rfactor obs: 0.189
Solvent computation
*PLUS
Displacement parameters
*PLUS

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