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- PDB-8bre: 1,6-anhydro-n-actetylmuramic acid kinase (AnmK) -

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Basic information

Entry
Database: PDB / ID: 8bre
Title1,6-anhydro-n-actetylmuramic acid kinase (AnmK)
ComponentsAnhydro-N-acetylmuramic acid kinase
KeywordsTRANSFERASE / Anhydro-sugar kinase Phosphotransferase ATP binding
Function / homology
Function and homology information


anhydro-N-acetylmuramic acid kinase / 1,6-anhydro-N-acetyl-beta-muramic acid catabolic process / amino sugar metabolic process / phosphotransferase activity, alcohol group as acceptor / peptidoglycan turnover / kinase activity / phosphorylation / response to antibiotic / ATP binding
Similarity search - Function
Anhydro-N-acetylmuramic acid kinase / Anhydro-N-acetylmuramic acid kinase / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Anhydro-N-acetylmuramic acid kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsJimenez-Faraco, E. / Hermoso, J.A.
Funding support Spain, 1items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)PID2020-115331GB_I00 Spain
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Catalytic process of anhydro-N-acetylmuramic acid kinase from Pseudomonas aeruginosa.
Authors: El-Araby, A.M. / Jimenez-Faraco, E. / Feltzer, R. / Martin-Garcia, J.M. / Karri, B.R. / Ramachandran, B. / Kim, C. / Fisher, J.F. / Hermoso, J.A. / Mobashery, S.
History
DepositionNov 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,0194
Polymers78,9482
Non-polymers712
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation, sedimentation velocity analytical ultracentrifugation (SV-AUC)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-27 kcal/mol
Surface area27290 Å2
Unit cell
Length a, b, c (Å)90.093, 90.093, 178.378
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Anhydro-N-acetylmuramic acid kinase / AnhMurNAc kinase


Mass: 39473.828 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: GAGAG tag in N-terminal (unobserved, disordered). These five residues should be renumbered from -4 to 0.
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: anmK, PA0666 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9I5Q5, anhydro-N-acetylmuramic acid kinase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.67 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 8% PEG 8000, 0.2M litium chloride, 0.05M magnesium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979264 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979264 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5749
pseudo-merohedral22-K, -H, -L20.4251
ReflectionResolution: 2→47.292 Å / Num. obs: 55214 / % possible obs: 100 % / Redundancy: 20.1 % / CC1/2: 1 / Net I/σ(I): 22.5
Reflection shellResolution: 2→2.05 Å / Redundancy: 20.5 % / Rmerge(I) obs: 1.688 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4056 / CC1/2: 0.667 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3QBX

3qbx


Resolution: 2→47.292 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.961 / WRfactor Rfree: 0.2 / WRfactor Rwork: 0.166 / SU B: 5.139 / SU ML: 0.085 / Average fsc free: 0.9678 / Average fsc work: 0.9789 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.03
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 2667 4.834 %RANDOM
Rwork0.1776 52500 --
all0.179 ---
obs-55167 99.978 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 51.715 Å2
Baniso -1Baniso -2Baniso -3
1--0.319 Å20 Å20 Å2
2---0.319 Å20 Å2
3---0.638 Å2
Refinement stepCycle: LAST / Resolution: 2→47.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5413 0 2 173 5588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125541
X-RAY DIFFRACTIONr_bond_other_d0.0090.0165033
X-RAY DIFFRACTIONr_angle_refined_deg1.041.647542
X-RAY DIFFRACTIONr_angle_other_deg0.4731.55711705
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995711
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.367549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.42610849
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.45210250
X-RAY DIFFRACTIONr_chiral_restr0.0550.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021091
X-RAY DIFFRACTIONr_nbd_refined0.210.21136
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.24678
X-RAY DIFFRACTIONr_nbtor_refined0.170.22700
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2230
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1410.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1260.216
X-RAY DIFFRACTIONr_nbd_other0.1870.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.29
X-RAY DIFFRACTIONr_mcbond_it2.4374.662853
X-RAY DIFFRACTIONr_mcbond_other2.4374.6592853
X-RAY DIFFRACTIONr_mcangle_it3.5256.9843561
X-RAY DIFFRACTIONr_mcangle_other3.5246.9833562
X-RAY DIFFRACTIONr_scbond_it2.4094.9522688
X-RAY DIFFRACTIONr_scbond_other2.4084.9512689
X-RAY DIFFRACTIONr_scangle_it3.5227.3233981
X-RAY DIFFRACTIONr_scangle_other3.5227.3223982
X-RAY DIFFRACTIONr_lrange_it5.52460.6946068
X-RAY DIFFRACTIONr_lrange_other5.48760.5126043
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.4711880.3973862X-RAY DIFFRACTION99.8521
2.052-2.1080.4521920.3133775X-RAY DIFFRACTION100
2.108-2.1690.371550.2633695X-RAY DIFFRACTION100
2.169-2.2360.3091650.2453592X-RAY DIFFRACTION100
2.236-2.3090.2181740.1913460X-RAY DIFFRACTION100
2.309-2.390.2121700.1953351X-RAY DIFFRACTION100
2.39-2.480.2571550.1933230X-RAY DIFFRACTION100
2.48-2.5820.2231320.1763125X-RAY DIFFRACTION100
2.582-2.6960.2141390.183008X-RAY DIFFRACTION100
2.696-2.8280.2461580.1842833X-RAY DIFFRACTION100
2.828-2.980.2081490.1872715X-RAY DIFFRACTION100
2.98-3.1610.2411670.1892506X-RAY DIFFRACTION100
3.161-3.3790.2011280.1942430X-RAY DIFFRACTION100
3.379-3.6490.2111350.1832212X-RAY DIFFRACTION100
3.649-3.9970.164790.1642102X-RAY DIFFRACTION100
3.997-4.4680.1831120.1411867X-RAY DIFFRACTION100
4.468-5.1570.184990.1391640X-RAY DIFFRACTION100
5.157-6.310.21780.161393X-RAY DIFFRACTION99.9321
6.31-8.9020.14530.1311090X-RAY DIFFRACTION100
8.902-47.2920.173390.143614X-RAY DIFFRACTION99.2401
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.18950.0931-0.15720.4254-0.07330.1432-0.0055-0.058-0.00510.1275-0.0252-0.0136-0.00670.04760.03070.05790.0054-0.0330.0342-0.02360.089813.312718.42690.8601
20.67630.21-0.19720.1562-0.12960.1116-0.05460.2103-0.0075-0.05430.04260.00790.0381-0.04640.01190.04220.0004-0.04420.0813-0.02760.085222.897524.2113-39.3492
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1-363 }A1 - 363
2X-RAY DIFFRACTION2{ B|1-363 }B1 - 363

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