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- PDB-4w1y: Crystal structure of Escherichia coli Tryptophanase in 'semi-holo... -

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Basic information

Entry
Database: PDB / ID: 4w1y
TitleCrystal structure of Escherichia coli Tryptophanase in 'semi-holo' form
Components(Tryptophanase) x 2
KeywordsLYASE / Tryptophanase
Function / homology
Function and homology information


indole metabolic process / tryptophanase activity / tryptophanase / cell pole / L-cysteine desulfhydrase activity / L-tryptophan catabolic process / potassium ion binding / pyridoxal phosphate binding / lyase activity / protein-containing complex ...indole metabolic process / tryptophanase activity / tryptophanase / cell pole / L-cysteine desulfhydrase activity / L-tryptophan catabolic process / potassium ion binding / pyridoxal phosphate binding / lyase activity / protein-containing complex / identical protein binding / membrane / cytosol
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
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 3.2 Å
AuthorsGoldgur, Y.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structures of Escherichia coli tryptophanase in holo and `semi-holo' forms.
Authors: Kogan, A. / Raznov, L. / Gdalevsky, G.Y. / Cohen-Luria, R. / Almog, O. / Parola, A.H. / Goldgur, Y.
History
DepositionAug 13, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 25, 2015Group: Database references
Revision 2.0Sep 27, 2017Group: Data collection / Derived calculations ...Data collection / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: diffrn_detector / entity ...diffrn_detector / entity / entity_src_gen / pdbx_struct_oper_list
Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _diffrn_detector.detector / _entity.formula_weight / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Tryptophanase
B: Tryptophanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,0464
Polymers104,8532
Non-polymers1922
Water1,928107
1
A: Tryptophanase
B: Tryptophanase
hetero molecules

A: Tryptophanase
B: Tryptophanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,0918
Polymers209,7074
Non-polymers3844
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area16710 Å2
ΔGint-108 kcal/mol
Surface area61100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.971, 109.971, 238.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Tryptophanase / L-tryptophan indole-lyase / TNase


Mass: 52540.801 Da / Num. of mol.: 1 / Fragment: UNP residues 5-471
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tnaA, ind, b3708, JW3686 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A853, tryptophanase
#2: Protein Tryptophanase / L-tryptophan indole-lyase / TNase


Mass: 52312.684 Da / Num. of mol.: 1 / Fragment: UNP residues 5-471
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: tnaA, ind, b3708, JW3686 / Production host: Escherichia coli (E. coli) / References: UniProt: P0A853, tryptophanase
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 13-16 % AMMONIUM SULFATE, 1-5 MM PLP, 50 MM TRIS / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 1, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.2→15 Å / Num. obs: 22389 / % possible obs: 94.8 % / Redundancy: 5.9 % / Rsym value: 0.124 / Net I/σ(I): 19.2
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 3.1 / % possible all: 97.2

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Processing

SoftwareName: REFMAC / Version: 5.4.0077 / Classification: refinement
RefinementResolution: 3.2→15 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.887 / SU B: 24.855 / SU ML: 0.419 / Cross valid method: THROUGHOUT / ESU R Free: 0.536 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28972 1207 5.1 %RANDOM
Rwork0.21377 ---
obs0.21772 22389 94.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 84.274 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å20 Å20 Å2
2--2.84 Å20 Å2
3----5.68 Å2
Refinement stepCycle: 1 / Resolution: 3.2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6840 0 10 107 6957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0226985
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.3851.9679438
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.45862
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15323.994323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.374151205
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4841545
X-RAY DIFFRACTIONr_chiral_restr0.150.21030
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215289
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9181.54303
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.73926908
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.13632682
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6884.52530
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.2→3.285 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.406 82 -
Rwork0.311 1655 -
obs--97.09 %

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