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- PDB-7bvk: UDP-N-acetylglucosamine 3-dehydrogenase GnnA from Acidithiobacill... -

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Basic information

Entry
Database: PDB / ID: 7bvk
TitleUDP-N-acetylglucosamine 3-dehydrogenase GnnA from Acidithiobacillus ferrooxidans (P212121)
ComponentsOxidoreductase, NAD-binding
KeywordsOXIDOREDUCTASE / GnnA / UDP-GlcNAc / lipopolysaccharide / UDP-N-acetylglucosamine 3-dehydrogenase
Function / homologyGfo/Idh/MocA-like oxidoreductase, N-terminal / Oxidoreductase family, NAD-binding Rossmann fold / NAD(P)-binding domain superfamily / nucleotide binding / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase, NAD-binding
Function and homology information
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsWangkanont, K.
Funding support Thailand, 1items
OrganizationGrant numberCountry
Chulalongkorn University Ratchadapisek Sompoch Endowment FundCU_GR_60_22_23_10 Thailand
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Biochemical and Structural Investigation of GnnA in the Lipopolysaccharide Biosynthesis Pathway of Acidithiobacillus ferrooxidans .
Authors: Manissorn, J. / Sitthiyotha, T. / Montalban, J.R.E. / Chunsrivirot, S. / Thongnuek, P. / Wangkanont, K.
History
DepositionApr 11, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 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: Oxidoreductase, NAD-binding
B: Oxidoreductase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9427
Polymers70,3272
Non-polymers1,6155
Water1,15364
1
A: Oxidoreductase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9233
Polymers35,1631
Non-polymers7592
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-7 kcal/mol
Surface area14350 Å2
MethodPISA
2
B: Oxidoreductase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0194
Polymers35,1631
Non-polymers8563
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-9 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.535, 80.489, 104.272
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Oxidoreductase, NAD-binding


Mass: 35163.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: synthetic gene, codon optimized
Source: (gene. exp.) Acidithiobacillus ferrooxidans (strain ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455) (bacteria)
Strain: ATCC 23270 / DSM 14882 / CIP 104768 / NCIMB 8455 / Gene: AFE_1457 / Plasmid: pET24a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): LEMO21 / References: UniProt: B7JA34
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.19 Å3/Da / Density % sol: 43.94 % / Mosaicity: 0.28 °
Crystal growTemperature: 289 K / Method: batch mode / pH: 5.5
Details: 100 mM Bis-Tris, 200 mM Ammonium Sulfate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.999999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 20, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999999 Å / Relative weight: 1
ReflectionResolution: 2.7→19.76 Å / Num. obs: 17552 / % possible obs: 99.7 % / Redundancy: 7.1 % / CC1/2: 0.99 / Rmerge(I) obs: 0.213 / Rpim(I) all: 0.086 / Rrim(I) all: 0.23 / Net I/σ(I): 6.5 / Num. measured all: 125291 / Scaling rejects: 86
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.837.31.0021674822920.8760.3971.0792.3100
8.96-19.7660.13529674920.9870.0590.14811.590.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.72 Å19.76 Å
Translation4.72 Å19.76 Å

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Processing

Software
NameVersionClassification
PHENIX1.17.1refinement
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7BVJ

7bvj


Resolution: 2.7→19.76 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 34.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2937 929 5.32 %
Rwork0.2154 16538 -
obs0.2195 17467 99.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 115.14 Å2 / Biso mean: 42.2284 Å2 / Biso min: 16.83 Å2
Refinement stepCycle: final / Resolution: 2.7→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4652 0 77 64 4793
Biso mean--55.66 39.88 -
Num. residues----604
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.840.35251400.26823062446100
2.84-3.020.35251400.260723062446100
3.02-3.250.34061320.24323332465100
3.25-3.580.37271180.233923472465100
3.58-4.090.26661280.199423852513100
4.09-5.140.23391280.179223842512100
5.14-19.760.27521430.20642477262099

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