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- PDB-4u8g: Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 4u8g
TitleCrystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus agalactiae
ComponentsPutative uncharacterized protein gbs1891
KeywordsOXIDOREDUCTASE / dehydrogenase / SDR family / rosman fold / NADH
Function / homology
Function and homology information


oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
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
Gluconate 5-dehydrogenase
Similarity search - Component
Biological speciesStreptococcus agalactiae NEM316 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsMaruyama, Y. / Oiki, S. / Takase, R. / Mikami, B. / Murata, K. / Hashimoto, W.
Funding support Japan, 3items
OrganizationGrant numberCountry
Grants-in-Aid for Scientific Research from the Japan Society for the Promotion of Science Japan
Targeted Proteins Research Program from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan Japan
Research Grant from Mizutani Foundation for Glycoscience Japan
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Metabolic Fate of Unsaturated Glucuronic/Iduronic Acids from Glycosaminoglycans: MOLECULAR IDENTIFICATION AND STRUCTURE DETERMINATION OF STREPTOCOCCAL ISOMERASE AND DEHYDROGENASE.
Authors: Maruyama, Y. / Oiki, S. / Takase, R. / Mikami, B. / Murata, K. / Hashimoto, W.
History
DepositionAug 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 1.3Jan 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / diffrn_source ...citation / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein gbs1891


Theoretical massNumber of molelcules
Total (without water)29,9421
Polymers29,9421
Non-polymers00
Water905
1
A: Putative uncharacterized protein gbs1891

A: Putative uncharacterized protein gbs1891

A: Putative uncharacterized protein gbs1891

A: Putative uncharacterized protein gbs1891


Theoretical massNumber of molelcules
Total (without water)119,7694
Polymers119,7694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation11_655-x+y+1,y,-z1
Buried area14840 Å2
ΔGint-122 kcal/mol
Surface area41020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.943, 83.943, 181.101
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Putative uncharacterized protein gbs1891


Mass: 29942.211 Da / Num. of mol.: 1 / Mutation: S150A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae NEM316 (bacteria)
Strain: NEM316 / Gene: gbs1891 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8E370
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% polyethylene glycol monomethyl ether 550, 0.1 M sodium chloride, and 0.1 M sodium N,N-bis(2-hydroxyethyl)glycine (pH 9.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 14, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 8964 / % possible obs: 99.8 % / Redundancy: 22.5 % / Net I/σ(I): 78.5

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Processing

SoftwareName: REFMAC / Version: 5.8.0049 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3cxr

3cxr


Resolution: 2.9→35.64 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.899 / SU B: 14.148 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R: 0.274 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2869 421 4.7 %RANDOM
Rwork0.21139 ---
obs0.21477 8454 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.396 Å2
Baniso -1Baniso -2Baniso -3
1-31.64 Å20 Å20 Å2
2--31.64 Å20 Å2
3----63.28 Å2
Refinement stepCycle: 1 / Resolution: 2.9→35.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1992 0 0 5 1997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192025
X-RAY DIFFRACTIONr_bond_other_d0.0010.021979
X-RAY DIFFRACTIONr_angle_refined_deg1.2191.9622736
X-RAY DIFFRACTIONr_angle_other_deg0.77934553
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0565265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80625.18183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.53715346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.552158
X-RAY DIFFRACTIONr_chiral_restr0.0650.2311
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022325
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02439
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.5457.3681063
X-RAY DIFFRACTIONr_mcbond_other3.4687.3671062
X-RAY DIFFRACTIONr_mcangle_it5.62611.0511327
X-RAY DIFFRACTIONr_mcangle_other5.63311.0551328
X-RAY DIFFRACTIONr_scbond_it3.3517.734961
X-RAY DIFFRACTIONr_scbond_other3.357.737962
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.48611.4481410
X-RAY DIFFRACTIONr_long_range_B_refined8.87469.9188496
X-RAY DIFFRACTIONr_long_range_B_other8.87369.9238495
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.901→2.976 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.476 34 -
Rwork0.33 586 -
obs--98.73 %

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