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- PDB-2ggk: The mutant A302C of Agrobacterium radiobacter N-carbamoyl-D-amino... -

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Basic information

Entry
Database: PDB / ID: 2ggk
TitleThe mutant A302C of Agrobacterium radiobacter N-carbamoyl-D-amino-acid amidohydrolase
ComponentsN-carbamoyl-D-amino acid amidohydrolase
KeywordsHYDROLASE / N-Carbamoyl-D-Amino-Acid Amidohydrolase
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 tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsWang, W.C. / Chiu, W.C. / You, J.Y.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structure-Stability-Activity Relationship in Covalently Cross-linked N-Carbamoyl d-Amino acid Amidohydrolase and N-Acylamino acid Racemase.
Authors: Chiu, W.C. / You, J.Y. / Liu, J.S. / Hsu, S.K. / Hsu, W.H. / Shih, C.H. / Hwang, J.K. / Wang, W.C.
History
DepositionMar 24, 2006Deposition site: RCSB / Processing site: PDBJ
SupersessionApr 11, 2006ID: 2FKV
Revision 1.0Apr 11, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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


Theoretical massNumber of molelcules
Total (without water)136,9654
Polymers136,9654
Non-polymers00
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-93 kcal/mol
Surface area38360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.091, 67.819, 138.037
Angle α, β, γ (deg.)90.00, 95.87, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe crystal structure of D-NCAase A302C mutant reveals a tetramer with 222 symmetry.

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Components

#1: Protein
N-carbamoyl-D-amino acid amidohydrolase


Mass: 34241.125 Da / Num. of mol.: 4 / Mutation: A302C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109
References: UniProt: Q44185, N-carbamoyl-D-amino-acid hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: lithium sulfate, HEPES buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 17, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 56903 / % possible obs: 95.6 %
Reflection shellResolution: 2.3→2.38 Å / % possible all: 95.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FO6

1fo6


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.935 / SU B: 6.225 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.333 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21963 2459 5 %RANDOM
Rwork0.17816 ---
all0.18 ---
obs0.18021 46601 86.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.184 Å2
Baniso -1Baniso -2Baniso -3
1-2.05 Å20 Å2-0.02 Å2
2--0.71 Å20 Å2
3----2.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9568 0 0 285 9853
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0229826
X-RAY DIFFRACTIONr_angle_refined_deg1.3151.94813316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74551204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.68623.109476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.608151596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8061576
X-RAY DIFFRACTIONr_chiral_restr0.0850.21412
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027632
X-RAY DIFFRACTIONr_nbd_refined0.2310.34692
X-RAY DIFFRACTIONr_nbtor_refined0.3240.56525
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.5823
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.270.347
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2690.55
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 168 -
Rwork0.231 3401 -
obs--86.1 %

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