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- PDB-9jff: Crystal structure of L-threonine-O-3-phosphate decarboxylase CobC... -

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Basic information

Entry
Database: PDB / ID: 9jff
TitleCrystal structure of L-threonine-O-3-phosphate decarboxylase CobC in complex with reaction intermediate
Componentsthreonine-phosphate decarboxylase
KeywordsLYASE / cobalamin / L-threonine-O-3-phosphate decarboxylase / PLP / aminopropanol phosphate
Function / homology
Function and homology information


threonine-phosphate decarboxylase / threonine-phosphate decarboxylase activity / cobalamin biosynthetic process / pyridoxal phosphate binding
Similarity search - Function
L-threonine-O-3-phosphate decarboxylase / Aminotransferases, class-I, pyridoxal-phosphate-binding site / Aminotransferases class-I pyridoxal-phosphate attachment site. / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-33P / threonine-phosphate decarboxylase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJiang, M. / Guo, S. / Chen, X. / Wei, Q. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
Other government2108085MC75 China
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Crystal structure of l-threonine-O-3-phosphate decarboxylase CobC from Sinorhizobium meliloti involved in vitamin B 12 biosynthesis.
Authors: Jiang, M. / Guo, S. / Chen, X. / Wei, Q. / Wang, M.
History
DepositionSep 4, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Oct 16, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: threonine-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,68317
Polymers36,1221
Non-polymers1,56016
Water8,773487
1
A: threonine-phosphate decarboxylase
hetero molecules

A: threonine-phosphate decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,36534
Polymers72,2442
Non-polymers3,12132
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation16_555x,-y,-z+1/21
Buried area10060 Å2
ΔGint-241 kcal/mol
Surface area26020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.074, 160.074, 160.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-416-

NA

21A-981-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein threonine-phosphate decarboxylase / L-threonine-O-3-phosphate decarboxylase


Mass: 36122.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (bacteria) / Gene: cobC / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A499W357, threonine-phosphate decarboxylase

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Non-polymers , 6 types, 503 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-33P / {3-[(3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YLMETHYL)-AMINO]-2-METHYL-PROPYL}-PHOSPHONIC ACID


Mass: 386.232 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H20N2O9P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 487 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 4.84 Å3/Da / Density % sol: 74.6 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.1 / Details: 0.1 M Bis-Tris pH 6.1 1.4 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL18U / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 30, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 37227 / % possible obs: 100 % / Redundancy: 10.1 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.165 / Rpim(I) all: 0.055 / Rrim(I) all: 0.174 / Χ2: 1.009 / Net I/σ(I): 3.7 / Num. measured all: 374317
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.15-2.2310.21.18437140.6710.8960.3911.2470.898100
2.23-2.3210.20.8636910.7940.9410.2840.9070.949100
2.32-2.4210.20.66436800.8680.9640.2190.6990.984100
2.42-2.5510.50.52337070.9130.9770.1690.551.076100
2.55-2.71100.38937040.9460.9860.1290.411.122100
2.71-2.92100.2836890.9680.9920.0930.2951.144100
2.92-3.2110.40.20337080.9830.9960.0660.2131.174100
3.21-3.689.90.1437360.990.9980.0470.1471.106100
3.68-4.639.90.10937510.9930.9980.0370.1150.966100
4.63-509.40.07938470.9960.9990.0270.0830.65399.7

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→25.31 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 1790 4.89 %
Rwork0.1563 --
obs0.1581 36571 98.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.15→25.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2476 0 86 487 3049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.664
X-RAY DIFFRACTIONf_dihedral_angle_d12.207967
X-RAY DIFFRACTIONf_chiral_restr0.047404
X-RAY DIFFRACTIONf_plane_restr0.007477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.210.29441220.23312488X-RAY DIFFRACTION91
2.21-2.270.25161250.21532602X-RAY DIFFRACTION96
2.27-2.340.23471380.20942646X-RAY DIFFRACTION98
2.34-2.430.23431110.20992703X-RAY DIFFRACTION99
2.43-2.530.23651450.18772635X-RAY DIFFRACTION99
2.53-2.640.2581480.18972639X-RAY DIFFRACTION99
2.64-2.780.18641470.17762678X-RAY DIFFRACTION99
2.78-2.950.2111340.16452691X-RAY DIFFRACTION99
2.95-3.180.19941280.16372723X-RAY DIFFRACTION99
3.18-3.50.17931510.13622696X-RAY DIFFRACTION100
3.5-40.16821450.12332736X-RAY DIFFRACTION100
4.01-5.040.14721500.11612740X-RAY DIFFRACTION100
5.05-25.310.16321460.14032804X-RAY DIFFRACTION99

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