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- PDB-9dtk: Crystal structure of UDP-N-acetylenolpyruvoylglucosamine reductas... -

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Basic information

Entry
Database: PDB / ID: 9dtk
TitleCrystal structure of UDP-N-acetylenolpyruvoylglucosamine reductase (MurB) from Brucella ovis
ComponentsUDP-N-acetylenolpyruvoylglucosamine reductase
KeywordsOXIDOREDUCTASE / flavoenzyme / peptidoglycan synthesis / cell wall / NADPH oxidation / Brucella ovis / FAD
Function / homology
Function and homology information


UDP-N-acetylmuramate dehydrogenase / UDP-N-acetylmuramate dehydrogenase activity / peptidoglycan biosynthetic process / FAD binding / cell wall organization / regulation of cell shape / cell division / cytosol
Similarity search - Function
UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain superfamily / UDP-N-acetylenolpyruvoylglucosamine reductase, C-terminal domain / FAD linked oxidase, N-terminal / FAD binding domain / FAD-binding, type PCMH, subdomain 1 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily
Similarity search - Domain/homology
Chem-EPU / FLAVIN-ADENINE DINUCLEOTIDE / UDP-N-acetylenolpyruvoylglucosamine reductase
Similarity search - Component
Biological speciesBrucella ovis ATCC 25840 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsMartinez-Julvez, M. / Medina, M. / Minjarez-Saenz, M.
Funding support Spain, 3items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)PID2022-136369NB-I00 Spain
Other governmentLMP13_21 Spain
Other governmentBiologia Estructural_E35_23R Spain
CitationJournal: Arch.Biochem.Biophys. / Year: 2025
Title: Structural and functional insights into UDP-N-acetylglucosamine-enolpyruvate reductase (MurB) from Brucella ovis.
Authors: Minjarez-Saenz, M. / Rivero, M. / Correa-Perez, V. / Boneta, S. / Suarez, P. / Polo, V. / Sadeghi, S.J. / Yruela, I. / Martinez-Julvez, M. / Medina, M.
History
DepositionOct 1, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UDP-N-acetylenolpyruvoylglucosamine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4984
Polymers34,9391
Non-polymers1,5593
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2690 Å2
ΔGint-22 kcal/mol
Surface area14060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.032, 37.533, 77.902
Angle α, β, γ (deg.)90.00, 91.09, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

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Components

#1: Protein UDP-N-acetylenolpyruvoylglucosamine reductase / UDP-N-acetylmuramate dehydrogenase


Mass: 34938.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella ovis ATCC 25840 (bacteria) / Gene: murB, BOV_1386 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A5VRH5, UDP-N-acetylmuramate dehydrogenase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#4: Chemical ChemComp-EPU / URIDINE-DIPHOSPHATE-2(N-ACETYLGLUCOSAMINYL) BUTYRIC ACID / ENOLPYRUVYL-URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE


Mass: 677.400 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29N3O19P2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.41 Å3/Da / Density % sol: 49.01 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 16% PEG4000, 0.200 M lithium sulfate, 0.100 M Tris-HCl, pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979185 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979185 Å / Relative weight: 1
ReflectionResolution: 2.23→77.89 Å / Num. obs: 15551 / % possible obs: 94.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.4
Reflection shellResolution: 2.23→2.35 Å / Rmerge(I) obs: 0.264 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 1638 / % possible all: 94.4

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.27→60.01 Å / Cross valid method: FREE R-VALUE / σ(F): 34.75 / Phase error: 34.2 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2472 825 5.31 %
Rwork0.2166 --
obs0.2473 15534 93.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→60.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2549 0 5 94 2648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.768
X-RAY DIFFRACTIONf_dihedral_angle_d11.129374
X-RAY DIFFRACTIONf_chiral_restr0.043378
X-RAY DIFFRACTIONf_plane_restr0.009457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.410.34531112502X-RAY DIFFRACTION91
2.41-2.590.34731370.33982519X-RAY DIFFRACTION93
2.59-2.850.3411230.30672158X-RAY DIFFRACTION79
2.85-3.270.31841290.27112522X-RAY DIFFRACTION93
3.27-4.120.25811490.21782527X-RAY DIFFRACTION91
4.12-50.2321300.18542527X-RAY DIFFRACTION89

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