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- PDB-3ado: Crystal Structure of the Rabbit L-Gulonate 3-Dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 3ado
TitleCrystal Structure of the Rabbit L-Gulonate 3-Dehydrogenase
ComponentsLambda-crystallin
KeywordsOXIDOREDUCTASE / L-Gulonate 3-Dehydrogenase / Structural Genomics / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Acetylation / Cytoplasm / Eye lens protein / NAD
Function / homology
Function and homology information


L-gulonate 3-dehydrogenase / L-gulonate 3-dehydrogenase activity / structural constituent of eye lens / NAD+ binding / fatty acid metabolic process / protein homodimerization activity / cytosol
Similarity search - Function
3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 ...3-hydroxyacyl-CoA dehydrogenase / 3-hydroxyacyl-CoA dehydrogenase, conserved site / 3-hydroxyacyl-CoA dehydrogenase signature. / 3-hydroxyacyl-CoA dehydrogenase, C-terminal / 3-hydroxyacyl-CoA dehydrogenase, NAD binding / 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain / 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 / 6-phosphogluconate dehydrogenase, domain 2 / 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesOryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAsada, Y. / Hara, A. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of the Rabbit L-Gulonate 3-Dehydrogenase
Authors: Asada, Y. / Hara, A. / Kunishima, N.
History
DepositionJan 26, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 9, 2010Provider: repository / Type: Initial release
SupersessionMay 26, 2010ID: 2DPO
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lambda-crystallin


Theoretical massNumber of molelcules
Total (without water)35,2461
Polymers35,2461
Non-polymers00
Water7,548419
1
A: Lambda-crystallin

A: Lambda-crystallin


Theoretical massNumber of molelcules
Total (without water)70,4922
Polymers70,4922
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area10170 Å2
ΔGint-90 kcal/mol
Surface area24860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.809, 69.079, 65.642
Angle α, β, γ (deg.)90.00, 102.729, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-737-

HOH

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Components

#1: Protein Lambda-crystallin / L-gulonate 3-dehydrogenase / Gul3DH


Mass: 35245.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oryctolagus cuniculus (rabbit) / Gene: CRYL1, GUL3DH / Plasmid: pCR T7/CT-TOPO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14755, L-gulonate 3-dehydrogenase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 4.6
Details: ammonium acetate, sodium acetate trihydrate, polyethylene glycol 4000, glycerol anhydrous, pH 4.6, MICROBATCH, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Jun 21, 2005 / Details: mirrors
RadiationMonochromator: Bending Magnet / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 34467 / Num. obs: 34467 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 18.901 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 9
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4 % / Rmerge(I) obs: 0.537 / Mean I/σ(I) obs: 3.3 / Num. unique all: 3421 / % possible all: 99.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3HDH

3hdh


Resolution: 1.7→28.96 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.206 1676 -RAMDOM
Rwork0.182 ---
all0.183 34455 --
obs0.183 34455 99.8 %-
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1-3.97 Å20 Å2-3.23 Å2
2---1.44 Å20 Å2
3----2.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.7→28.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2403 0 0 419 2822
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
LS refinement shellResolution: 1.7→1.78 Å / Rfactor Rfree error: 0.019
RfactorNum. reflection% reflection
Rfree0.276 211 -
Rwork0.252 --
obs--99.3 %

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