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- PDB-1spx: Crystal Structure of Glucose Dehydrogenase of Caenorhabditis Eleg... -

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Basic information

Entry
Database: PDB / ID: 1spx
TitleCrystal Structure of Glucose Dehydrogenase of Caenorhabditis Elegans in the Apo-Form
Componentsshort-chain reductase family member (5L265)
KeywordsOXIDOREDUCTASE / Parallel beta-sheet of seven strands in the order 3214567 / three alpha-helices on either side of beta-sheet / seventh alpha-helix on top of beta-sheet / Structural Genomics / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG
Function / homology
Function and homology information


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
DeHydrogenases, Short chain
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchormann, N. / Zhou, J. / McCombs, D. / Bray, T. / Symersky, J. / Huang, W.-Y. / Luan, C.-H. / Gray, R. / Luo, D. / Arabashi, A. ...Schormann, N. / Zhou, J. / McCombs, D. / Bray, T. / Symersky, J. / Huang, W.-Y. / Luan, C.-H. / Gray, R. / Luo, D. / Arabashi, A. / Bunzel, B. / Nagy, L. / Lu, S. / Li, S. / Lin, G. / Zhang, Y. / Qiu, S. / Tsao, J. / Luo, M. / Carson, M. / Southeast Collaboratory for Structural Genomics (SECSG)
CitationJournal: To be Published
Title: Crystal Structure of Glucose Dehydrogenase of Caenorhabditis Elegans in the Apo-Form: A Member of the SDR-Family
Authors: Schormann, N. / Zhou, J. / McCombs, D. / Bray, T. / Symersky, J. / Huang, W.-Y. / Luan, C.-H. / Gray, R. / Luo, D. / Arabashi, A. / Bunzel, B. / Nagy, L. / Lu, S. / Li, S. / Lin, G. / Zhang, ...Authors: Schormann, N. / Zhou, J. / McCombs, D. / Bray, T. / Symersky, J. / Huang, W.-Y. / Luan, C.-H. / Gray, R. / Luo, D. / Arabashi, A. / Bunzel, B. / Nagy, L. / Lu, S. / Li, S. / Lin, G. / Zhang, Y. / Qiu, S. / Tsao, J. / Luo, M. / Carson, M.
History
DepositionMar 17, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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: short-chain reductase family member (5L265)


Theoretical massNumber of molelcules
Total (without water)29,3981
Polymers29,3981
Non-polymers00
Water2,612145
1
A: short-chain reductase family member (5L265)

A: short-chain reductase family member (5L265)

A: short-chain reductase family member (5L265)

A: short-chain reductase family member (5L265)


Theoretical massNumber of molelcules
Total (without water)117,5944
Polymers117,5944
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area10820 Å2
ΔGint-81 kcal/mol
Surface area34340 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.682, 89.287, 108.153
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsThe biological unit is a tetramer (point group symmetry 222) generated by the following 4 operators: x,y,z; -x+1,-y+1,z; x,-y+1,-z+1; -x+1,y,-z+1

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Components

#1: Protein short-chain reductase family member (5L265) / Glucose Dehydrogenase


Mass: 29398.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: D1054.8 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q18946, glucose 1-dehydrogenase [NAD(P)+]
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.17 Å3/Da / Density % sol: 60.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2M Ammonium Sulfate, 5% Isopropanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 12, 2004 / Details: Osmic Mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 17897 / Num. obs: 17897 / % possible obs: 95.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 7.7 % / Biso Wilson estimate: 19.5 Å2 / Rmerge(I) obs: 0.086 / Rsym value: 0.086 / Net I/σ(I): 16.4
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4 % / Rmerge(I) obs: 0.239 / Num. unique all: 1460 / Rsym value: 0.239 / % possible all: 79.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Starting model was a homology model from Swiss-Model based on PDB entries 1RWB and 1G6K

1rwb

1g6k


Resolution: 2.1→19.54 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 316099.25 / Data cutoff high rms absF: 316099.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: The following residues are disordered and not visible in the electron density: 1; 96-108; 199-212; 266-278
RfactorNum. reflection% reflectionSelection details
Rfree0.25 834 4.9 %RANDOM
Rwork0.202 ---
all0.203 17779 --
obs0.202 17064 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.5179 Å2 / ksol: 0.383461 e/Å3
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å20 Å20 Å2
2--7.51 Å20 Å2
3----5.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1759 0 0 145 1904
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it2.272
X-RAY DIFFRACTIONc_scangle_it3.142.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 105 4.7 %
Rwork0.199 2149 -
obs-2149 73.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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