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- PDB-4z9x: Crystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase fro... -

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Basic information

Entry
Database: PDB / ID: 4z9x
TitleCrystal structure of 2-keto-3-deoxy-D-gluconate dehydrogenase from Streptococcus pyogenes
ComponentsGluconate 5-dehydrogenase
KeywordsOXIDOREDUCTASE / Glycosaminoglycan metabolism / Short-chain dehydrogenase/reductase / Rossmann fold / NADH specificity
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / 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
Putative 5-keto-D-gluconate 5-reductase
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsMaruyama, Y. / Takase, R. / Oiki, S. / Mikami, B. / Murata, K. / Hashimoto, W.
Funding support Japan, 4items
OrganizationGrant numberCountry
Grants-in-aid from the Japan Society for the Promotion of Science Japan
Program for Promotion of Basic Research Activities for Innovative Biosciences (PROBRAIN) of Japan Japan
Targeted Proteins Research Program from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT) of Japan Japan
Research fellowships from the Japan Society for the Promotion of Science for Young Scientists Japan
CitationJournal: Proteins / Year: 2016
Title: Structural determinants in bacterial 2-keto-3-deoxy-D-gluconate dehydrogenase KduD for dual-coenzyme specificity
Authors: Takase, R. / Maruyama, Y. / Oiki, S. / Mikami, B. / Murata, K. / Hashimoto, W.
History
DepositionApr 13, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Feb 19, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Nov 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
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: Gluconate 5-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)28,2081
Polymers28,2081
Non-polymers00
Water1,72996
1
A: Gluconate 5-dehydrogenase

A: Gluconate 5-dehydrogenase

A: Gluconate 5-dehydrogenase

A: Gluconate 5-dehydrogenase


Theoretical massNumber of molelcules
Total (without water)112,8334
Polymers112,8334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area16070 Å2
ΔGint-107 kcal/mol
Surface area34270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.621, 67.621, 108.907
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-366-

HOH

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Components

#1: Protein Gluconate 5-dehydrogenase / / 2-keto-3-deoxy-D-gluconic acid 5-dehydrogenase / Putative 5-keto-D-gluconate 5-reductase


Mass: 28208.229 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: idnO, M5005_Spy0524, SPy_0636 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9A0T1, EC: 1.1.1.127
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG 4000, sodium citrate, ammonium sulfate, nicotinamide adenine dinucleotide, 5-keto-D-gluconic acid potassium salt

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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: Apr 20, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 28162 / % possible obs: 99.8 % / Redundancy: 12 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 58
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.1 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data scaling
SCALEPACKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CXR

3cxr


Resolution: 1.7→32.01 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.829 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20066 1420 5 %RANDOM
Rwork0.18234 ---
obs0.18326 26769 98.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.612 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å2-0 Å2
2--0.59 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 1.7→32.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 0 96 2024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0191967
X-RAY DIFFRACTIONr_bond_other_d0.0010.021916
X-RAY DIFFRACTIONr_angle_refined_deg1.1021.9622662
X-RAY DIFFRACTIONr_angle_other_deg0.72634403
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5475257
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8825.0683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.25115331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.23159
X-RAY DIFFRACTIONr_chiral_restr0.0660.2303
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212263
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02430
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_it0.9112.2171028
X-RAY DIFFRACTIONr_mcbond_other0.9092.2151027
X-RAY DIFFRACTIONr_mcangle_it1.5213.3131282
X-RAY DIFFRACTIONr_mcangle_other1.523.3151283
X-RAY DIFFRACTIONr_scbond_it1.2772.493939
X-RAY DIFFRACTIONr_scbond_other1.2772.495940
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1173.6661380
X-RAY DIFFRACTIONr_long_range_B_refined3.36818.1372252
X-RAY DIFFRACTIONr_long_range_B_other3.32218.0552226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.233 97 -
Rwork0.205 1938 -
obs--98.36 %

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