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- PDB-2we5: Carbamate kinase from Enterococcus faecalis bound to MgADP -

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Basic information

Entry
Database: PDB / ID: 2we5
TitleCarbamate kinase from Enterococcus faecalis bound to MgADP
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
ACETATE ION / ADENOSINE-5'-DIPHOSPHATE / Carbamate kinase 1
Similarity search - Component
Biological speciesENTEROCOCCUS FAECALIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsRamon-Maiques, S. / Marina, A. / 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 ...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: Database references / Derived calculations ...Database references / Derived calculations / Other / Structure summary / 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 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Dec 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,28910
Polymers98,8763
Non-polymers1,4147
Water15,133840
1
A: CARBAMATE KINASE 1
B: CARBAMATE KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8797
Polymers65,9172
Non-polymers9625
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5860 Å2
ΔGint-50.8 kcal/mol
Surface area25170 Å2
MethodPISA
2
C: CARBAMATE KINASE 1
hetero molecules

C: CARBAMATE KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,8206
Polymers65,9172
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area5620 Å2
ΔGint-50.3 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.522, 103.522, 155.414
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein CARBAMATE KINASE 1 / CARBAMATE KINASE


Mass: 32958.578 Da / Num. of mol.: 3
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): BL21(DE3) / References: UniProt: P0A2X7, carbamate kinase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / 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: 2.25 Å3/Da / Density % sol: 45 % / 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 MIRCROLITERS OF A 10 MG/ML PROTEIN SOLUTION IN 5 MM SODIUM CACODYLATE PH 6.5, 2 MM ADP, 5 MM ...Details: CRYSTALS WERE OBTAINED AT 4 DEGREES USING THE HANGING DROP VAPOUR DIFFUSION METHOD BY MIXING 1.5 MIRCROLITERS OF A 10 MG/ML PROTEIN SOLUTION IN 5 MM SODIUM CACODYLATE PH 6.5, 2 MM ADP, 5 MM MGCL2 AND 50 MM SODIUM PHOPHONOACETATE, AND 1.5 MICROLITERS OF THE RESERVOIR BUFFER CONTAINING 13-16% PEG 8000, 130-160 MM MAGNESIUM ACETATE AND 0.1 M SODIUM CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9067
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9067 Å / Relative weight: 1
ReflectionResolution: 1.39→50 Å / Num. obs: 172839 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 7
Reflection shellResolution: 1.39→1.47 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 87.1

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Processing

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

1b7b


Resolution: 1.39→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2103 8668 4.5 %RANDOM
Rwork0.2012 ---
obs0.2012 172736 89.7 %-
Solvent computationBsol: 46.1408 Å2 / ksol: 0.342447 e/Å3
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å2-0.683 Å20 Å2
2---0.22 Å20 Å2
3---0.441 Å2
Refinement stepCycle: LAST / Resolution: 1.39→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6909 0 88 840 7837
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
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_deg1.228
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 fileTopol file
X-RAY DIFFRACTION1WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3PROTEIN_REP.PARAM
X-RAY DIFFRACTION4ACY.PARAM
X-RAY DIFFRACTION5ADP_PFU_COMILLAS.PARAM
X-RAY DIFFRACTION6EDO.PARAM

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