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- PDB-5kmy: Crystal structure of tryptophan synthase subunit alpha from Legio... -

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Basic information

Entry
Database: PDB / ID: 5kmy
TitleCrystal structure of tryptophan synthase subunit alpha from Legionella pneumophila str. Paris
ComponentsTryptophan synthase alpha chain
KeywordsLYASE / L-tryptophan biosynthesis / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.908 Å
AuthorsNocek, B. / 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 subunit alpha from Legionella pneumophila str. Paris
Authors: Nocek, B. / Hatzos-Skintges, C. / Endres, M. / Anderson, W.F. / Joachimiak, A.
History
DepositionJun 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Database references
Revision 1.2Nov 23, 2016Group: Database references
Revision 1.3Feb 8, 2017Group: Database references / Structure summary
Revision 1.4Nov 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)30,7581
Polymers30,7581
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.707, 69.654, 75.075
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Tryptophan synthase alpha chain


Mass: 30758.441 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (strain Paris) (bacteria)
Strain: Paris / Gene: trpA, lpp1269 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5X5Q1, tryptophan synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 1.89 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: sodium chloride (0.2M) bis-tris ph 6.5 (0.1M) peg 3350 (25%)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2015
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.908→37.538 Å / Num. obs: 31628 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 20
Reflection shellResolution: 1.908→1.93 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.49 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIXdev_1888refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.908→37.538 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 20.41
RfactorNum. reflection% reflection
Rfree0.2067 1521 4.81 %
Rwork0.1759 --
obs0.1775 31628 92.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.908→37.538 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2024 0 0 204 2228
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052084
X-RAY DIFFRACTIONf_angle_d0.8972833
X-RAY DIFFRACTIONf_dihedral_angle_d12.671790
X-RAY DIFFRACTIONf_chiral_restr0.032324
X-RAY DIFFRACTIONf_plane_restr0.004368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.908-1.96960.2847910.22491588X-RAY DIFFRACTION54
1.9696-2.040.22971070.21352100X-RAY DIFFRACTION71
2.04-2.12170.28441390.20362662X-RAY DIFFRACTION89
2.1217-2.21820.20971340.19872926X-RAY DIFFRACTION97
2.2182-2.33510.23241540.18812948X-RAY DIFFRACTION100
2.3351-2.48140.22411320.17883025X-RAY DIFFRACTION100
2.4814-2.6730.23431550.1892945X-RAY DIFFRACTION100
2.673-2.94190.17481670.17952983X-RAY DIFFRACTION100
2.9419-3.36730.20951670.17222967X-RAY DIFFRACTION100
3.3673-4.24150.16841410.14592966X-RAY DIFFRACTION100
4.2415-37.54470.19151340.16522997X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.51881.3636-5.92712.2982-1.94966.48890.273-0.7164-0.01630.4403-0.1587-0.3733-0.07720.6578-0.02070.1351-0.0214-0.00760.2034-0.00470.125523.21459.033964.7069
23.26250.30780.15360.8590.05771.2881-0.0289-0.01690.3241-0.069-0.00010.0641-0.0672-0.07840.02270.10290.0073-0.01050.0884-0.00260.08885.70667.808352.1782
32.10280.03840.32141.86910.63512.5782-0.1143-0.27180.02950.15780.00580.29950.0756-0.22050.08360.0948-0.0050.00640.12440.01770.12193.30735.900264.9035
41.76690.7758-0.45263.0585-1.26450.52760.0574-0.09020.19760.2164-0.06370.2473-0.1143-0.04280.00510.17260.0106-0.00830.1218-0.03410.129210.556922.312864.5015
51.82010.5213-0.0523.49591.21432.136-0.00610.00940.135-0.26990.0059-0.0045-0.1-0.07460.00780.11570.0032-0.01140.10670.02130.142919.573322.00750.061
65.42961.63031.61913.09020.65121.8456-0.04140.18650.0464-0.24360.0481-0.0311-0.0168-0.00940.03630.16730.01470.02820.11990.00530.058311.53084.92842.0636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 14 )
2X-RAY DIFFRACTION2chain 'A' and (resid 15 through 74 )
3X-RAY DIFFRACTION3chain 'A' and (resid 75 through 121 )
4X-RAY DIFFRACTION4chain 'A' and (resid 122 through 190 )
5X-RAY DIFFRACTION5chain 'A' and (resid 191 through 234 )
6X-RAY DIFFRACTION6chain 'A' and (resid 235 through 269 )

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