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- PDB-8zo3: The crystal structures of MurK in complex with N-acetylglucosamin... -

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Basic information

Entry
Database: PDB / ID: 8zo3
TitleThe crystal structures of MurK in complex with N-acetylglucosamine from Clostridium acetobutylicum
ComponentsN-acetylmuramic acid/N-acetylglucosamine kinase
KeywordsTRANSFERASE / N-acetylmuramic acid/N-acetylglucosamine kinase / MurK / Nucleotide-binding
Function / homology
Function and homology information


N-acetylmuramic acid metabolic process / carbohydrate kinase activity / N-acetylglucosamine kinase / N-acetylglucosamine kinase activity / carbohydrate phosphorylation / N-acetylglucosamine metabolic process / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / peptidoglycan turnover / ATP binding / cytoplasm
Similarity search - Function
: / ATPase, BadF/BadG/BcrA/BcrD type / BadF/BadG/BcrA/BcrD ATPase family / ATPase, nucleotide binding domain
Similarity search - Domain/homology
N-acetylmuramic acid/N-acetylglucosamine kinase
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 Å
AuthorsYang, X.Y. / Liu, X.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Int.J.Biol.Macromol. / Year: 2024
Title: Structural and biochemical insights into the molecular mechanism of N-acetylglucosamine/N-Acetylmuramic acid kinase MurK from Clostridium acetobutylicum.
Authors: He, X. / Liu, C. / Li, X. / Yang, Q. / Niu, F. / An, L. / Fan, Y. / Li, Y. / Zhou, Z. / Zhou, H. / Yang, X. / Liu, X.
History
DepositionMay 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: N-acetylmuramic acid/N-acetylglucosamine kinase
B: N-acetylmuramic acid/N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3884
Polymers66,9462
Non-polymers4422
Water10,305572
1
A: N-acetylmuramic acid/N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6942
Polymers33,4731
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: N-acetylmuramic acid/N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6942
Polymers33,4731
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: N-acetylmuramic acid/N-acetylglucosamine kinase
hetero molecules

B: N-acetylmuramic acid/N-acetylglucosamine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,3884
Polymers66,9462
Non-polymers4422
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+3/2,-y,z+1/21
Buried area4830 Å2
ΔGint-2 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.028, 103.829, 108.864
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/N-acetylglucosamine kinase / MurNAc/GlcNAc kinase / Murein sugar kinase


Mass: 33472.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium acetobutylicum (strain ATCC 824 / DSM 792 / JCM 1419 / IAM 19013 / LMG 5710 / NBRC 13948 / NRRL B-527 / VKM B-1787 / 2291 / W) (bacteria)
Gene: murK, CA_C0183 / Production host: Escherichia coli (E. coli)
References: UniProt: Q97ML3, Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor, N-acetylglucosamine kinase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 572 / 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: 2.2 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 0.2 M Potassium sodium tartrate 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Aug 15, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.88→75.14 Å / Num. obs: 48285 / % possible obs: 98.6 % / Redundancy: 7.1 % / CC1/2: 0.995 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.061 / Rrim(I) all: 0.163 / Χ2: 0.95 / Net I/σ(I): 8 / Num. measured all: 340700
Reflection shellResolution: 1.88→1.98 Å / % possible obs: 99.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.735 / Num. measured all: 47134 / Num. unique obs: 6980 / CC1/2: 0.884 / Rpim(I) all: 0.297 / Rrim(I) all: 0.797 / Χ2: 0.71 / Net I/σ(I) obs: 2.8

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.88→46.94 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 30.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2692 2440 5.08 %
Rwork0.2125 --
obs0.2153 48073 98.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.88→46.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4618 0 30 572 5220
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074696
X-RAY DIFFRACTIONf_angle_d0.946300
X-RAY DIFFRACTIONf_dihedral_angle_d5.692670
X-RAY DIFFRACTIONf_chiral_restr0.059744
X-RAY DIFFRACTIONf_plane_restr0.008786
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.88-1.920.31811170.24572667X-RAY DIFFRACTION98
1.92-1.960.30291450.24632673X-RAY DIFFRACTION99
1.96-20.29431630.22442697X-RAY DIFFRACTION100
2-2.050.28951500.2192654X-RAY DIFFRACTION100
2.05-2.110.2211540.21862682X-RAY DIFFRACTION100
2.11-2.170.26141360.21632702X-RAY DIFFRACTION99
2.17-2.240.24371370.20712708X-RAY DIFFRACTION99
2.24-2.320.27311620.2152682X-RAY DIFFRACTION99
2.32-2.410.34551480.21762703X-RAY DIFFRACTION99
2.41-2.520.33491730.22142656X-RAY DIFFRACTION99
2.52-2.660.27591660.22372676X-RAY DIFFRACTION99
2.66-2.820.26891520.21612687X-RAY DIFFRACTION99
2.82-3.040.30481090.2252737X-RAY DIFFRACTION99
3.04-3.350.25811230.21132759X-RAY DIFFRACTION99
3.35-3.830.25071150.1952310X-RAY DIFFRACTION83
3.83-4.820.2271700.18142732X-RAY DIFFRACTION98
4.82-46.940.26661200.22162908X-RAY DIFFRACTION98

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