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- PDB-3qbx: Crystal structure of pseudomonas aeruginosa 1,6-anhydro-n-actetyl... -

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Basic information

Entry
Database: PDB / ID: 3qbx
TitleCrystal structure of pseudomonas aeruginosa 1,6-anhydro-n-actetylmuramic acid kinase (ANMK) bound to 1,6-anhydro-n-actetylmuramic acid
ComponentsAnhydro-N-acetylmuramic acid kinase
KeywordsTRANSFERASE / Acetate and sugar kinases / hsp70 / actin superfamily / kinase / 1 / 6-anhydro-n-actetylmuramic acid binding / glycoside hydrolase / atp-binding / carbohydrate metabolism / peptidoglycan recycling
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 / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AH0 / Anhydro-N-acetylmuramic acid kinase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBacik, J.P. / Martin, D.R. / Mark, B.L.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular Basis of 1,6-Anhydro Bond Cleavage and Phosphoryl Transfer by Pseudomonas aeruginosa 1,6-Anhydro-N-acetylmuramic Acid Kinase.
Authors: Bacik, J.P. / Whitworth, G.E. / Stubbs, K.A. / Yadav, A.K. / Martin, D.R. / Bailey-Elkin, B.A. / Vocadlo, D.J. / Mark, B.L.
History
DepositionJan 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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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)81,0106
Polymers80,2672
Non-polymers7434
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-8 kcal/mol
Surface area26360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.480, 91.480, 173.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A2 - 654
2112B2 - 654

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Components

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


Mass: 40133.523 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: anmK, PA0666 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I5Q5, hexokinase
#2: 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
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 166 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.84 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG 4000, 0.2 M (NH4)2SO4, 0.1 M tri-Sodium Citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 12, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
111.000H, 1.000K, L10.578
111.000H+1.000K, -1.000K, -L20.422
ReflectionResolution: 2.1→46.68 Å / Num. all: 61441 / Num. obs: 47575 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 5.1 % / Biso Wilson estimate: 34.5 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.087 / Net I/σ(I): 11.3
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 3.9 / Num. unique all: 6974 / Rsym value: 0.369 / % possible all: 100

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Processing

Software
NameVersionClassification
MxDCdata collection
PHASERphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CQY

3cqy


Resolution: 2.1→40.45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.564 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R Free: 0.034 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21533 2055 4.3 %RANDOM
Rwork0.19332 ---
all0.19431 47575 --
obs0.19431 45429 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.92 Å2
Baniso -1Baniso -2Baniso -3
1-8.43 Å20 Å20 Å2
2--8.43 Å20 Å2
3----16.87 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5332 0 48 166 5546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0215515
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1261.9727519
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.265713
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42423.077234
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35815807
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6261546
X-RAY DIFFRACTIONr_chiral_restr0.0720.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214266
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4311.53553
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80225628
X-RAY DIFFRACTIONr_scbond_it1.2631962
X-RAY DIFFRACTIONr_scangle_it2.0024.51890
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1411tight positional0.020.05
1194medium positional0.030.5
1411tight thermal0.070.5
1194medium thermal0.082
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 153 -
Rwork0.235 3328 -
obs--98.64 %

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