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- PDB-8zcx: Crystal Structure of a novel Aldehyde Dehydrogenase from Klebsiel... -

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Basic information

Entry
Database: PDB / ID: 8zcx
TitleCrystal Structure of a novel Aldehyde Dehydrogenase from Klebsiella pneumoniae
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / catalysis / Aldehyde dehydrogenase
Function / homology
Function and homology information


benzaldehyde dehydrogenase (NAD+) activity / aldehyde dehydrogenase (NAD+)
Similarity search - Function
Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
Aldehyde dehydrogenase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsZhang, J. / Han, Y. / Liu, W. / Zhang, W.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
CitationJournal: To Be Published
Title: Crystal Structure of a novel Aldehyde Dehydrogenase from Klebsiella pneumoniae
Authors: Zhang, J. / Han, Y. / Liu, W. / Zhang, W.
History
DepositionApr 30, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)210,9344
Polymers210,9344
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12070 Å2
ΔGint-52 kcal/mol
Surface area67150 Å2
MethodPISA
2
A: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)105,4672
Polymers105,4672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3120 Å2
ΔGint-15 kcal/mol
Surface area36070 Å2
MethodPISA
3
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)105,4672
Polymers105,4672
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-14 kcal/mol
Surface area35960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.669, 146.744, 149.528
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Aldehyde dehydrogenase / Aldehyde dehydrogenase family protein / Putative aldehyde dehydrogenase


Mass: 52733.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Sequence reference for Klebsiella pneumoniae (573) is not available in UniProt at the time of biocuration. Current sequence reference is from UniProt ID A0A069Q1D5.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: yfmT, xylC_1, CAZ10_02010, DT376_04100, IPC1295_07430, NCTC13621_03651, PAERUG_P19_London_7_VIM_2_05_10_05035
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A069Q1D5, aldehyde dehydrogenase (NAD+), benzaldehyde dehydrogenase (NAD+)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.82 Å3/Da / Density % sol: 56.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1M MMT, pH6.0, 25% PEG1500, 10% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL10U2 / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.44→50 Å / Num. obs: 83594 / % possible obs: 98.7 % / Redundancy: 17.5 % / CC1/2: 0.999 / Net I/σ(I): 12.8
Reflection shellResolution: 2.44→2.5 Å / Redundancy: 9 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5452 / CC1/2: 0.596

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimlessdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.44→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.799 / SU ML: 0.231 / Cross valid method: THROUGHOUT / ESU R: 0.462 / ESU R Free: 0.27 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25205 4316 5.2 %RANDOM
Rwork0.22197 ---
obs0.22354 78549 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.343 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å20 Å20 Å2
2--2.49 Å2-0 Å2
3----1.67 Å2
Refinement stepCycle: 1 / Resolution: 2.44→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13869 0 0 192 14061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01214523
X-RAY DIFFRACTIONr_bond_other_d0.0020.01613907
X-RAY DIFFRACTIONr_angle_refined_deg0.9971.81719715
X-RAY DIFFRACTIONr_angle_other_deg0.3631.74931833
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.41751860
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.8485149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.734102272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0530.22192
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217790
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023466
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_it5.5935.9387470
X-RAY DIFFRACTIONr_mcbond_other5.5935.9387470
X-RAY DIFFRACTIONr_mcangle_it8.68810.6719320
X-RAY DIFFRACTIONr_mcangle_other8.68710.6719321
X-RAY DIFFRACTIONr_scbond_it5.8676.5737053
X-RAY DIFFRACTIONr_scbond_other5.8676.5737054
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.34211.76610396
X-RAY DIFFRACTIONr_long_range_B_refined16.82872.0659561
X-RAY DIFFRACTIONr_long_range_B_other16.83472.0559502
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.44→2.503 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 225 -
Rwork0.339 4886 -
obs--82.54 %

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