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

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Basic information

Entry
Database: PDB / ID: 7bvj
TitleUDP-N-acetylglucosamine 3-dehydrogenase GnnA from Acidithiobacillus ferrooxidans (P21)
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 / Chem-F8U / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase, NAD-binding
Function and homology information
Biological speciesAcidithiobacillus ferrooxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 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 10, 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
C: Oxidoreductase, NAD-binding
D: Oxidoreductase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,5589
Polymers140,6544
Non-polymers2,9045
Water14,376798
1
A: Oxidoreductase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0773
Polymers35,1631
Non-polymers9142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area680 Å2
ΔGint-2 kcal/mol
Surface area14870 Å2
MethodPISA
2
B: Oxidoreductase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8272
Polymers35,1631
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area660 Å2
ΔGint-2 kcal/mol
Surface area14140 Å2
MethodPISA
3
C: Oxidoreductase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8272
Polymers35,1631
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint-1 kcal/mol
Surface area13890 Å2
MethodPISA
4
D: Oxidoreductase, NAD-binding
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8272
Polymers35,1631
Non-polymers6631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-3 kcal/mol
Surface area14100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.809, 80.057, 107.211
Angle α, β, γ (deg.)90.000, 95.020, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Oxidoreductase, NAD-binding /


Mass: 35163.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
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 / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-F8U / (2R,3R)-2,3-bis(oxidanyl)butane-1,4-disulfonic acid


Mass: 250.247 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O8S2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 798 / 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: 2.21 Å3/Da / Density % sol: 44.42 % / Mosaicity: 0.29 °
Crystal growTemperature: 289 K / Method: batch mode / pH: 5.5 / Details: 100 mM Bis-Tris, 200 mM NaCl, 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 21, 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: 2.15→19.8 Å / Num. obs: 66811 / % possible obs: 99.8 % / Redundancy: 7.5 % / CC1/2: 0.976 / Rmerge(I) obs: 0.293 / Rpim(I) all: 0.115 / Rrim(I) all: 0.315 / Net I/σ(I): 5.1 / Num. measured all: 499713 / Scaling rejects: 1804
Reflection shell

Diffraction-ID: 1 / Redundancy: 6.7 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.15-2.21.1062992444770.2290.4751.2082.2100
10.08-19.80.22839645930.9630.0950.2488.686.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.15 Å19.8 Å
Translation2.15 Å19.8 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.3data scaling
PHASER2.8.2phasing
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4koa, 4h3v, 4fb5, 5yab, 4hkt, 3ezy

4koa

4h3v

4fb5

5yab

4hkt

3ezy


Resolution: 2.15→19.8 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 33.63
RfactorNum. reflection% reflection
Rfree0.2719 3270 4.9 %
Rwork0.2158 --
obs0.2186 66725 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 81.15 Å2 / Biso mean: 30.5095 Å2 / Biso min: 9.85 Å2
Refinement stepCycle: final / Resolution: 2.15→19.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9373 0 122 798 10293
Biso mean--30.13 35.35 -
Num. residues----1219
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.15-2.230.32853090.257563266635
2.23-2.320.33033070.246163046611
2.32-2.420.32623310.231963416672
2.42-2.550.29533170.226463206637
2.55-2.710.26892910.241963656656
2.71-2.920.32213290.243663146643
2.92-3.210.2993320.228463416673
3.21-3.670.27073460.214463436689
3.67-4.610.21783720.180463506722
4.61-19.80.24733360.196964516787

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