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- PDB-1ax4: TRYPTOPHANASE FROM PROTEUS VULGARIS -

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Basic information

Entry
Database: PDB / ID: 1ax4
TitleTRYPTOPHANASE FROM PROTEUS VULGARIS
ComponentsTRYPTOPHANASE
KeywordsTRYPTOPHAN BIOSYNTHESIS / TRYPTOPHAN INDOLE-LYASE / PYRIDOXAL 5'-PHOSPHATE / MONOVALENT CATION BINDING SITE
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
Biological speciesProteus vulgaris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsIsupov, M.N. / Antson, A.A. / Dodson, E.J. / Dodson, G.G. / Dementieva, I.S. / Zakomirdina, L.N. / Wilson, K.S. / Dauter, Z. / Lebedev, A.A. / Harutyunyan, E.H.
Citation
#1: Journal: Biochemistry of Vitamin B6 and Pqq / Year: 1994
Title: X-Ray Study of Tryptophanase at 2.1 Angstrom Resolution
Authors: Isupov, M. / Dementieva, I. / Zakomirdina, L. / Wilson, K.S. / Dauter, Z. / Antson, A.A. / Dodson, G.G. / Harutyunyan, E.H.
#2: Journal: J.Mol.Biol. / Year: 1994
Title: Crystallization and Preliminary X-Ray Investigation of Holotryptophanases from Escherichia Coli and Proteus Vulgaris
Authors: Dementieva, I.S. / Zakomirdina, L.N. / Sinitzina, N.I. / Antson, A.A. / Wilson, K.S. / Isupov, M.N. / Lebedev, A.A. / Harutyunyan, E.H.
History
DepositionOct 28, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: database_2 / diffrn_source ...database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _diffrn_source.pdbx_synchrotron_site / _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.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.pdbx_leaving_atom_flag / _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_ref_seq_dif.details / _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)211,3058
Polymers211,1484
Non-polymers1564
Water16,934940
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18180 Å2
ΔGint-86 kcal/mol
Surface area58440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.990, 118.230, 153.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.01, -0.212, 0.977), (-0.214, -0.955, -0.205), (0.977, -0.208, -0.055)-46.10084, 127.67617, 75.14806
2given(-0.009, 0.263, -0.965), (0.229, -0.939, -0.257), (-0.973, -0.223, -0.052)43.11463, 129.55736, 76.94052
3given(-1, -0.018, 0.002), (-0.015, 0.887, 0.462), (-0.01, 0.462, -0.887)2.05439, -21.19797, 86.3586

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Components

#1: Protein
TRYPTOPHANASE / / TRYPTOPHAN INDOLE-LYASE


Mass: 52787.102 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: PYRIDOXAL 5'-DEPENDENT ENZYME, REQUIRES MONOVALENT CATIONS FOR ACTIVITY, DEGRADES L-TRYPTOPHAN TO INDOLE, PYRUVATE AND AMMONIA
Source: (gene. exp.) Proteus vulgaris (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P28796, tryptophanase
#2: Chemical
ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 940 / 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: 2.49 Å3/Da / Density % sol: 51 %
Crystal growpH: 7.8
Details: 27 % PEG 4000, 0.1 M POTASSIUM PHOSPHATE BUFFER PH 7.8, 0.25 MM PYRIDOXAL 5'-PHOSPHATE, 5MM DTT, 0.1 M CSCL.
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
10.25 mMPLP1reservoir
25 mMdithiothreitol1reservoir
30.1 M1reservoirCsCl
40.1 Mpotassium phosphate1reservoir
527 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.95
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 2.1→18 Å / Num. obs: 397510 / % possible obs: 97.6 % / Redundancy: 3.33 % / Rmerge(I) obs: 0.098 / Rsym value: 0.098 / Net I/σ(I): 11
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 2.49 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 3.2 / Rsym value: 0.273 / % possible all: 97.3
Reflection
*PLUS
Num. obs: 117863 / Num. measured all: 397510
Reflection shell
*PLUS
% possible obs: 97.3 %

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Processing

Software
NameClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TYROSINE PHENOL LYASE, PDB ENTRY 1TPL

1tpl


Resolution: 2.1→18 Å / Cross valid method: FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.22749 2364 2 %RANDOM
Rwork0.18688 ---
obs-115498 97.6 %-
Refinement stepCycle: LAST / Resolution: 2.1→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14772 0 64 941 15777
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 117863 / Rfactor obs: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.030.04
X-RAY DIFFRACTIONp_dihedral_angle_d
X-RAY DIFFRACTIONp_dihedral_angle_deg4.17
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_plane_restr0.0210.02
X-RAY DIFFRACTIONp_chiral_restr0.1180.15
X-RAY DIFFRACTIONp_mcbond_it2.84
X-RAY DIFFRACTIONp_scbond_it5.78
X-RAY DIFFRACTIONp_mcangle_it3.76
X-RAY DIFFRACTIONp_scangle_it7.710

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