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- PDB-8c0u: 1,6-anhydro-n-actetylmuramic acid kinase (AnmK) in complex with t... -

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Basic information

Entry
Database: PDB / ID: 8c0u
Title1,6-anhydro-n-actetylmuramic acid kinase (AnmK) in complex with their natural substrates and products
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
ADENOSINE-5'-DIPHOSPHATE / Chem-AH0 / Chem-VW0 / Anhydro-N-acetylmuramic acid kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.112 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
DepositionDec 19, 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

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)80,4516
Polymers78,9482
Non-polymers1,5034
Water3,135174
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-18 kcal/mol
Surface area25730 Å2
Unit cell
Length a, b, c (Å)90.583, 90.583, 174.478
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: tag GAGAG in N-terminal. These 5 residues are not observed in the structure, but are present in the used sample. They have to be included in the sequence between numbers -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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*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.: 1 / Source method: isolated from a natural source / Formula: C11H17NO7 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-VW0 / (2~{R})-2-[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-acetamido-2,5-bis(oxidanyl)-6-(phosphonooxymethyl)oxan-4-yl]oxypropanoic acid


Mass: 373.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20NO11P / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O
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: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 20% PEG 3350, Bis-Tris 0.1 M, pH 6.0, Li2SO4 0.2 M

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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: Jan 22, 2022
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.11→46.764 Å / Num. obs: 42080 / % possible obs: 94.6 % / Redundancy: 24.8 % / CC1/2: 0.99 / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.041 / Net I/σ(I): 18.41
Reflection shellResolution: 2.11→2.19 Å / Mean I/σ(I) obs: 1.555 / Num. unique obs: 2106 / CC1/2: 0.518 / Rpim(I) all: 0.785 / % possible all: 64

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
XDS2022data reduction
STARANISOv3.347 1-Sep-2022data scaling
PHASER7.1.016phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.112→46.764 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.248 / WRfactor Rwork: 0.215 / SU B: 15.792 / SU ML: 0.2 / Average fsc free: 0.9406 / Average fsc work: 0.9563 / Cross valid method: THROUGHOUT / ESU R: 0.299 / ESU R Free: 0.226
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2681 2057 4.891 %RANDOM
Rwork0.2303 40004 --
all0.232 ---
obs-42061 90.69 %-
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: 48.191 Å2
Baniso -1Baniso -2Baniso -3
1--0.136 Å2-0.068 Å20 Å2
2---0.136 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 2.112→46.764 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5502 0 97 174 5773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0125734
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165362
X-RAY DIFFRACTIONr_angle_refined_deg0.8491.6417818
X-RAY DIFFRACTIONr_angle_other_deg0.2891.56512316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8945724
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.25554
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.48754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.71510866
X-RAY DIFFRACTIONr_dihedral_angle_6_deg12.60910254
X-RAY DIFFRACTIONr_chiral_restr0.0420.2864
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026874
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021318
X-RAY DIFFRACTIONr_nbd_refined0.1950.21190
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.25064
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22774
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.22927
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.2243
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1390.26
X-RAY DIFFRACTIONr_nbd_other0.1530.236
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.211
X-RAY DIFFRACTIONr_mcbond_it1.794.7132904
X-RAY DIFFRACTIONr_mcbond_other1.794.7132904
X-RAY DIFFRACTIONr_mcangle_it2.9418.4783625
X-RAY DIFFRACTIONr_mcangle_other2.9418.4783626
X-RAY DIFFRACTIONr_scbond_it1.664.9472830
X-RAY DIFFRACTIONr_scbond_other1.6534.9462825
X-RAY DIFFRACTIONr_scangle_it2.7719.0024193
X-RAY DIFFRACTIONr_scangle_other2.779.0014194
X-RAY DIFFRACTIONr_lrange_it4.73944.1916313
X-RAY DIFFRACTIONr_lrange_other4.6843.9916273
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.112-2.1670.349390.34710230.34734140.9340.92631.10720.338
2.167-2.2260.3811230.35123040.35333090.9120.92173.34540.347
2.226-2.2910.3831280.32427520.32732430.9040.93188.80670.302
2.291-2.3610.341390.30329230.30531290.9250.93897.85870.279
2.361-2.4380.3291840.27228970.27630820.9210.95199.96760.246
2.438-2.5240.3511600.26427880.26929480.9280.9561000.236
2.524-2.6190.3181370.25927070.26228440.9360.9581000.231
2.619-2.7250.3051200.25221280.25527430.9430.95981.95410.224
2.725-2.8460.2661340.2424970.24226310.9560.9621000.22
2.846-2.9840.2841110.24523830.24724940.9420.9611000.224
2.984-3.1450.251200.23222950.23324150.9590.9661000.216
3.145-3.3350.2531180.24221540.24322730.9590.96399.9560.226
3.335-3.5640.2671060.22220120.22521180.9550.971000.215
3.564-3.8480.309780.22719160.2319940.9270.9681000.222
3.848-4.2120.267730.21916110.22118050.9550.96993.29640.216
4.212-4.7040.202880.18815770.18816660.9740.97699.940.188
4.704-5.4230.227710.18813930.1914640.9720.9781000.187
5.423-6.6190.205710.2211710.21912440.9730.97499.83920.22
6.619-9.2690.279310.1969420.1989780.9550.97699.48880.205
9.269-46.7640.243260.2145310.2155650.9630.96898.58410.229
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)
10.1829-0.03210.02230.06860.02040.17450.003-0.03290.00160.0102-0.01630.0263-0.0020.01030.01330.0096-0.00410.01220.0162-0.00730.0195-22.52612.19541.6415
20.118-0.0290.06770.1821-0.1170.15410.00450.0142-0.0147-0.0506-0.0259-0.02380.02620.00940.02130.01890.00330.0130.0124-0.0080.0192-32.20967.7487-37.9837
Refinement TLS groupSelection: ALL

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