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- PDB-2oqx: Crystal Structure of the apo form of E. coli tryptophanase at 1.9... -

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Basic information

Entry
Database: PDB / ID: 2oqx
TitleCrystal Structure of the apo form of E. coli tryptophanase at 1.9 A resolution
ComponentsTryptophanase
KeywordsLYASE / PYRIDOXAL PHOSPHATE / TRYPTOPHAN CATABOLISM
Function / homology
Function and homology information


indole metabolic process / tryptophanase activity / tryptophanase / cell pole / L-cysteine desulfhydrase activity / tryptophan catabolic process / potassium ion binding / pyridoxal phosphate binding / protein-containing complex / identical protein binding ...indole metabolic process / tryptophanase activity / tryptophanase / cell pole / L-cysteine desulfhydrase activity / tryptophan catabolic process / potassium ion binding / pyridoxal phosphate binding / 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
Tryptophanase / Tryptophanase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGoldgur, Y. / Kogan, A. / Gdalevsky, G. / Parola, A. / Cohen-Luria, R. / Almog, O.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2007
Title: The structure of apo tryptophanase from Escherichia coli reveals a wide-open conformation.
Authors: Tsesin, N. / Kogan, A. / Gdalevsky, G.Y. / Himanen, J.P. / Cohen-Luria, R. / Parola, A.H. / Goldgur, Y. / Almog, O.
History
DepositionFeb 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 20, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tryptophanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7634
Polymers52,4651
Non-polymers2983
Water6,557364
1
A: Tryptophanase
hetero molecules

A: Tryptophanase
hetero molecules

A: Tryptophanase
hetero molecules

A: Tryptophanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,05216
Polymers209,8604
Non-polymers1,19212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area20680 Å2
ΔGint-113 kcal/mol
Surface area64460 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)118.422, 120.116, 171.209
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-1001-

CL

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Components

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


Mass: 52464.926 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli)
References: UniProt: P0A853, UniProt: Q5UES8*PLUS, tryptophanase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / 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: 2.9 Å3/Da / Density % sol: 57.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 400, 100mM HEPES, 100 mM magnesium sulfate, pH 7.5, 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
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 1, 2003 / Details: osmic mirrors
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 88583 / % possible obs: 95.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 42.54
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.25 / Num. unique all: 9268 / % possible all: 99.3

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
PDB_EXTRACT2data extraction
MAR345345DTBdata collection
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→14.82 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1074113.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.232 2631 3 %RANDOM
Rwork0.203 ---
all0.21 ---
obs0.21 88583 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.89 Å2 / ksol: 0.468 e/Å3
Displacement parametersBiso mean: 27 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--2.66 Å20 Å2
3----3.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.9→14.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3670 0 17 364 4051
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.612
X-RAY DIFFRACTIONc_scbond_it1.932
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 419 2.9 %
Rwork0.261 14095 -
obs-14514 93.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep_bs.paramprotein_bs.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3cis_peptide.paramepe_xplor.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5epe_xplor.par

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