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- PDB-1erz: CRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH ... -

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Basic information

Entry
Database: PDB / ID: 1erz
TitleCRYSTAL STRUCTURE OF N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE WITH A NOVEL CATALYTIC FRAMEWORK COMMON TO AMIDOHYDROLASES
ComponentsN-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE
KeywordsHYDROLASE / four-layer sandwich
Function / homology
Function and homology information


N-carbamoyl-D-amino-acid hydrolase / N-carbamoyl-D-amino acid hydrolase activity
Similarity search - Function
: / Nitrilase/N-carbamoyl-D-aminoacid amidohydrolase / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase domain profile. / Carbon-nitrogen hydrolase superfamily / Carbon-nitrogen hydrolase / Carbon-nitrogen hydrolase / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
N-carbamoyl-D-amino acid hydrolase
Similarity search - Component
Biological speciesAgrobacterium sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsNakai, T. / Hasegawa, T. / Yamashita, E. / Yamamoto, M. / Kumasaka, T. / Ueki, T. / Nanba, H. / Ikenaka, Y. / Takahashi, S. / Sato, M. / Tsukihara, T.
Citation
Journal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of N-carbamyl-D-amino acid amidohydrolase with a novel catalytic framework common to amidohydrolases.
Authors: Nakai, T. / Hasegawa, T. / Yamashita, E. / Yamamoto, M. / Kumasaka, T. / Ueki, T. / Nanba, H. / Ikenaka, Y. / Takahashi, S. / Sato, M. / Tsukihara, T.
#1: Journal: BIOSCI.BIOTECHNOL.BIOCHEM. / Year: 1998
Title: Isolation of Agrobacterium sp. Strain KNK712 that Produces N-carbamyl-D-amino acid Amidohydrolase, Cloning of the Gene for this Enzyme, and Properties of the Enzyme.
Authors: Nanba, H. / Ikenaka, Y. / Yamada, Y. / Yajima, K. / Takano, M. / Takahashi, S.
#2: Journal: PATENT / Year: 1999
Title: Crystals and Three-dimensional Structure of DCase, and their Use
Authors: Nakai, T. / Morikawa, S. / Ishii, K. / Nanba, H. / Yajima, K. / Ikenaka, Y. / Takahashi, S.
History
DepositionApr 6, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev / _citation.pdbx_database_id_patent
Revision 1.4Feb 7, 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

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Assembly

Deposited unit
A: N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE
B: N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)68,3982
Polymers68,3982
Non-polymers00
Water13,673759
1
A: N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE
B: N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE

A: N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE
B: N-CARBAMYL-D-AMINO ACID AMIDOHYDROLASE


Theoretical massNumber of molelcules
Total (without water)136,7964
Polymers136,7964
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)67.84, 137.83, 68.39
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-601-

HOH

21B-699-

HOH

DetailsThe biological assembly is a tetramer constructed from chain A and B. A symmetry partner generated by the two-fold.

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Components

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


Mass: 34199.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium sp. (bacteria) / Strain: KNK712 / Plasmid: PAD108 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: P60327, N-carbamoyl-D-amino-acid hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 759 / 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: 2.34 Å3/Da / Density % sol: 47.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG 6000, lithium chloride, HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.2 M1reservoirLiSO4
20.1 MHEPES1reservoir
320 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.9341
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 13, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9341 Å / Relative weight: 1
ReflectionResolution: 1.7→69 Å / Num. all: 68606 / Num. obs: 68596 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Biso Wilson estimate: 22.87 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.207 / Num. unique all: 6418 / % possible all: 91.4
Reflection
*PLUS
Num. measured all: 189832
Reflection shell
*PLUS
% possible obs: 91.4 %

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→69 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.201 3492 -RANDOM
Rwork0.176 ---
all-68596 --
obs-65104 91.3 %-
Refinement stepCycle: LAST / Resolution: 1.7→69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4814 0 0 759 5573
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.38

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