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- PDB-8cpb: 1,6-anhydro-n-actetylmuramic acid kinase (AnmK) in complex with A... -

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Basic information

Entry
Database: PDB / ID: 8cpb
Title1,6-anhydro-n-actetylmuramic acid kinase (AnmK) in complex with AMPPNP, and AnhMurNAc at 1.7 Angstroms resolution.
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 / 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
Chem-AH0 / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / L(+)-TARTARIC ACID / Anhydro-N-acetylmuramic acid kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
DepositionMar 2, 2023Deposition 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

Downloads & links

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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)80,99510
Polymers78,9482
Non-polymers2,0478
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation, sedimentation velocity analytical ultracentrifugation (SV-AUC)
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-9 kcal/mol
Surface area25970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.670, 90.670, 171.686
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 2 molecules AB

#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 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

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Non-polymers , 5 types, 269 molecules

#2: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-AH0 / 2-(2-ACETYLAMINO-4-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCT-3-YLOXY)-PROPIONIC ACID / 1,6-anhydro-N-acetylmuramic acid


Mass: 275.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.58 Å3/Da / Density % sol: 52.33 % / Description: hexagonal crystals
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, Na/K tartrate 0.2M

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 16, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5214
pseudo-merohedral22-K, -H, -L20.4786
ReflectionResolution: 1.7→46.25 Å / Num. obs: 87575 / % possible obs: 100 % / Redundancy: 20.7 % / CC1/2: 0.99 / Rpim(I) all: 0.24 / Net I/σ(I): 17.4
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 20.9 % / Mean I/σ(I) obs: 1.9 / Num. unique obs: 4470 / CC1/2: 0.81 / Rpim(I) all: 0.398 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
PHASERphasing
REFMAC5.8.0352refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→46.249 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.658 / SU ML: 0.048 / Cross valid method: FREE R-VALUE / ESU R: 0.02 / ESU R Free: 0.02
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2046 4235 4.839 %
Rwork0.1689 83286 -
all0.171 --
obs-87521 99.979 %
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: 28.328 Å2
Baniso -1Baniso -2Baniso -3
1-5.196 Å20 Å20 Å2
2--5.196 Å20 Å2
3----10.392 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.249 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5494 0 132 261 5887
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125807
X-RAY DIFFRACTIONr_bond_other_d0.0170.0165199
X-RAY DIFFRACTIONr_angle_refined_deg1.0711.6217925
X-RAY DIFFRACTIONr_angle_other_deg0.7071.55912101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3855727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.396553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74710867
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.1210255
X-RAY DIFFRACTIONr_chiral_restr0.0550.2871
X-RAY DIFFRACTIONr_chiral_restr_other0.1410.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026727
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021132
X-RAY DIFFRACTIONr_nbd_refined0.2130.21186
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1870.24809
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22800
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.22920
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2273
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2030.219
X-RAY DIFFRACTIONr_nbd_other0.2490.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1270.213
X-RAY DIFFRACTIONr_mcbond_it1.2852.5382909
X-RAY DIFFRACTIONr_mcbond_other1.2842.5382909
X-RAY DIFFRACTIONr_mcangle_it1.9643.8073632
X-RAY DIFFRACTIONr_mcangle_other1.9643.8073633
X-RAY DIFFRACTIONr_scbond_it1.5152.7452898
X-RAY DIFFRACTIONr_scbond_other1.5152.7452897
X-RAY DIFFRACTIONr_scangle_it2.2964.0474292
X-RAY DIFFRACTIONr_scangle_other2.2964.0474292
X-RAY DIFFRACTIONr_lrange_it3.59133.7636402
X-RAY DIFFRACTIONr_lrange_other3.55333.5786369
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.5142940.4786198X-RAY DIFFRACTION99.7848
1.744-1.7920.4053160.3685911X-RAY DIFFRACTION99.9839
1.792-1.8440.3553000.2895837X-RAY DIFFRACTION100
1.844-1.90.2722740.2555651X-RAY DIFFRACTION99.9831
1.9-1.9620.272430.2085549X-RAY DIFFRACTION99.9827
1.962-2.0310.2163030.1785238X-RAY DIFFRACTION100
2.031-2.1080.2123030.185113X-RAY DIFFRACTION100
2.108-2.1940.2012380.1684908X-RAY DIFFRACTION100
2.194-2.2910.2242440.1594739X-RAY DIFFRACTION99.9799
2.291-2.4020.2152140.1624537X-RAY DIFFRACTION100
2.402-2.5320.2162230.1594298X-RAY DIFFRACTION100
2.532-2.6850.1922020.1554058X-RAY DIFFRACTION100
2.685-2.870.1881940.1623835X-RAY DIFFRACTION100
2.87-3.0990.2021720.1593576X-RAY DIFFRACTION100
3.099-3.3930.1661770.1533272X-RAY DIFFRACTION100
3.393-3.7910.1731540.1512977X-RAY DIFFRACTION100
3.791-4.3730.1711560.1332605X-RAY DIFFRACTION100
4.373-5.3430.179850.1292271X-RAY DIFFRACTION100
5.343-7.5070.1981060.1651711X-RAY DIFFRACTION100
7.507-46.2490.128370.1511002X-RAY DIFFRACTION100
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)
10.17820.00220.15480.11910.02430.36420.05870.0685-0.00540.0058-0.0235-0.00460.0210.0273-0.03520.02870.01260.00520.0605-0.00380.006122.6261.7436-1.2983
20.10640.05560.08530.21860.21110.41560.04350.01920.00290.09590.0001-0.01150.0668-0.0069-0.04360.062-0.0107-0.0040.02830.01180.010232.52217.554137.9136
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1-363 }A1 - 363
2X-RAY DIFFRACTION2{ B|2-363 }B2 - 363

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