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- PDB-5k9x: Crystal structure of Tryptophan synthase alpha chain from Legione... -

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Basic information

Entry
Database: PDB / ID: 5k9x
TitleCrystal structure of Tryptophan synthase alpha chain from Legionella pneumophila subsp. pneumophila
ComponentsTryptophan synthase alpha chain
KeywordsLYASE / Tryptophan synthase / structural genomics / CSGID / trpA / Center for Structural Genomics of Infectious Diseases
Function / homology
Function and homology information


L-tryptophan metabolic process / tryptophan synthase / tryptophan synthase activity / cytosol
Similarity search - Function
Tryptophan synthase, alpha chain / Tryptophan synthase, alpha chain, active site / Tryptophan synthase alpha chain / Tryptophan synthase alpha chain signature. / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Tryptophan synthase alpha chain
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.016 Å
AuthorsChang, C. / Hatzos-Skintges, C. / Endres, M. / ANDERSON, W.F. / JOACHIMIAK, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: Crystal structure of Tryptophan synthase alpha chain from Legionella pneumophila subsp. pneumophila
Authors: Chang, C. / Hatzos-Skintges, C. / Endres, M. / ANDERSON, W.F. / JOACHIMIAK, A.
History
DepositionJun 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 6, 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 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophan synthase alpha chain


Theoretical massNumber of molelcules
Total (without water)30,8021
Polymers30,8021
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.021, 71.046, 71.818
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tryptophan synthase alpha chain


Mass: 30802.492 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: trpA, lpg1305
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q5ZVY3, tryptophan synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / Details: 0.01 M Sodium citrate,33% PEG 6000,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97924 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97924 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 16344 / % possible obs: 99.4 % / Redundancy: 11.3 % / Biso Wilson estimate: 24.07 Å2 / Rmerge(I) obs: 0.058 / Net I/av σ(I): 38 / Net I/σ(I): 10.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.038.40.893193.1
2.03-2.079.20.736198
2.07-2.119.80.633199.3
2.11-2.1510.60.6041100
2.15-2.211.30.4951100
2.2-2.2511.80.4341100
2.25-2.31120.3751100
2.31-2.3712.10.3061100
2.37-2.44120.2441100
2.44-2.5212.10.2041100
2.52-2.6112.10.1611100
2.61-2.7112.10.1241100
2.71-2.84120.0911100
2.84-2.99120.0721100
2.99-3.1711.90.0581100
3.17-3.4211.80.0531100
3.42-3.7611.80.0511100
3.76-4.3111.60.0451100
4.31-5.4311.30.0321100
5.43-5010.60.029198.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXdev_2056refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.016→39.211 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.58
RfactorNum. reflection% reflection
Rfree0.2379 1411 5.03 %
Rwork0.1909 --
obs0.1933 15279 91.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.59 Å2 / Biso mean: 34.5078 Å2 / Biso min: 11.45 Å2
Refinement stepCycle: final / Resolution: 2.016→39.211 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2010 0 0 130 2140
Biso mean---41.43 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032094
X-RAY DIFFRACTIONf_angle_d0.6582843
X-RAY DIFFRACTIONf_chiral_restr0.032324
X-RAY DIFFRACTIONf_plane_restr0.004370
X-RAY DIFFRACTIONf_dihedral_angle_d10.2441284
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0162-2.08830.2718810.23441365144647
2.0883-2.17190.3051050.25282188229375
2.1719-2.27070.34161440.24582742288694
2.2707-2.39040.27931510.229129123063100
2.3904-2.54010.24241540.223829093063100
2.5401-2.73620.31451520.219729203072100
2.7362-3.01150.24971600.209328893049100
3.0115-3.4470.2821530.190929233076100
3.447-4.3420.1941730.153328923065100
4.342-39.21840.16421380.15232903304199

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