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- PDB-1b7b: Carbamate kinase from Enterococcus faecalis -

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Basic information

Entry
Database: PDB / ID: 1b7b
TitleCarbamate kinase from Enterococcus faecalis
ComponentsCARBAMATE KINASE
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE / ARGININE CATABOLISM / ATP SYNTHESYS / ACYLPHOSPHATE-MAKING ENZYMES / OPEN ALPHA/BETA SHEET
Function / homology
Function and homology information


carbamate kinase / carbamate kinase activity / L-arginine deiminase pathway / ATP binding / cytosol
Similarity search - Function
Carbamate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Acetylglutamate kinase-like superfamily / Amino acid kinase family / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEnterococcus faecium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 2.8 Å
AuthorsMarina, A. / Alzari, P.M. / Bravo, J. / Uriarte, M. / Barcelona, B. / Fita, I. / Rubio, V.
CitationJournal: Protein Sci. / Year: 1999
Title: Carbamate kinase: New structural machinery for making carbamoyl phosphate, the common precursor of pyrimidines and arginine.
Authors: Marina, A. / Alzari, P.M. / Bravo, J. / Uriarte, M. / Barcelona, B. / Fita, I. / Rubio, V.
History
DepositionJan 20, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jan 26, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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

Downloads & links

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Assembly

Deposited unit
A: CARBAMATE KINASE
B: CARBAMATE KINASE
C: CARBAMATE KINASE
D: CARBAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,2198
Polymers131,8344
Non-polymers3844
Water1,22568
1
A: CARBAMATE KINASE
C: CARBAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1094
Polymers65,9172
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4480 Å2
ΔGint-57 kcal/mol
Surface area25480 Å2
MethodPISA
2
B: CARBAMATE KINASE
D: CARBAMATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1094
Polymers65,9172
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4490 Å2
ΔGint-57 kcal/mol
Surface area25520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.860, 172.920, 98.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
/ NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(-0.999953, 0.009657, -0.001168), (0.008817, 0.849089, -0.528177), (-0.004109, -0.528162, -0.849134)28.049, 13.1245, 46.2127
2given(-0.997496, -0.043989, -0.055375), (-0.011779, 0.875414, -0.483231), (0.069733, -0.481369, -0.87374)33.4157, 47.7554, 81.4565
3given(0.997176, 0.03716, 0.065267), (-0.040201, 0.998136, 0.045918), (-0.063439, -0.048412, 0.996811)-5.6123, 11.0275, -48.0873

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Components

#1: Protein
CARBAMATE KINASE / EC 2.7.2.2


Mass: 32958.578 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: COMPLEXED WITH SULPHATE ANION / Source: (natural) Enterococcus faecium (bacteria) / Cellular location: CYTOPLASM / Plasmid: PCK41 / Strain: D10 / References: UniProt: P0A2X8, carbamate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 68 / 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: 2.62 Å3/Da / Density % sol: 52.62 %
Crystal growpH: 6.4 / Details: PEG 4000, (NH4)2SO4, SODIUM CACODYLATE, pH 6.4
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 400011
2(NH4)2SO411
3sodium CACODylate11
Crystal grow
*PLUS
Method: other / Details: Marina, A., (1994) J. Mol. Biol., 235, 1345.
Components of the solutions
*PLUS
IDCrystal-ID
11
21
31

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.928
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1996
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.928 Å / Relative weight: 1
ReflectionResolution: 2.8→15 Å / Num. obs: 31935 / % possible obs: 89.5 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 8.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.851refinement
RefinementMethod to determine structure: MIRAS / Resolution: 2.8→15 Å / Data cutoff low absF: 200 / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.283 2893 10.2 %RANDOM
Rwork0.224 ---
obs-28366 89.5 %-
Displacement parametersBiso mean: 28 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9424 0 20 68 9512
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Rms dev Biso : _ / Rms dev position: _ / Weight Biso : 2 / Weight position: 30

Ens-IDDom-IDNCS model details
11RESTRAINTS
22
33
44
LS refinement shellResolution: 2.8→2.93 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.344 279 11 %
Rwork0.287 2531 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM11.WATTOPH11.WAT
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 15 Å / σ(F): 2 / % reflection Rfree: 10.2 % / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28 Å2
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 1.4
LS refinement shell
*PLUS
Highest resolution: 2.8 Å / Rfactor Rfree: 0.344 / % reflection Rfree: 11 % / Rfactor Rwork: 0.287

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