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- PDB-4lzj: Crystal Structure of MurQ from H.influenzae with bound inhibitor -

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Basic information

Entry
Database: PDB / ID: 4lzj
TitleCrystal Structure of MurQ from H.influenzae with bound inhibitor
ComponentsN-acetylmuramic acid 6-phosphate etherase
KeywordsLYASE/LYASE INHIBITOR / Alpha-Beta-Alpha sandwich / MurQ / YfeU / Protein-Ligand complex / NAD(P)/FAD-binding Rossmann fold / D-muramitol 6-phosphate / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


amino sugar catabolic process / N-acetylmuramic acid 6-phosphate etherase / N-acetylmuramic acid catabolic process / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / ether hydrolase activity / carbon-oxygen lyase activity / peptidoglycan turnover / carbohydrate derivative binding / carbohydrate metabolic process
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
Chem-22H / PHOSPHATE ION / N-acetylmuramic acid 6-phosphate etherase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.405 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
DepositionJul 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,1998
Polymers130,2594
Non-polymers9404
Water9,530529
1
A: N-acetylmuramic acid 6-phosphate etherase
D: N-acetylmuramic acid 6-phosphate etherase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6004
Polymers65,1292
Non-polymers4702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-26 kcal/mol
Surface area21940 Å2
MethodPISA
2
B: N-acetylmuramic acid 6-phosphate etherase
C: N-acetylmuramic acid 6-phosphate etherase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,6004
Polymers65,1292
Non-polymers4702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8870 Å2
ΔGint-38 kcal/mol
Surface area20880 Å2
MethodPISA
3
B: N-acetylmuramic acid 6-phosphate etherase
C: N-acetylmuramic acid 6-phosphate etherase
hetero molecules

A: N-acetylmuramic acid 6-phosphate etherase
D: N-acetylmuramic acid 6-phosphate etherase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,1998
Polymers130,2594
Non-polymers9404
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area17870 Å2
ΔGint-79 kcal/mol
Surface area41450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.492, 113.335, 143.917
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11B-508-

HOH

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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) / Gene: murQ / Production host: Escherichia coli (E. coli)
References: UniProt: P44862, N-acetylmuramic acid 6-phosphate etherase
#2: Chemical ChemComp-22H / 2-(acetylamino)-3-O-[(1R)-1-carboxyethyl]-2-deoxy-6-O-phosphono-D-glucitol


Mass: 375.266 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H22NO11P
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 529 / 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: 2.39 Å3/Da / Density % sol: 48.63 %
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: 298 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: 2.4→42.52 Å / Num. all: 49352 / Num. obs: 48045

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NRI

1nri


Resolution: 2.405→44.52 Å / SU ML: 0.28 / σ(F): 1.34 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2251 2422 5.04 %
Rwork0.1657 --
obs0.1687 48045 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.405→44.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8766 0 58 529 9353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088938
X-RAY DIFFRACTIONf_angle_d1.19712086
X-RAY DIFFRACTIONf_dihedral_angle_d16.3313438
X-RAY DIFFRACTIONf_chiral_restr0.0751491
X-RAY DIFFRACTIONf_plane_restr0.0051547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4048-2.45390.27961180.17031957X-RAY DIFFRACTION73
2.4539-2.50720.27621160.18092404X-RAY DIFFRACTION88
2.5072-2.56550.24171520.19112605X-RAY DIFFRACTION97
2.5655-2.62970.3011260.19172735X-RAY DIFFRACTION99
2.6297-2.70080.26811420.18712692X-RAY DIFFRACTION100
2.7008-2.78030.27151420.19462727X-RAY DIFFRACTION100
2.7803-2.870.28551400.19182737X-RAY DIFFRACTION100
2.87-2.97250.30411580.19722744X-RAY DIFFRACTION100
2.9725-3.09150.23611430.18712726X-RAY DIFFRACTION100
3.0915-3.23220.25451370.18752746X-RAY DIFFRACTION100
3.2322-3.40250.24141520.17732745X-RAY DIFFRACTION100
3.4025-3.61560.24161470.17592758X-RAY DIFFRACTION100
3.6156-3.89460.191450.1542774X-RAY DIFFRACTION100
3.8946-4.28630.23731410.15412711X-RAY DIFFRACTION98
4.2863-4.90580.16181510.12382785X-RAY DIFFRACTION100
4.9058-6.17820.19021520.15442823X-RAY DIFFRACTION100
6.1782-44.52760.16181600.14082954X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -16.758 Å / Origin y: 27.7892 Å / Origin z: 171.7257 Å
111213212223313233
T0.099 Å2-0.0397 Å20.0486 Å2-0.0765 Å2-0.003 Å2--0.0833 Å2
L0.4675 °2-0.1544 °20.2119 °2-0.2685 °2-0.0243 °2--0.406 °2
S-0.0011 Å °0.0197 Å °-0.0353 Å °0.0024 Å °0.0227 Å °0.0365 Å °-0.0181 Å °-0.0138 Å °-0.0183 Å °
Refinement TLS groupSelection details: all

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