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- PDB-4m0d: Crystal structure of MurQ from H.influenzae in apo form -

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Basic information

Entry
Database: PDB / ID: 4m0d
TitleCrystal structure of MurQ from H.influenzae in apo form
ComponentsN-acetylmuramic acid 6-phosphate etherase
KeywordsLYASE / NAD(P)/FAD- binding Rossmann fold / Alpha-Beta-Alpha sandwich / MurQ / YfeU
Function / homology
Function and homology information


N-acetylmuramic acid 6-phosphate etherase / N-acetylmuramic acid catabolic process / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / amino sugar catabolic process / ether hydrolase activity / carbon-oxygen lyase activity / fructose-6-phosphate binding / peptidoglycan turnover / response to fructose / enzyme inhibitor activity ...N-acetylmuramic acid 6-phosphate etherase / N-acetylmuramic acid catabolic process / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / amino sugar catabolic process / ether hydrolase activity / carbon-oxygen lyase activity / fructose-6-phosphate binding / peptidoglycan turnover / response to fructose / enzyme inhibitor activity / glucose homeostasis / carbohydrate binding / enzyme binding / cytosol
Similarity search - Function
N-acetylmuramic acid 6-phosphate etherase MurQ / Helicase, Ruva Protein; domain 3 - #1080 / C-terminal lid domain of glucokinase regulatory protein / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Glucokinase regulatory protein family signature. / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily ...N-acetylmuramic acid 6-phosphate etherase MurQ / Helicase, Ruva Protein; domain 3 - #1080 / C-terminal lid domain of glucokinase regulatory protein / Glucokinase regulatory protein, conserved site / N-acetylmuramic acid 6-phosphate etherase/glucokinase regulatory protein / Glucokinase regulatory protein family signature. / SIS domain / SIS domain / SIS domain profile. / SIS domain superfamily / Glucose-6-phosphate isomerase like protein; domain 1 / Helicase, Ruva Protein; domain 3 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
N-acetylmuramic acid 6-phosphate etherase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.577 Å
AuthorsHazra, S. / Blanchard, J.
CitationJournal: Biochemistry / Year: 2013
Title: Structure of MurNAc 6-phosphate hydrolase (MurQ) from Haemophilus influenzae with a bound inhibitor.
Authors: Hadi, T. / Hazra, S. / Tanner, M.E. / Blanchard, J.S.
History
DepositionAug 1, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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: N-acetylmuramic acid 6-phosphate etherase
B: N-acetylmuramic acid 6-phosphate etherase
C: N-acetylmuramic acid 6-phosphate etherase
D: N-acetylmuramic acid 6-phosphate etherase


Theoretical massNumber of molelcules
Total (without water)130,2594
Polymers130,2594
Non-polymers00
Water5,098283
1
A: N-acetylmuramic acid 6-phosphate etherase
D: N-acetylmuramic acid 6-phosphate etherase


Theoretical massNumber of molelcules
Total (without water)65,1292
Polymers65,1292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8410 Å2
ΔGint-32 kcal/mol
Surface area21840 Å2
MethodPISA
2
B: N-acetylmuramic acid 6-phosphate etherase
C: N-acetylmuramic acid 6-phosphate etherase


Theoretical massNumber of molelcules
Total (without water)65,1292
Polymers65,1292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8190 Å2
ΔGint-33 kcal/mol
Surface area21520 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17890 Å2
ΔGint-76 kcal/mol
Surface area42080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.127, 111.650, 134.509
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
N-acetylmuramic acid 6-phosphate etherase / / MurNAc-6-P etherase / N-acetylmuramic acid 6-phosphate hydrolase / N-acetylmuramic acid 6-phosphate lyase


Mass: 32564.734 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: Rd KW20 / Gene: murQ / Production host: Escherichia coli (E. coli)
References: UniProt: P44862, N-acetylmuramic acid 6-phosphate etherase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 283 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Nacl, 0.1 M Bis-Tris:HCl, pH 5.5, 25% (w/v) PEG-3350, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 65 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorDetector: IMAGE PLATE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.58→32.56 Å / Num. all: 35231 / Num. obs: 34265 / Redundancy: 5.5 %
Reflection shellHighest resolution: 2.58 Å

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIXmodel building
PHENIX1.8.1_1168refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NRI

1nri


Resolution: 2.577→32.563 Å / SU ML: 0.42 / σ(F): 0.11 / Phase error: 30.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2859 2000 5.84 %
Rwork0.1828 --
obs0.1888 34265 92.84 %
all-35231 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.577→32.563 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8838 0 0 283 9121
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088830
X-RAY DIFFRACTIONf_angle_d1.26711955
X-RAY DIFFRACTIONf_dihedral_angle_d15.7883301
X-RAY DIFFRACTIONf_chiral_restr0.0821498
X-RAY DIFFRACTIONf_plane_restr0.0051537
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5773-2.64180.41161130.29881822X-RAY DIFFRACTION75
2.6418-2.71320.35971370.25242220X-RAY DIFFRACTION91
2.7132-2.79290.33491410.22492257X-RAY DIFFRACTION92
2.7929-2.8830.31281390.21272256X-RAY DIFFRACTION93
2.883-2.9860.32511420.21372299X-RAY DIFFRACTION94
2.986-3.10550.33981440.21432306X-RAY DIFFRACTION94
3.1055-3.24670.34581440.20942323X-RAY DIFFRACTION95
3.2467-3.41770.34731450.2032352X-RAY DIFFRACTION95
3.4177-3.63160.28241470.19142364X-RAY DIFFRACTION94
3.6316-3.91150.27631460.16762347X-RAY DIFFRACTION96
3.9115-4.30440.25141480.14692398X-RAY DIFFRACTION95
4.3044-4.92540.2391470.14232366X-RAY DIFFRACTION95
4.9254-6.19840.24561530.17122491X-RAY DIFFRACTION98
6.1984-32.5660.23861540.15662464X-RAY DIFFRACTION93

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