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- PDB-4jz7: Carbamate kinase from Giardia lamblia bound to AMP-PNP -

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Basic information

Entry
Database: PDB / ID: 4jz7
TitleCarbamate kinase from Giardia lamblia bound to AMP-PNP
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / 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: 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)137,9268
Polymers135,9014
Non-polymers2,0254
Water8,557475
1
A: Carbamate kinase
B: Carbamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9634
Polymers67,9502
Non-polymers1,0122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-36 kcal/mol
Surface area21920 Å2
MethodPISA
2
C: Carbamate kinase
D: Carbamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9634
Polymers67,9502
Non-polymers1,0122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5890 Å2
ΔGint-38 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.630, 97.050, 102.120
Angle α, β, γ (deg.)90.00, 106.69, 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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.47 Å3/Da / Density % sol: 50.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.4 M ammonium citrate dibasic, pH 5.0, 21% PEG 3350, crystal soaked in 50mM AMP-PNP for 4 hours, 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→48.9 Å / Num. all: 40467 / Num. obs: 40467 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 8.1
Reflection shellResolution: 2.6→2.73 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 3.6 / Num. unique all: 5834 / % possible all: 99.2

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Processing

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

3kzf

2we4


Resolution: 2.6→48.9 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.292 1616 RANDOM
Rwork0.217 --
all-40450 -
obs-40450 -
Displacement parametersBiso mean: 24 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8968 0 124 475 9567
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.2
LS refinement shellResolution: 2.6→2.73 Å
RfactorNum. reflection% reflection
Rfree0.332 226 -
Rwork0.26 --
obs-5832 99.2 %

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