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- PDB-4jz9: Carbamate kinase from Giardia lamblia bound to citric acid -

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Basic information

Entry
Database: PDB / ID: 4jz9
TitleCarbamate kinase from Giardia lamblia bound to citric acid
ComponentsCarbamate kinase
KeywordsTRANSFERASE / modified Rossmann fold / ATP carbamate phosphotransferase / ADP / Mg2+ / carbamoyl phosphate
Function / homology
Function and homology information


carbamate kinase activity / L-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 / Carbamate kinase
Similarity search - Component
Biological speciesGiardia lamblia (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLim, K. / Herzberg, O.
Citation
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.
#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.
History
DepositionApr 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 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_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_ref_seq_dif.details / _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)136,6698
Polymers135,9014
Non-polymers7684
Water4,954275
1
A: Carbamate kinase
B: Carbamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3354
Polymers67,9502
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-34 kcal/mol
Surface area25110 Å2
MethodPISA
2
C: Carbamate kinase
D: Carbamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,3354
Polymers67,9502
Non-polymers3842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint-38 kcal/mol
Surface area24940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.922, 92.740, 101.836
Angle α, β, γ (deg.)90.00, 106.22, 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.4 M ammonium citrate dibasic, pH 5.0, 21% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 5, 2010 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→46.1 Å / Num. all: 48667 / Num. obs: 48667 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 31 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 7.2
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 3.3 / Num. unique all: 4869 / % possible all: 99.9

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Processing

Software
NameClassification
CrystalCleardata collection
PHASERphasing
PHENIXrefinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 3KZF AND 2WE4

3kzf

2we4


Resolution: 2.4→46.1 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.28 2009 RANDOM
Rwork0.218 --
all-48666 -
obs-48666 -
Displacement parametersBiso mean: 44 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9464 0 52 275 9791
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d1.4
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection% reflection
Rfree0.368 187 -
Rwork0.3 --
obs-4869 99.9 %

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