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- PDB-3kzf: Structure of Giardia Carbamate Kinase -

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Basic information

Entry
Database: PDB / ID: 3kzf
TitleStructure of Giardia Carbamate Kinase
ComponentsCarbamate kinase
KeywordsTRANSFERASE / Carbamate kinase / arginine dihydrolase pathway / Giardia lamblia / drug target / Kinase
Function / homology
Function and homology information


carbamate kinase activity / arginine deiminase pathway / phosphorylation / nucleotide binding / cytosol
Similarity search - Function
Carbamate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesGiardia lamblia ATCC 50803 (unknown)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGalkin, A. / Herzberg, O.
CitationJournal: 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
DepositionDec 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references

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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)136,2698
Polymers135,9014
Non-polymers3684
Water0
1
A: Carbamate kinase
B: Carbamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1354
Polymers67,9502
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-40 kcal/mol
Surface area23530 Å2
MethodPISA
2
C: Carbamate kinase
hetero molecules

D: Carbamate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1354
Polymers67,9502
Non-polymers1842
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area4870 Å2
ΔGint-36 kcal/mol
Surface area22780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.77, 85.41, 102.10
Angle α, β, γ (deg.)90.00, 106.80, 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 ATCC 50803 (unknown) / Strain: WB / Gene: CK, GL50803_16453 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: A8BB85, carbamate kinase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3

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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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350 and 0.2 M ammonium citrate, VAPOR DIFFUSION, HANGING DROP, temperature 298.0 K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Oct 13, 2006 / 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: 3→20 Å / Num. all: 23098 / Num. obs: 20419 / % possible obs: 88.4 % / Rmerge(I) obs: 0.095
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.193 / % possible all: 87

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1e19
Resolution: 3→10 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.902 / Cross valid method: THROUGHOUT / ESU R Free: 0.611 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28305 998 5 %RANDOM
Rwork0.22672 ---
obs-18918 88.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8701 0 24 0 8725
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONc_bond_d0.0180.0228828
X-RAY DIFFRACTIONc_angle_d2.11.98211921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg51148
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.78327
X-RAY DIFFRACTIONr_dihedral_angle_3_deg151603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg1535
X-RAY DIFFRACTIONr_chiral_restr0.21420
X-RAY DIFFRACTIONr_gen_planes_refined0.026384
X-RAY DIFFRACTIONr_nbd_refined0.24900
X-RAY DIFFRACTIONr_nbtor_refined0.25977
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2381
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2193
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.25
LS refinement shellResolution: 3→3.071 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 70 -
Rwork0.239 1293 -
obs--87.54 %

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