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- PDB-8cp9: 1,6-anhydro-n-actetylmuramic acid kinase (AnmK)in complex with no... -

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Basic information

Entry
Database: PDB / ID: 8cp9
Title1,6-anhydro-n-actetylmuramic acid kinase (AnmK)in complex with non-hydrolyzable AMPPNP.
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Anhydro-N-acetylmuramic acid kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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
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)80,0096
Polymers78,9482
Non-polymers1,0614
Water2,216123
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 area5400 Å2
ΔGint-33 kcal/mol
Surface area26570 Å2
Unit cell
Length a, b, c (Å)89.940, 89.940, 176.958
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 expresion tag in N-terminal. These five aminoacids 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-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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.62 Å3/Da / Density % sol: 54.32 % / 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, L10.5356
pseudo-merohedral22-K, -H, -L20.4644
ReflectionResolution: 2.2→47.024 Å / Num. obs: 41089 / % possible obs: 100 % / Redundancy: 20.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Net I/σ(I): 21
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 21.3 % / Rmerge(I) obs: 1.717 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 3557 / CC1/2: 0.701 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
XDSv0.86data reduction
Aimless0.7.9data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→47.024 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.172 / SU B: 8.792 / SU ML: 0.126 / Average fsc free: 0.9577 / Average fsc work: 0.9763 / Cross valid method: FREE R-VALUE / ESU R: 0.05 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.231 2042 4.975 %
Rwork0.1833 39006 -
all0.186 --
obs-41048 99.981 %
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: 53.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.845 Å20 Å20 Å2
2--0.845 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5401 0 64 123 5588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125594
X-RAY DIFFRACTIONr_bond_other_d0.0150.0165054
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.6257626
X-RAY DIFFRACTIONr_angle_other_deg0.641.55211750
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2775709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.784549
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51910847
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.29410248
X-RAY DIFFRACTIONr_chiral_restr0.0580.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021097
X-RAY DIFFRACTIONr_nbd_refined0.2210.21268
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1960.24833
X-RAY DIFFRACTIONr_nbtor_refined0.1730.22712
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22991
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2207
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0080.22
X-RAY DIFFRACTIONr_metal_ion_refined0.0420.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.213
X-RAY DIFFRACTIONr_nbd_other0.2360.241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2360.29
X-RAY DIFFRACTIONr_mcbond_it3.3874.9512847
X-RAY DIFFRACTIONr_mcbond_other3.3854.9512847
X-RAY DIFFRACTIONr_mcangle_it4.8227.4173551
X-RAY DIFFRACTIONr_mcangle_other4.8227.4173552
X-RAY DIFFRACTIONr_scbond_it3.2765.252747
X-RAY DIFFRACTIONr_scbond_other3.2755.252747
X-RAY DIFFRACTIONr_scangle_it4.697.774075
X-RAY DIFFRACTIONr_scangle_other4.697.774076
X-RAY DIFFRACTIONr_lrange_it6.94464.4986245
X-RAY DIFFRACTIONr_lrange_other6.93264.3666235
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.2570.481690.3942872X-RAY DIFFRACTION99.9014
2.257-2.3190.3661470.3032795X-RAY DIFFRACTION100
2.319-2.3860.4041600.2632712X-RAY DIFFRACTION100
2.386-2.4590.3141340.2212639X-RAY DIFFRACTION100
2.459-2.540.3211390.2162563X-RAY DIFFRACTION100
2.54-2.6290.31110.1892509X-RAY DIFFRACTION100
2.629-2.7280.2641040.1822420X-RAY DIFFRACTION100
2.728-2.840.2751340.1952306X-RAY DIFFRACTION100
2.84-2.9660.2591430.1782178X-RAY DIFFRACTION100
2.966-3.110.238980.1962132X-RAY DIFFRACTION100
3.11-3.2780.2071070.1962004X-RAY DIFFRACTION100
3.278-3.4770.272820.191944X-RAY DIFFRACTION100
3.477-3.7160.255930.2031782X-RAY DIFFRACTION100
3.716-4.0140.1961200.181629X-RAY DIFFRACTION100
4.014-4.3960.195680.1531548X-RAY DIFFRACTION100
4.396-4.9130.159680.1371402X-RAY DIFFRACTION100
4.913-5.670.228680.1711236X-RAY DIFFRACTION99.9234
5.67-6.9370.142340.1641062X-RAY DIFFRACTION100
6.937-9.7810.153400.133814X-RAY DIFFRACTION100
9.781-47.0240.155230.152459X-RAY DIFFRACTION99.177
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)
10.2614-0.02740.01170.3599-0.14040.2822-0.0011-0.0030.0134-0.117-0.01130.00610.03090.03470.01240.0516-0.00420.01820.0225-0.0240.054513.2817-18.287-1.4109
20.4507-0.06960.27080.0704-0.01320.2123-0.0282-0.1231-0.00040.02330.01030.0479-0.0177-0.0430.01790.04080.00070.04470.0711-0.00830.065122.8217-24.217238.6282
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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