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- PDB-4up2: Crystal structure of Escherichia coli tryptophanase purified from... -

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Basic information

Entry
Database: PDB / ID: 4up2
TitleCrystal structure of Escherichia coli tryptophanase purified from alkaline stressed bacterial culture.
ComponentsTRYPTOPHANASE
KeywordsLYASE / ALKALINE STRESS / PROTEIN PURIFICATION
Function / homology
Function and homology information


tryptophanase activity / tryptophanase
Similarity search - Function
Tryptophanase / Beta-eliminating lyase family / Tryptophanase, conserved site / Beta-eliminating lyases pyridoxal-phosphate attachment site. / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) ...Tryptophanase / Beta-eliminating lyase family / Tryptophanase, conserved site / Beta-eliminating lyases pyridoxal-phosphate attachment site. / Aromatic amino acid beta-eliminating lyase/threonine aldolase / Beta-eliminating lyase / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Tryptophanase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsRety, S. / Deschamps, P. / Leulliot, N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of Escherichia Coli Tryptophanase Purified from an Alkaline-Stressed Bacterial Culture.
Authors: Rety, S. / Deschamps, P. / Leulliot, N.
History
DepositionJun 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 11, 2015Group: Database references
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)214,16933
Polymers211,4014
Non-polymers2,76829
Water2,036113
1
A: TRYPTOPHANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4277
Polymers52,8501
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TRYPTOPHANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,69710
Polymers52,8501
Non-polymers8479
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TRYPTOPHANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6199
Polymers52,8501
Non-polymers7698
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TRYPTOPHANASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4277
Polymers52,8501
Non-polymers5766
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.240, 158.240, 387.766
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein
TRYPTOPHANASE / L-TRYPTOPHAN INDOLE-LYASE


Mass: 52850.266 Da / Num. of mol.: 4 / Fragment: RESIDUES 6-476
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 / References: UniProt: C3SLI7, tryptophanase
#2: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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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: 3.32 Å3/Da / Density % sol: 63.02 % / Description: NONE
Crystal growDetails: 25% PEG 4000 30MM AMMONIUM SULFATE 20MM B-MERCAPTOETHANOL 100MM TRIS-HCL PH 9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97625
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.78→47.01 Å / Num. obs: 72775 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 42.6 % / Biso Wilson estimate: 56.34 Å2 / Rmerge(I) obs: 0.175 / Net I/σ(I): 25.72
Reflection shellResolution: 2.78→2.88 Å / Redundancy: 43.7 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.54 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2C44

2c44


Resolution: 2.78→47.014 Å / SU ML: 0.37 / σ(F): 1.35 / Phase error: 23.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2457 3672 5.1 %
Rwork0.2155 --
obs0.217 72774 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 60.9 Å2
Refinement stepCycle: LAST / Resolution: 2.78→47.014 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12841 0 144 113 13098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313211
X-RAY DIFFRACTIONf_angle_d0.69617835
X-RAY DIFFRACTIONf_dihedral_angle_d10.7694869
X-RAY DIFFRACTIONf_chiral_restr0.0281921
X-RAY DIFFRACTIONf_plane_restr0.0032287
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-2.81660.37861580.32392580X-RAY DIFFRACTION100
2.8166-2.85520.31281360.30042612X-RAY DIFFRACTION100
2.8552-2.89590.34231370.2852610X-RAY DIFFRACTION100
2.8959-2.93920.29391330.27652604X-RAY DIFFRACTION100
2.9392-2.98510.31111310.27372652X-RAY DIFFRACTION100
2.9851-3.0340.30531350.26262627X-RAY DIFFRACTION100
3.034-3.08630.30171310.26422593X-RAY DIFFRACTION100
3.0863-3.14240.27621280.24632628X-RAY DIFFRACTION100
3.1424-3.20290.2761530.24422616X-RAY DIFFRACTION100
3.2029-3.26820.26581410.25292623X-RAY DIFFRACTION100
3.2682-3.33930.28851420.25152623X-RAY DIFFRACTION100
3.3393-3.41690.28961540.2432623X-RAY DIFFRACTION100
3.4169-3.50230.27261360.24852653X-RAY DIFFRACTION100
3.5023-3.5970.27641500.24622630X-RAY DIFFRACTION100
3.597-3.70280.26241470.23122628X-RAY DIFFRACTION100
3.7028-3.82230.2471490.22032614X-RAY DIFFRACTION100
3.8223-3.95880.24531460.21292666X-RAY DIFFRACTION100
3.9588-4.11720.23831170.20732665X-RAY DIFFRACTION100
4.1172-4.30450.22441320.18782673X-RAY DIFFRACTION100
4.3045-4.53130.19761530.17122668X-RAY DIFFRACTION100
4.5313-4.81490.21171460.18042684X-RAY DIFFRACTION100
4.8149-5.18620.21411440.17912674X-RAY DIFFRACTION100
5.1862-5.70730.20921340.18792745X-RAY DIFFRACTION100
5.7073-6.53130.22931470.20422724X-RAY DIFFRACTION100
6.5313-8.22160.2061500.18462761X-RAY DIFFRACTION99
8.2216-47.02120.22011420.19682926X-RAY DIFFRACTION98

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