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- PDB-7xb6: Crystal structure of the O-carbamoyltransferase VtdB in complex w... -

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Basic information

Entry
Database: PDB / ID: 7xb6
TitleCrystal structure of the O-carbamoyltransferase VtdB in complex with carbamoyl adenylate intermediate
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, C-terminal domain / Carbamoyltransferase / Carbamoyltransferase, C-terminal / Carbamoyltransferase, C-terminal domain superfamily / : / Carbamoyltransferase N-terminus / Carbamoyltransferase C-terminus / DHBP synthase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain ...Carbamoyltransferase, C-terminal domain / Carbamoyltransferase / Carbamoyltransferase, C-terminal / Carbamoyltransferase, C-terminal domain superfamily / : / Carbamoyltransferase N-terminus / Carbamoyltransferase C-terminus / DHBP synthase / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CA0 / Carbamoyltransferase
Similarity search - Component
Biological speciesStreptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.901 Å
AuthorsZhang, H. / 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 from Streptomyces sp. NO1W98 in complex with carbamoyladenylate
Authors: Zhang, H. / Teng, Y.
History
DepositionMar 20, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 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

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Assembly

Deposited unit
A: Carbamoyltransferase
B: Carbamoyltransferase
C: Carbamoyltransferase
D: Carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,10512
Polymers263,4474
Non-polymers1,6588
Water2,918162
1
A: Carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2763
Polymers65,8621
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2763
Polymers65,8621
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2763
Polymers65,8621
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Carbamoyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2763
Polymers65,8621
Non-polymers4152
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.391, 245.567, 96.946
Angle α, β, γ (deg.)90.000, 92.042, 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.: 4
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.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-CA0 / 5'-O-[(S)-(carbamoyloxy)(hydroxy)phosphoryl]adenosine


Mass: 390.246 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H15N6O8P / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.46 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop
Details: 27% w/v PEG 4000, 0.1 M HEPES pH 7.0, 0.2 M sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→48.19 Å / Num. obs: 372765 / % possible obs: 98.24 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.149 / Rsym value: 0.149 / Net I/σ(I): 7.77
Reflection shellResolution: 2.9→3 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.533 / Num. unique obs: 3578 / % possible all: 99.4

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Processing

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

Resolution: 2.901→48.189 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.896 / SU B: 0.005 / SU ML: 0 / Cross valid method: NONE / ESU R: 0.333 / ESU R Free: 0.479
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2688 2743 4.983 %
Rwork0.1868 52306 -
all0.191 --
obs-55049 98.242 %
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: 62.607 Å2
Baniso -1Baniso -2Baniso -3
1-0.122 Å2-0 Å20.081 Å2
2---4.035 Å20 Å2
3---3.898 Å2
Refinement stepCycle: LAST / Resolution: 2.901→48.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18568 0 108 162 18838
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.901-2.9760.362040.3063578X-RAY DIFFRACTION91.0886
2.976-3.0580.372040.2663793X-RAY DIFFRACTION99.3044
3.058-3.1460.3441980.2553701X-RAY DIFFRACTION99.4897
3.146-3.2430.3431870.2493592X-RAY DIFFRACTION99.1863
3.243-3.3490.3111750.2293396X-RAY DIFFRACTION97.329
3.349-3.4670.321740.2243403X-RAY DIFFRACTION99.7212
3.467-3.5970.31770.2063268X-RAY DIFFRACTION99.6529
3.597-3.7440.2791960.1953081X-RAY DIFFRACTION99.8172
3.744-3.910.2851590.1813054X-RAY DIFFRACTION99.3814
3.91-4.1010.2561390.1532776X-RAY DIFFRACTION97.0696
4.101-4.3230.2621230.1472740X-RAY DIFFRACTION99.1344
4.323-4.5850.2291500.1422603X-RAY DIFFRACTION99.53
4.585-4.9010.2051040.1422458X-RAY DIFFRACTION99.5725
4.901-5.2930.223910.1652250X-RAY DIFFRACTION98.5684
5.293-5.7970.2771170.1862029X-RAY DIFFRACTION97.7231
5.797-6.4790.293890.1891920X-RAY DIFFRACTION99.7022
6.479-7.4780.222900.1631667X-RAY DIFFRACTION99.1535
7.478-9.150.191690.1431389X-RAY DIFFRACTION97.3298
9.15-12.9040.17630.1551083X-RAY DIFFRACTION99.4792
12.904-48.1890.29340.253525X-RAY DIFFRACTION84.5688

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