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- PDB-8apz: Crystal structure of wild-type L-N-Carbamoylase from Sinorhizobiu... -

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Basic information

Entry
Database: PDB / ID: 8apz
TitleCrystal structure of wild-type L-N-Carbamoylase from Sinorhizobium meliloti
ComponentsN-carbamoyl-L-amino-acid hydrolase
KeywordsHYDROLASE / peptidase family M20/M25/M40
Function / homology
Function and homology information


N-carbamoyl-L-amino-acid hydrolase / N-carbamoyl-L-amino-acid hydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines / amino acid biosynthetic process / metal ion binding
Similarity search - Function
Amidase, carbamoylase-type / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40
Similarity search - Domain/homology
ACETATE ION / : / D-ORNITHINE / N-carbamoyl-L-amino-acid hydrolase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsRozeboom, H.J. / Mayer, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)VENI 722.017.007 Netherlands
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Selecting Better Biocatalysts by Complementing Recoded Bacteria.
Authors: Rubini, R. / Jansen, S.C. / Beekhuis, H. / Rozeboom, H.J. / Mayer, C.
History
DepositionAug 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 11, 2023Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.year
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N-carbamoyl-L-amino-acid hydrolase
B: N-carbamoyl-L-amino-acid hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,28118
Polymers94,0792
Non-polymers1,20316
Water8,287460
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7100 Å2
ΔGint-113 kcal/mol
Surface area27530 Å2
Unit cell
Length a, b, c (Å)133.250, 41.801, 133.996
Angle α, β, γ (deg.)90.000, 94.080, 90.000
Int Tables number5
Space group name H-MI121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N-carbamoyl-L-amino-acid hydrolase / / Hydantoin utilization protein C / L-N-carbamoylase


Mass: 47039.250 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: First 21 residues are expression tag / Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: hyuC / Plasmid: pACYCDUET-1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q6DTN4, N-carbamoyl-L-amino-acid hydrolase

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Non-polymers , 6 types, 476 molecules

#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-ORD / D-ORNITHINE / Ornithine


Type: D-peptide linking / Mass: 132.161 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12N2O2
#5: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M sodium acetate, 0.1 M Bis-tris propane and 20 % PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.9655 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9655 Å / Relative weight: 1
ReflectionResolution: 1.75→45.53 Å / Num. obs: 74615 / % possible obs: 99.5 % / Redundancy: 6.5 % / CC1/2: 0.997 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.037 / Rrim(I) all: 0.095 / Net I/σ(I): 13.3 / Num. measured all: 482305
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.778 / Num. unique obs: 3970 / CC1/2: 0.836 / Rpim(I) all: 0.332 / Rrim(I) all: 0.848 / % possible all: 97.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.68 Å43.18 Å
Translation6.68 Å43.18 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.7data scaling
PHASER2.8.3phasing
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AF model

Resolution: 1.75→43.22 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.916 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.104 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1855 3687 4.9 %RANDOM
Rwork0.1495 ---
obs0.1513 70922 99.46 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 83.18 Å2 / Biso mean: 25.558 Å2 / Biso min: 13.88 Å2
Baniso -1Baniso -2Baniso -3
1--1.81 Å20 Å2-1.21 Å2
2--1.49 Å2-0 Å2
3---0.49 Å2
Refinement stepCycle: final / Resolution: 1.75→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6221 0 56 460 6737
Biso mean--43.33 31.62 -
Num. residues----822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0126436
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165818
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.6378683
X-RAY DIFFRACTIONr_angle_other_deg0.5161.55313546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8735822
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.1491044
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.967101047
X-RAY DIFFRACTIONr_chiral_restr0.2110.2943
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027437
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021243
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 245 -
Rwork0.238 5087 -
all-5332 -
obs--97.26 %
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)
11.15020.13440.11180.05960.05690.37620.03490.1031-0.0970.0386-0.0044-0.00520.035-0.043-0.03050.0296-0.0080.00910.024-0.00330.0479-30.9351-5.3349-55.8673
20.9307-0.01060.48140.0436-0.00260.7964-0.0003-0.014-0.06330.00920.01350.0303-0.01030.0578-0.01320.01540.00060.01920.02620.00570.040111.11712.1714-35.5698
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 416
2X-RAY DIFFRACTION2B7 - 416

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