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- PDB-2we4: Carbamate kinase from Enterococcus faecalis bound to a sulfate io... -

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Basic information

Entry
Database: PDB / ID: 2we4
TitleCarbamate kinase from Enterococcus faecalis bound to a sulfate ion and two water molecules, which mimic the substrate carbamyl phosphate
ComponentsCARBAMATE KINASE 1
KeywordsTRANSFERASE / ARGININE CATABOLISM / ARGININE METABOLISM / ATP SYNTHESYS / KINASE / OPEN ALPHA/BETA SHEET / PHOSPHOTRANSFERASE
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 FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsRamon-Maiques, S. / Marina, A. / Gil-Ortiz, F. / Rubio, V.
Citation
Journal: J.Mol.Biol. / Year: 2010
Title: Substrate Binding and Catalysis in Carbamate Kinase Ascertained by Crystallographic and Site-Directed Mutagenesis Studies. Movements and Significance of a Unique Globular Subdomain of This Key ...Title: Substrate Binding and Catalysis in Carbamate Kinase Ascertained by Crystallographic and Site-Directed Mutagenesis Studies. Movements and Significance of a Unique Globular Subdomain of This Key Enzyme for Fermentative ATP Production in Bacteria.
Authors: Ramon-Maiques, S. / Marina, A. / Guinot, A. / Gil-Ortiz, F. / Uriarte, M. / Fita, I. / Rubio, V.
#1: Journal: 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.
#2: Journal: J.Mol.Biol. / Year: 2000
Title: The 1.5 A Resolution Crystal Structure of the Carbamate Kinase-Like Carbamoyl Phosphate Synthetase from the Hyperthermophilic Archaeon Pyrococcus Furiosus, Bound to Adp, Confirms that This ...Title: The 1.5 A Resolution Crystal Structure of the Carbamate Kinase-Like Carbamoyl Phosphate Synthetase from the Hyperthermophilic Archaeon Pyrococcus Furiosus, Bound to Adp, Confirms that This Thermostable Enzyme is a Carbamate Kinase, and Provides Insight Into Substrate Binding and Stability in Carbamate Kinases
Authors: Ramon-Maiques, S. / Marina, A. / Uriarte, M. / Fita, I. / Rubio, V.
History
DepositionMar 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Version format compliance
Revision 1.2Apr 3, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 1.4Dec 13, 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

Downloads & links

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Assembly

Deposited unit
A: CARBAMATE KINASE 1
B: CARBAMATE KINASE 1
C: CARBAMATE KINASE 1
D: CARBAMATE KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,27519
Polymers131,8344
Non-polymers1,44115
Water16,340907
1
B: CARBAMATE KINASE 1
D: CARBAMATE KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,68610
Polymers65,9172
Non-polymers7698
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5620 Å2
ΔGint-137.1 kcal/mol
Surface area24790 Å2
MethodPISA
2
A: CARBAMATE KINASE 1
C: CARBAMATE KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5909
Polymers65,9172
Non-polymers6727
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-116.7 kcal/mol
Surface area25210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.888, 172.600, 98.627
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-1, 0.0047, -0.0067), (0.0075, 0.8565, -0.51604), (0.00337, -0.5161, -0.8566)28.2197, 12.6385, 45.7711
2given(-0.9985, -0.0539, -0.0074), (-0.0456, 0.9033, -0.4266), (0.0296, -0.4256, -0.9044)27.8538, 30.644, 133.472

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Components

#1: Protein
CARBAMATE KINASE 1 / CARBAMATE KINASE


Mass: 32958.578 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROCOCCUS FAECALIS (bacteria) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): DE3 / References: UniProt: P0A2X7, carbamate kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 907 / 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: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: CRYSTALS WERE OBTAINED AT 4 DEGREES USING THE HANGING DROP VAPOUR DIFFUSION METHOD BY MIXING 1.5 MICROLITERS OF A 10 MG/ML PROTEIN SOLUTION IN 5 MM SODIUM CACODYLATE PH 6.5 AND 1.5 ...Details: CRYSTALS WERE OBTAINED AT 4 DEGREES USING THE HANGING DROP VAPOUR DIFFUSION METHOD BY MIXING 1.5 MICROLITERS OF A 10 MG/ML PROTEIN SOLUTION IN 5 MM SODIUM CACODYLATE PH 6.5 AND 1.5 MICROLITERS OF THE RESERVOIR BUFFER CONTAINING 16-20% PEG 8000, 25-100 MM AMMONIUM SULFATE AND 0.1 M SODIUM CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 20, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 88372 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.6
Reflection shellResolution: 2.02→2.12 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.6 / % possible all: 82

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B7B

1b7b


Resolution: 2.02→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.234 4439 4.8 %RANDOM
Rwork0.195 ---
obs0.195 88173 96.1 %-
Solvent computationBsol: 47.8 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 28.8 Å2
Baniso -1Baniso -2Baniso -3
1--5.219 Å20 Å20 Å2
2--5.436 Å20 Å2
3----0.216 Å2
Refinement stepCycle: LAST / Resolution: 2.02→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9208 0 75 907 10190
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.15
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2SO4.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM

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