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- PDB-4za2: Crystal structure of Pectobacterium carotovorum 2-keto-3-deoxy-D-... -

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Basic information

Entry
Database: PDB / ID: 4za2
TitleCrystal structure of Pectobacterium carotovorum 2-keto-3-deoxy-D-gluconate dehydrogenase complexed with NAD+
Components2-deoxy-D-gluconate 3-dehydrogenase
KeywordsOXIDOREDUCTASE / Pectin metabolism / Short-chain dehydrogenase/reductase / Rossmann fold / dual coenzyme specificity
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / :
Function and homology information
Biological speciesPectobacterium carotovorum subsp. carotovorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsTakase, R. / Maruyama, Y. / 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 Scienc Japan
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

Downloads & links

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Assembly

Deposited unit
A: 2-deoxy-D-gluconate 3-dehydrogenase
B: 2-deoxy-D-gluconate 3-dehydrogenase
C: 2-deoxy-D-gluconate 3-dehydrogenase
D: 2-deoxy-D-gluconate 3-dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,8325
Polymers109,1694
Non-polymers6631
Water10,737596
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15330 Å2
ΔGint-105 kcal/mol
Surface area32430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.663, 72.654, 98.991
Angle α, β, γ (deg.)90.00, 90.81, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
2-deoxy-D-gluconate 3-dehydrogenase / 2-keto-3-deoxy-D-gluconic acid dehydrogenase


Mass: 27292.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pectobacterium carotovorum subsp. carotovorum (bacteria)
Gene: RD01_02285, RD02_01035 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A093RP61, EC: 1.1.1.127
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 596 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: PEG 4000, isopropanol, nicotinamide adenine dinucleotide

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 18, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 140618 / % possible obs: 99.7 % / Redundancy: 4.1 % / Net I/σ(I): 40.5
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 4.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data scaling
SCALEPACKdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Z9Y

4z9y


Resolution: 1.55→34.13 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.764 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22581 7048 5 %RANDOM
Rwork0.19909 ---
obs0.20042 133535 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.487 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0 Å20.36 Å2
2--0.07 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.55→34.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7374 0 44 596 8014
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197535
X-RAY DIFFRACTIONr_bond_other_d0.0010.027346
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.95510183
X-RAY DIFFRACTIONr_angle_other_deg0.735316827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6165973
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65224.645310
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.976151296
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0371543
X-RAY DIFFRACTIONr_chiral_restr0.0670.21163
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028621
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021707
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_it1.0352.3193913
X-RAY DIFFRACTIONr_mcbond_other1.0352.3193912
X-RAY DIFFRACTIONr_mcangle_it1.6343.4714879
X-RAY DIFFRACTIONr_mcangle_other1.6343.4724880
X-RAY DIFFRACTIONr_scbond_it1.2682.543622
X-RAY DIFFRACTIONr_scbond_other1.2672.543623
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0483.7455305
X-RAY DIFFRACTIONr_long_range_B_refined3.75119.1188898
X-RAY DIFFRACTIONr_long_range_B_other3.75119.1218899
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 519 -
Rwork0.272 9824 -
obs--99.08 %

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