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- PDB-8hiu: Crystal structure of O-carbamoyltransferase VtdB and the compound... -

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Basic information

Entry
Database: PDB / ID: 8hiu
TitleCrystal structure of O-carbamoyltransferase VtdB and the compound VtdB with carbamoyladenylate from Streptomyces sp. NO1W98
ComponentsCarbamoyltransferase
KeywordsTRANSFERASE / carboxyl- or carbamoyltransferase activity / catalytic activity / transferase activity / ligase activity / magnesium ion binding / metal ion binding
Function / homology
Function and homology information


biosynthetic process / transferase activity / metal ion binding
Similarity search - Function
Carbamoyltransferase / Carbamoyltransferase, C-terminal / Carbamoyltransferase, C-terminal domain superfamily / : / Carbamoyltransferase N-terminus / Carbamoyltransferase C-terminus / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Carbamoyltransferase
Similarity search - Component
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsRao, D. / Teng, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31700650 China
CitationJournal: To Be Published
Title: Crystal structure of O-carbamoyltransferase VtdB and the compound VtdB with carbamoyladenylate from Streptomyces sp. NO1W98
Authors: Rao, D. / Teng, Y.
History
DepositionNov 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbamoyltransferase
B: Carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,7724
Polymers131,7232
Non-polymers492
Water2,342130
1
A: Carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8862
Polymers65,8621
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8862
Polymers65,8621
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.804, 216.678, 70.573
Angle α, β, γ (deg.)90.000, 113.389, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbamoyltransferase


Mass: 65861.648 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7U3NFH8
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 6.6 / Details: 30% w/v PEG 2000, 0.1 M MES pH 6.6

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 18-ID / Wavelength: 0.988 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.988 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 247145 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rpim(I) all: 0.045 / Net I/σ(I): 13.67
Reflection shellResolution: 3→3.05 Å / Num. unique obs: 35766 / Rpim(I) all: 0.164 / Rsym value: 0.406

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold 2

Resolution: 2.99→31.049 Å / Cor.coef. Fo:Fc: 0.917 / Cor.coef. Fo:Fc free: 0.861 / SU B: 0.005 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.344 / ESU R Free: 0.44
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2736 1830 5.129 %
Rwork0.2137 33848 -
all0.217 --
obs-35678 99.084 %
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: 50.448 Å2
Baniso -1Baniso -2Baniso -3
1-6.718 Å20 Å21.187 Å2
2---2.991 Å20 Å2
3----3.46 Å2
Refinement stepCycle: LAST / Resolution: 2.99→31.049 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9284 0 2 130 9416
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.99-3.0670.3921150.2912396X-RAY DIFFRACTION94.1507
3.067-3.1510.351240.2892411X-RAY DIFFRACTION99.4898
3.151-3.2430.3711250.2782435X-RAY DIFFRACTION99.5334
3.243-3.3420.3831160.272290X-RAY DIFFRACTION99.6273
3.342-3.4520.3061270.252234X-RAY DIFFRACTION99.6203
3.452-3.5730.3411120.2522161X-RAY DIFFRACTION99.2143
3.573-3.7080.2981210.2292104X-RAY DIFFRACTION99.6864
3.708-3.8590.2741340.2141961X-RAY DIFFRACTION99.8094
3.859-4.030.251180.1931925X-RAY DIFFRACTION99.7559
4.03-4.2270.217970.1861854X-RAY DIFFRACTION99.6425
4.227-4.4550.252870.1871777X-RAY DIFFRACTION99.7859
4.455-4.7250.274800.1751673X-RAY DIFFRACTION99.6023
4.725-5.050.224810.1711586X-RAY DIFFRACTION99.8204
5.05-5.4540.251690.1841467X-RAY DIFFRACTION99.5463
5.454-5.9730.239790.1951324X-RAY DIFFRACTION99.6449
5.973-6.6750.243920.2131186X-RAY DIFFRACTION99.7658
6.675-7.7030.279570.2041073X-RAY DIFFRACTION99.9116
7.703-9.4220.143430.168932X-RAY DIFFRACTION99.4898

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