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- PDB-4olc: Carbamate kinase from Giardia lamblia thiocarbamoylated by disulf... -

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Basic information

Entry
Database: PDB / ID: 4olc
TitleCarbamate kinase from Giardia lamblia thiocarbamoylated by disulfiram on Cys242
ComponentsCarbamate kinase
KeywordsTRANSFERASE / ADP / Mg2+ / carbamate / carbamoyl phosphate
Function / homology
Function and homology information


carbamate kinase activity / arginine deiminase pathway / 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
CITRIC ACID / DIETHYLCARBAMODITHIOIC ACID / Carbamate kinase
Similarity search - Component
Biological speciesGiardia lamblia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLim, K. / Herzberg, O.
Citation
Journal: J.Biol.Chem. / Year: 2014
Title: Structural Basis for Inactivation of Giardia lamblia Carbamate Kinase by Disulfiram.
Authors: Galkin, A. / Kulakova, L. / Lim, K. / Chen, C.Z. / Zheng, W. / Turko, I.V. / Herzberg, O.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: X-ray structure and characterization of carbamate kinase from the human parasite Giardia lamblia.
Authors: Galkin, A. / Kulakova, L. / Wu, R. / Nash, T.E. / Dunaway-Mariano, D. / Herzberg, O.
#2: Journal: Plos One / Year: 2013
Title: Crystal structures of carbamate kinase from Giardia lamblia bound with citric acid and AMP-PNP.
Authors: Lim, K. / Kulakova, L. / Galkin, A. / Herzberg, O.
History
DepositionJan 23, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Apr 30, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 20, 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)137,11711
Polymers135,9014
Non-polymers1,2167
Water4,774265
1
A: Carbamate kinase
B: Carbamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,6336
Polymers67,9502
Non-polymers6834
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-34 kcal/mol
Surface area23510 Å2
MethodPISA
2
C: Carbamate kinase
D: Carbamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4845
Polymers67,9502
Non-polymers5343
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-37 kcal/mol
Surface area24090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.297, 98.178, 102.674
Angle α, β, γ (deg.)90.00, 107.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Carbamate kinase


Mass: 33975.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Giardia lamblia (eukaryote) / Strain: ATCC 50803 / WB clone C6 / Gene: GL50803_16453 / Plasmid: pDEST-HisMBP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Star / References: UniProt: A8BB85, carbamate kinase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-DCD / DIETHYLCARBAMODITHIOIC ACID


Mass: 149.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H11NS2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.4 M ammonium citrate dibasic, 21% PEG3350, crystal soaked in 2 mM disulfiram overnight, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2011 / Details: mirrors
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.6→49 Å / Num. all: 40662 / Num. obs: 40662 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.8
Reflection shellResolution: 2.6→2.71 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4635 / % possible all: 99.7

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Processing

Software
NameClassification
JBluIce-EPICSdata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4JZ7

4jz7


Resolution: 2.6→49 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.274 2013 RANDOM
Rwork0.206 --
all-40662 -
obs-40453 -
Displacement parametersBiso mean: 43 Å2
Refinement stepCycle: LAST / Resolution: 2.6→49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9184 0 76 265 9525
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_deg1.2
LS refinement shellResolution: 2.6→2.71 Å
RfactorNum. reflection% reflection
Rfree0.32 227 -
Rwork0.238 --
obs-4604 99.7 %

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