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- PDB-2z8o: Structural basis for the catalytic mechanism of phosphothreonine lyase -

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Basic information

Entry
Database: PDB / ID: 2z8o
TitleStructural basis for the catalytic mechanism of phosphothreonine lyase
Components27.5 kDa virulence protein
KeywordsLYASE / short three-helix bundle / distorted beta-strand sheet
Function / homology
Function and homology information


Lyases; Carbon-oxygen lyases; Acting on phosphates / lyase activity / extracellular region
Similarity search - Function
Phosphothreonine lyase fold / phosphothreonine lyase / OspF/SpvC / OspF/SpvC superfamily / Salmonella virulence-associated 28kDa protein / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / MAPK phosphothreonine lyase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2.4 Å
AuthorsChen, L. / Wang, H. / Gu, L. / Huang, N. / Zhou, J.M. / Chai, J.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2008
Title: Structural basis for the catalytic mechanism of phosphothreonine lyase.
Authors: Chen, L. / Wang, H. / Zhang, J. / Gu, L. / Huang, N. / Zhou, J.M. / Chai, J.
History
DepositionSep 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 27.5 kDa virulence protein
B: 27.5 kDa virulence protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,3563
Polymers56,2062
Non-polymers1501
Water3,081171
1
A: 27.5 kDa virulence protein


Theoretical massNumber of molelcules
Total (without water)28,1031
Polymers28,1031
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 27.5 kDa virulence protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2532
Polymers28,1031
Non-polymers1501
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.755, 70.755, 200.710
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein 27.5 kDa virulence protein / Spvc / phosphothreonine lyase


Mass: 28103.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: mkaD, spvC, vsdD / Plasmid: pGEX6p-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P0A2M9
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.23 Å3/Da / Density % sol: 44.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.8M Na, K-tartrate, 100mM Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
RadiationMonochromator: Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→99 Å / Num. all: 20794 / Num. obs: 20394 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.05 / Net I/σ(I): 63.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 41.2 % / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 17.3 / % possible all: 90.9

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Processing

Software
NameClassification
CrystalCleardata collection
SOLVEphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 2.4→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.253 --RANDOM
Rwork0.243 ---
obs0.243 20394 98.1 %-
all-20794 --
Displacement parametersBiso mean: 33.3323 Å2
Baniso -1Baniso -2Baniso -3
1--3.918 Å20 Å20 Å2
2---3.918 Å20 Å2
3---7.837 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3400 0 10 171 3581
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_angle_refined_deg1.346
LS refinement shellResolution: 2.4→2.49 Å
RfactorNum. reflection% reflection
Rfree0.351 83 -
Rwork0.267 --
obs-1843 90.9 %

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