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- PDB-3vtz: Structure of Thermoplasma volcanium aldohexose dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 3vtz
TitleStructure of Thermoplasma volcanium aldohexose dehydrogenase
ComponentsGlucose 1-dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold / NAD binding
Function / homology
Function and homology information


oxidoreductase activity
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
Glucose 1-dehydrogenase
Similarity search - Component
Biological speciesThermoplasma volcanium (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYasutake, Y. / Nishioka, T. / Tamura, T.
CitationJournal: To be Published
Title: Structure of Thermoplasma volcanium aldohexose dehydrogenase
Authors: Yasutake, Y. / Nishioka, T. / Tamura, T.
History
DepositionJun 12, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucose 1-dehydrogenase
B: Glucose 1-dehydrogenase
C: Glucose 1-dehydrogenase
D: Glucose 1-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)116,9864
Polymers116,9864
Non-polymers00
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17450 Å2
ΔGint-112 kcal/mol
Surface area33700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.018, 110.018, 77.172
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Glucose 1-dehydrogenase /


Mass: 29246.398 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma volcanium (archaea) / Strain: JCM 9571 / Gene: TV0074 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q97CM7, EC: 1.1.1.118
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.3 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 0.2M Li2SO4, 28% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 43989 / % possible obs: 100 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 24.1
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.509 / Mean I/σ(I) obs: 3.5 / Num. unique all: 4645 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DTD

2dtd


Resolution: 2.3→44.79 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.928 / SU B: 13.348 / SU ML: 0.153 / Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.228 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23201 2342 5.1 %RANDOM
Rwork0.16682 ---
obs0.17007 43989 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.351 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å2-0.57 Å2-0 Å2
2---1.13 Å20 Å2
3---1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7633 0 0 87 7720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197749
X-RAY DIFFRACTIONr_angle_refined_deg2.0421.96610514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.07551002
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54324.478297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.247151349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7191544
X-RAY DIFFRACTIONr_chiral_restr0.1520.21262
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215664
LS refinement shellResolution: 2.301→2.361 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 194 -
Rwork0.197 3227 -
obs--99.16 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1578-0.4554-0.13720.9604-0.13460.84130.0174-0.0570.22160.0648-0.0142-0.2271-0.16020.1146-0.00320.08750.0182-0.01920.062-0.04040.1143-13.908427.2167-0.2117
21.3499-0.23470.01470.6812-0.21740.7585-0.00140.0682-0.2777-0.0502-0.00360.04940.1862-0.06150.0050.06050.0058-0.02510.0986-0.03960.1113-30.3378-3.8395-18.6315
31.0291-0.14490.48581.1883-0.05981.47920.0375-0.2551-0.06980.2714-0.00840.31880.0399-0.4204-0.02910.08890.00160.04670.1705-0.02030.1187-34.85488.43478.2387
41.17740.0846-0.25961.03850.36751.5826-0.02920.21590.3121-0.26510.05770.1604-0.4063-0.2087-0.02850.14450.0393-0.04990.11280.030.1274-26.599224.0259-27.0316
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 256
2X-RAY DIFFRACTION2B2 - 256
3X-RAY DIFFRACTION3C2 - 256
4X-RAY DIFFRACTION4D2 - 256

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