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- PDB-2c44: Crystal Structure of E. coli Tryptophanase -

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Basic information

Entry
Database: PDB / ID: 2c44
TitleCrystal Structure of E. coli Tryptophanase
ComponentsTRYPTOPHANASE
KeywordsLYASE / PYRIDOXAL PHOSPHATE / TRYPTOPHAN CATABOLISM
Function / homology
Function and homology information


indole metabolic process / tryptophanase activity / tryptophanase / cell pole / L-cysteine desulfhydrase activity / L-tryptophan catabolic process / L-tryptophan metabolic process / potassium ion binding / pyridoxal phosphate binding / protein-containing complex ...indole metabolic process / tryptophanase activity / tryptophanase / cell pole / L-cysteine desulfhydrase activity / L-tryptophan catabolic process / L-tryptophan metabolic 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKu, S.-Y. / Yip, P. / Howell, P.L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of Escherichia Coli Tryptophanase
Authors: Ku, S.-Y. / Yip, P. / Howell, P.L.
History
DepositionOct 15, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 28, 2006Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_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)212,40418
Polymers211,4014
Non-polymers1,00314
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)215.510, 215.510, 107.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 471
2115B1 - 471
3115C1 - 471
4115D1 - 471

NCS oper:
IDCodeMatrixVector
1given(-0.97343, 0.11196, -0.19977), (0.11037, -0.53496, -0.83764), (-0.20065, -0.83743, 0.50839)508.05426, 83.78087, 114.00939
2given(-0.92671, 0.33053, 0.17876), (0.31706, 0.43247, 0.84406), (0.20168, 0.83888, -0.50558)490.16437, 4.5027, -196.30457
3given(0.9024, -0.43089, 0.00248), (-0.43089, -0.9024, 0.00061), (0.00198, -0.00162, -1)67.61022, 298.05063, -82.36967

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Components

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


Mass: 52850.266 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Details: ONE SULFATE IN THE PLP BINDING SITE, AND THE OTHER SULFATE IN THE TRYPTOPHAN BINDING SITE
Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: JM109
References: UniProt: Q8XB34, UniProt: P0A853*PLUS, tryptophanase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.96 Å3/Da / Density % sol: 58.4 %
Crystal growpH: 7.9
Details: 1.6M AMMONIUM SULFATE, 0.5%(V/V)PEG400, 0.1M SODIUM HEPES PH 7.9

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 31, 2002 / Details: RH-COATED FUSED SILICA COLLIMATING MIRROR
RadiationMonochromator: SI (111) DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→500 Å / Num. obs: 62257 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 26.9
Reflection shellResolution: 2.8→2.91 Å / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 8.7 / % possible all: 98.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AX4

1ax4


Resolution: 2.8→500 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.858 / SU B: 11.546 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE NOT MODELED. RESIDUES WITH DISORDERED SIDE CHAINS WERE MODELED AS ALANINE (ALA).
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3150 5.1 %RANDOM
Rwork0.196 ---
obs0.164 62257 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.529 Å20 Å20 Å2
2---1.529 Å20 Å2
3---3.058 Å2
Refinement stepCycle: LAST / Resolution: 2.8→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14282 0 46 518 14846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0310.02214607
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6831.96119825
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.36151853
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89523.665644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.423152308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0011590
X-RAY DIFFRACTIONr_chiral_restr0.1870.22201
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211206
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2890.28436
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.340.210145
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2953
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.236
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8471.59237
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.613214739
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9135470
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.6144.55086
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1748medium positional0.180.5
2B1748medium positional0.210.5
3C1748medium positional0.180.5
4D1748medium positional0.230.5
1A1614loose positional0.345
2B1614loose positional0.325
3C1614loose positional0.325
4D1614loose positional0.365
1A1748medium thermal1.452
2B1748medium thermal2.142
3C1748medium thermal2.122
4D1748medium thermal3.22
1A1614loose thermal2.8910
2B1614loose thermal3.6410
3C1614loose thermal3.8310
4D1614loose thermal5.4610
LS refinement shellResolution: 2.81→2.88 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.364 250
Rwork0.209 4216

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