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- PDB-1fo6: CRYSTAL STRUCTURE ANALYSIS OF N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE -

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Basic information

Entry
Database: PDB / ID: 1fo6
TitleCRYSTAL STRUCTURE ANALYSIS OF N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE
ComponentsN-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE
KeywordsHYDROLASE / four layer a/b fold
Function / homology
Function and homology information


N-carbamoyl-D-amino-acid hydrolase / N-carbamoyl-D-amino acid hydrolase activity / beta-alanine biosynthetic process via 3-ureidopropionate / beta-ureidopropionase activity
Similarity search - Function
Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
XENON / N-carbamoyl-D-amino acid hydrolase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.95 Å
AuthorsWang, W.-C. / Hsu, W.-H. / Chien, F.-T. / Chen, C.-Y.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: Crystal structure and site-directed mutagenesis studies of N-carbamoyl-D-amino-acid amidohydrolase from Agrobacterium radiobacter reveals a homotetramer and insight into a catalytic cleft.
Authors: Wang, W.C. / Hsu, W.H. / Chien, F.T. / Chen, C.Y.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Expression, crystallization and preliminary X-ray diffraction studies of N-carbamyl-D-amino-acid amidohydrolase from Agrobacterium radiobacter
Authors: Hsu, W.-H. / Chien, F.-T. / Hsu, C.L. / Wang, T.C. / Yuan, H.S. / Wang, W.-C.
History
DepositionAug 25, 2000Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 29, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE
B: N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE
C: N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE
D: N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,0996
Polymers136,8364
Non-polymers2632
Water13,007722
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13550 Å2
ΔGint-83 kcal/mol
Surface area38250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.230, 67.530, 137.480
Angle α, β, γ (deg.)90.00, 96.12, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
N-CARBAMoYL-D-AMINO-ACID AMIDOHYDROLASE


Mass: 34209.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / References: UniProt: Q44185, EC: 3.4.22.12
#2: Chemical ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Xe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / 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: 6

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.05 %
Crystal growTemperature: 296.5 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Lithium sulfate, HEPES , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 296.5K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115 mg/mlprotein1drop
210 mMHEPES1drop
31 mMEDTA1drop
40.02 %(w/v)sodium azide1drop
51.15 Mlithium sulfate1reservoir
6100 mMHEPES1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11131
21
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU RU30011.5418
SYNCHROTRONSSRL BL7-121.08
Detector
TypeIDDetectorDate
RIGAKU RAXIS IV1IMAGE PLATEAug 12, 1998
MARRESEARCH2IMAGE PLATEDec 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.081
ReflectionResolution: 1.95→30 Å / Num. all: 93420 / Num. obs: 93415 / % possible obs: 99.9 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.5
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.459 / Num. unique all: 6865 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 99.8 %

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Processing

Software
NameVersionClassification
SHARPphasing
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.95→30 Å / σ(F): 0 / σ(I): 0
Details: Refinement of Macromolecular Structures by the Maximum-Likelihood Method
RfactorNum. reflection% reflectionSelection details
Rfree0.23929 4682 5 %RANDOM
all0.18668 93501 --
obs0.18668 88788 94.9 %-
Refinement stepCycle: LAST / Resolution: 1.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9564 0 2 722 10288
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.018
X-RAY DIFFRACTIONo_angle_deg1.7
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONp_bond_d
X-RAY DIFFRACTIONp_angle_deg

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