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- PDB-3va7: Crystal structure of the Kluyveromyces lactis Urea Carboxylase -

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Basic information

Entry
Database: PDB / ID: 3va7
TitleCrystal structure of the Kluyveromyces lactis Urea Carboxylase
ComponentsKLLA0E08119p
KeywordsLIGASE / Carboxylase
Function / homology
Function and homology information


small molecule metabolic process / urea carboxylase activity / methylcrotonoyl-CoA carboxylase activity / propionyl-CoA carboxylase activity / hydrolase activity / mitochondrion / ATP binding / metal ion binding
Similarity search - Function
Urea carboxylase / Allophanate hydrolase / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Gyrase A; domain 2 - #40 / Amidase signature domain ...Urea carboxylase / Allophanate hydrolase / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Gyrase A; domain 2 - #40 / Amidase signature domain / Amidase signature (AS) superfamily / Amidase / Biotin-binding site / Biotin-requiring enzymes attachment site. / Biotin carboxylase-like, N-terminal domain / Biotin carboxylase, C-terminal / Biotin carboxylation domain / Biotin carboxylase, N-terminal domain / Biotin carboxylase C-terminal domain / Biotin carboxylation domain profile. / Biotin carboxylase C-terminal domain / Rossmann fold - #20 / Carbamoyl-phosphate synthase subdomain signature 1. / Carbamoyl-phosphate synthetase large subunit-like, ATP-binding domain / Carbamoyl-phosphate synthase L chain, ATP binding domain / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / Cyclophilin-like / Cyclophilin / Biotin-requiring enzyme / Rudiment single hybrid motif / Biotinyl/lipoyl domain profile. / Biotin/lipoyl attachment / Single hybrid motif / ATP-grasp fold, B domain / Pre-ATP-grasp domain superfamily / Cyclophilin-like domain superfamily / ATP-grasp fold / ATP-grasp fold profile. / Gyrase A; domain 2 / D-amino Acid Aminotransferase; Chain A, domain 1 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Carbamoyl-phosphate synthase subdomain signature 2. / Beta Barrel / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-BTI / UREA / KLLA0E08119p
Similarity search - Component
Biological speciesKluyveromyces lactis (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsFan, C. / Xiang, S.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of urea carboxylase provides insights into the carboxyltransfer reaction
Authors: Fan, C. / Chou, C.Y. / Tong, L. / Xiang, S.
History
DepositionDec 29, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 1, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KLLA0E08119p
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,90411
Polymers136,9481
Non-polymers95610
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.660, 126.660, 217.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-2186-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein KLLA0E08119p / urea carboxylase


Mass: 136947.938 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 617-1829
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis (yeast) / Strain: NRRL Y-1140 / Gene: KLLA0E08119g / Production host: Escherichia coli (E. coli) / References: UniProt: Q6CP22, EC: 6.3.4.6

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Non-polymers , 5 types, 387 molecules

#2: Chemical ChemComp-BTI / 5-(HEXAHYDRO-2-OXO-1H-THIENO[3,4-D]IMIDAZOL-6-YL)PENTANAL


Mass: 228.311 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O2S
#3: Chemical ChemComp-URE / UREA


Mass: 60.055 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH4N2O
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 3.19 Å3/Da / Density % sol: 61.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4M ammonium sulfate, 0.1M Bis-Tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 54762 / Num. obs: 51949 / % possible obs: 99.4 % / Observed criterion σ(I): 1.9 / Redundancy: 4.7 %
Reflection shell
Resolution (Å)Rmerge(I) obsDiffraction-ID
2.6-2.740.3881
2.74-2.910.2711
2.91-3.110.181
3.11-3.360.1241
3.36-3.680.0851
3.68-4.111

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.898 / SU B: 8.968 / SU ML: 0.195 / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25524 2790 5.1 %RANDOM
Rwork0.18738 ---
obs0.19081 51949 99.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.426 Å2
Baniso -1Baniso -2Baniso -3
1-1.48 Å20 Å20 Å2
2--1.48 Å20 Å2
3----2.96 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8829 0 62 377 9268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0229072
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9221.9712284
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.18351127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.31124.512410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.598151546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0751553
X-RAY DIFFRACTIONr_chiral_restr0.130.21353
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216872
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8891.55622
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70429078
X-RAY DIFFRACTIONr_scbond_it2.70833450
X-RAY DIFFRACTIONr_scangle_it4.3734.53206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 211 -
Rwork0.264 3756 -
obs--99.13 %

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