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- PDB-4axs: Structure of Carbamate Kinase from Mycoplasma penetrans -

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Basic information

Entry
Database: PDB / ID: 4axs
TitleStructure of Carbamate Kinase from Mycoplasma penetrans
ComponentsCARBAMATE KINASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


carbamate kinase activity / arginine metabolic process
Similarity search - Function
Carbamate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMYCOPLASMA PENETRANS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGallego, P. / Planell, R. / Benach, J. / Querol, E. / PerezPons, J.A. / Reverter, D.
CitationJournal: Plos One / Year: 2012
Title: Structural Characterization of the Enzymes Composing the Arginine Deiminase Pathway in Mycoplasma Penetrans.
Authors: Gallego, P. / Planell, R. / Benach, J. / Querol, E. / Perez-Pons, J.A. / Reverter, D.
History
DepositionJun 14, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 31, 2012Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CARBAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7553
Polymers35,5631
Non-polymers1922
Water59433
1
A: CARBAMATE KINASE
hetero molecules

A: CARBAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,5096
Polymers71,1252
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5360 Å2
ΔGint-96.1 kcal/mol
Surface area24030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.800, 51.800, 174.162
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein CARBAMATE KINASE /


Mass: 35562.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOPLASMA PENETRANS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8EVF4
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 33 / 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: 1.9 Å3/Da / Density % sol: 35.15 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.38→44.86 Å / Num. obs: 11222 / % possible obs: 97.7 % / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Biso Wilson estimate: 45.29 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.8
Reflection shellResolution: 2.38→2.51 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2.5 / % possible all: 92.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E19

1e19


Resolution: 2.5→44.86 Å / SU ML: 0.38 / σ(F): 1.35 / Phase error: 30.52 / Stereochemistry target values: ML / Details: RESIDUES 134 TO 143 AND 151 TO 156 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2872 465 4.7 %
Rwork0.2306 --
obs0.2332 9818 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.096 Å2 / ksol: 0.356 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-11.9406 Å20 Å20 Å2
2--11.9406 Å20 Å2
3----23.8811 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 10 33 2198
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082213
X-RAY DIFFRACTIONf_angle_d1.1093001
X-RAY DIFFRACTIONf_dihedral_angle_d20.881795
X-RAY DIFFRACTIONf_chiral_restr0.077351
X-RAY DIFFRACTIONf_plane_restr0.004390
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5001-2.86190.34521620.27112998X-RAY DIFFRACTION97
2.8619-3.60540.29971490.22293067X-RAY DIFFRACTION98
3.6054-44.86730.26251540.22113288X-RAY DIFFRACTION99

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