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- PDB-8c46: N-Carbamoyl-beta-Alanine Amidohydrolases from Rhizobium radiobact... -

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Basic information

Entry
Database: PDB / ID: 8c46
TitleN-Carbamoyl-beta-Alanine Amidohydrolases from Rhizobium radiobacter MDC 8606
ComponentsN-carbamoyl-beta-alanine amidohydrolase
KeywordsHYDROLASE / Amidohydrolase / N-Carbamoyl-beta-Alanine / carbamoylase / Rhizobium radiobacter / N-carbamoyl amino acid
Function / homology
Function and homology information


beta-ureidopropionase / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / metal ion binding
Similarity search - Function
Amidase, carbamoylase-type / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40
Similarity search - Domain/homology
N-carbamoyl-beta-alanine amidohydrolase
Similarity search - Component
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBasle, A. / Marles-Wright, J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Febs J. / Year: 2023
Title: Structural and biochemical characterisation of the N-carbamoyl-beta-alanine amidohydrolase from Rhizobium radiobacter MDC 8606.
Authors: Paloyan, A. / Sargsyan, A. / Karapetyan, M.D. / Hambardzumyan, A. / Kocharov, S. / Panosyan, H. / Dyukova, K. / Kinosyan, M. / Krueger, A. / Piergentili, C. / Stanley, W.A. / Djoko, K.Y. / ...Authors: Paloyan, A. / Sargsyan, A. / Karapetyan, M.D. / Hambardzumyan, A. / Kocharov, S. / Panosyan, H. / Dyukova, K. / Kinosyan, M. / Krueger, A. / Piergentili, C. / Stanley, W.A. / Djoko, K.Y. / Basle, A. / Marles-Wright, J. / Antranikian, G.
History
DepositionJan 2, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 6, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-carbamoyl-beta-alanine amidohydrolase
B: N-carbamoyl-beta-alanine amidohydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,0068
Polymers88,3542
Non-polymers6526
Water6,521362
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-166 kcal/mol
Surface area27830 Å2
Unit cell
Length a, b, c (Å)53.231, 104.622, 145.372
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: GLN / End label comp-ID: GLN / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 7 - 415 / Label seq-ID: 1 - 409

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein N-carbamoyl-beta-alanine amidohydrolase


Mass: 44176.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8F7I7M8
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.29 Å3/Da / Density % sol: 46.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / Details: 23 % (w/v) PEG1500 and 100 mM MMT pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.91188 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91188 Å / Relative weight: 1
ReflectionResolution: 2→84.92 Å / Num. obs: 55817 / % possible obs: 100 % / Redundancy: 7 % / CC1/2: 0.996 / Net I/σ(I): 7.1
Reflection shellResolution: 2→2.05 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4087 / CC1/2: 0.786

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Processing

Software
NameVersionClassification
xia2data reduction
DIALSdata reduction
Aimlessdata scaling
MoRDaphasing
MolProbitymodel building
BUCCANEERmodel building
Cootmodel building
BUSTERrefinement
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→84.917 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.918 / SU B: 13.3 / SU ML: 0.185 / Cross valid method: FREE R-VALUE / ESU R: 0.232 / ESU R Free: 0.194
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2698 2802 5.035 %
Rwork0.2287 52849 -
all0.231 --
obs-55651 99.801 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 29.238 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0 Å2
2---0.448 Å20 Å2
3---0.588 Å2
Refinement stepCycle: LAST / Resolution: 2→84.917 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6196 0 28 362 6586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0126358
X-RAY DIFFRACTIONr_bond_other_d0.0030.0165778
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.6438622
X-RAY DIFFRACTIONr_angle_other_deg0.7061.56113432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7575816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg12.167548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58101012
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.66310280
X-RAY DIFFRACTIONr_chiral_restr0.0930.2958
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027392
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021248
X-RAY DIFFRACTIONr_nbd_refined0.1990.21405
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.25936
X-RAY DIFFRACTIONr_nbtor_refined0.1670.23176
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.23595
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2390
X-RAY DIFFRACTIONr_metal_ion_refined0.040.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.233
X-RAY DIFFRACTIONr_nbd_other0.1920.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.210
X-RAY DIFFRACTIONr_mcbond_it1.8551.7553270
X-RAY DIFFRACTIONr_mcbond_other1.8511.7553270
X-RAY DIFFRACTIONr_mcangle_it2.6522.6254084
X-RAY DIFFRACTIONr_mcangle_other2.6512.6264085
X-RAY DIFFRACTIONr_scbond_it2.5121.983088
X-RAY DIFFRACTIONr_scbond_other2.5121.9793086
X-RAY DIFFRACTIONr_scangle_it3.4832.8824538
X-RAY DIFFRACTIONr_scangle_other3.4832.8824539
X-RAY DIFFRACTIONr_lrange_it5.01225.887298
X-RAY DIFFRACTIONr_lrange_other4.99325.6297235
X-RAY DIFFRACTIONr_ncsr_local_group_10.0870.0513354
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.087130.05008
12AX-RAY DIFFRACTIONLocal ncs0.087130.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2-2.0520.3432030.34338640.34340840.9140.91299.58370.303
2.052-2.1080.3342100.31737170.31839370.9240.92999.7460.279
2.108-2.1690.3071700.28936680.28938520.9320.94399.63660.253
2.169-2.2360.3151790.27235510.27437340.9210.94899.89290.233
2.236-2.3090.3051900.26434760.26636760.9360.95399.7280.23
2.309-2.390.3381890.23533020.2434960.9240.96499.8570.2
2.39-2.480.271780.24332150.24534020.9480.96499.73550.205
2.48-2.5820.2871820.21830880.22232770.9520.97199.78640.183
2.582-2.6960.3131520.22629970.2331510.9330.96999.93650.187
2.696-2.8280.2861510.20928680.21330230.9530.97599.86770.177
2.828-2.980.2691110.22127630.22328780.950.97199.8610.189
2.98-3.1610.2521390.19625980.19927400.9660.97899.89050.169
3.161-3.3790.2561350.20924300.21125660.9580.97499.9610.185
3.379-3.6490.2721490.21222430.21623960.9550.97299.83310.194
3.649-3.9970.2391180.20821080.2122290.9590.97399.86540.197
3.997-4.4670.2651070.19919140.20220220.9510.97599.95050.194
4.467-5.1560.219870.20517060.20517960.9660.97399.8330.204
5.156-6.3090.23720.22114590.22115340.970.97199.80440.214
6.309-8.8980.198500.211870.212400.9740.97699.75810.2
8.898-84.9170.187300.2196960.2177300.9720.97199.45210.227
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.52430.83610.173.07310.70070.2725-0.12610.15850.0183-0.52220.10310.0686-0.0711-0.01150.0230.1155-0.0203-0.00810.12150.01440.0056-25.004788.733419.2828
20.34490.7654-0.11162.5852-0.46930.3352-0.11330.1636-0.081-0.40650.1271-0.12660.02290.0394-0.01380.0843-0.02150.0180.1512-0.0490.0327-1.5456132.135819.1822
Refinement TLS groupSelection: ALL

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