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- PDB-6hg6: Clostridium beijerinckii aldo-keto reductase Cbei_3974 with NADPH -

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Basic information

Entry
Database: PDB / ID: 6hg6
TitleClostridium beijerinckii aldo-keto reductase Cbei_3974 with NADPH
ComponentsL-glyceraldehyde 3-phosphate reductase
KeywordsOXIDOREDUCTASE / Aldo keto reductase / AKR / Clostridium beijerinckii / Cbei_3974 / aldehyde reductase / methylglyoxal / TIM barrel / NADPH / furfural resistance / 3D Structure determination
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
Potassium channel, voltage-dependent, beta subunit, KCNAB-related / NADP-dependent oxidoreductase domain / NADP-dependent oxidoreductase domain / Aldo/keto reductase family / NADP-dependent oxidoreductase domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / L-glyceraldehyde 3-phosphate reductase
Similarity search - Component
Biological speciesClostridium beijerinckii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsScott, A.F. / Cresser-Brown, J. / Rizkallah, P.J. / Jin, Y. / Allemann, R.K.
CitationJournal: Appl.Environ.Microbiol. / Year: 2019
Title: Crystal Structure and Biophysical Analysis of Furfural-Detoxifying Aldehyde Reductase from Clostridium beijerinckii.
Authors: Scott, A.F. / Cresser-Brown, J. / Williams, T.L. / Rizkallah, P.J. / Jin, Y. / Luk, L.Y. / Allemann, R.K.
History
DepositionAug 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 17, 2024Group: 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: L-glyceraldehyde 3-phosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,52710
Polymers37,2851
Non-polymers1,2429
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint10 kcal/mol
Surface area14210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.165, 109.165, 72.157
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number79
Space group name H-MI4

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Components

#1: Protein L-glyceraldehyde 3-phosphate reductase


Mass: 37285.402 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium beijerinckii (bacteria) / Gene: gpr_2, CBEIJ_11710 / Plasmid: pET-14b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1S8QGT2, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 90 mM MOPS pH 7.6, 271 mM NH4Cl2, 2.7% PEG 8K, 10 mM NADPH, 2 mM 4-pyridine methanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 27, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 1.75→54.58 Å / Num. obs: 42762 / % possible obs: 100 % / Redundancy: 7.4 % / Biso Wilson estimate: 19.4 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.094 / Net I/σ(I): 13.3
Reflection shellResolution: 1.75→1.8 Å / Redundancy: 7 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3169 / CC1/2: 0.725 / Rrim(I) all: 0.963 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
xia2data reduction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T79

5t79


Resolution: 1.75→54.58 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.428 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.091 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19274 2105 4.9 %RANDOM
Rwork0.16471 ---
obs0.16605 40627 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.821 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refinement stepCycle: 1 / Resolution: 1.75→54.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2467 0 80 264 2811
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0132667
X-RAY DIFFRACTIONr_bond_other_d0.0040.0172437
X-RAY DIFFRACTIONr_angle_refined_deg1.9831.6513597
X-RAY DIFFRACTIONr_angle_other_deg1.5581.585685
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81823.603136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.53615474
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5481513
X-RAY DIFFRACTIONr_chiral_restr0.0960.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022994
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02536
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_it0.9861.4241294
X-RAY DIFFRACTIONr_mcbond_other0.9841.4221293
X-RAY DIFFRACTIONr_mcangle_it1.6432.121628
X-RAY DIFFRACTIONr_mcangle_other1.6432.1231629
X-RAY DIFFRACTIONr_scbond_it1.5461.7381373
X-RAY DIFFRACTIONr_scbond_other1.5461.741374
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.352.5091970
X-RAY DIFFRACTIONr_long_range_B_refined6.35318.9023134
X-RAY DIFFRACTIONr_long_range_B_other6.22418.1673071
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 166 -
Rwork0.287 2982 -
obs--99.27 %
Refinement TLS params.Method: refined / Origin x: 83.7297 Å / Origin y: 63.4506 Å / Origin z: -3.0832 Å
111213212223313233
T0.0213 Å2-0.0197 Å20.0075 Å2-0.0874 Å20.0737 Å2--0.1784 Å2
L1.3883 °20.3968 °2-0.3777 °2-2.0618 °2-0.0889 °2--1.0083 °2
S-0.0718 Å °0.038 Å °0.0854 Å °-0.0857 Å °-0.0223 Å °-0.4553 Å °-0.0882 Å °0.2209 Å °0.0941 Å °

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