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- PDB-6v6h: Crystal structure of histidine ammonia-lyase from Trypanosoma cruzi -

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Basic information

Entry
Database: PDB / ID: 6v6h
TitleCrystal structure of histidine ammonia-lyase from Trypanosoma cruzi
ComponentsHistidine ammonia-lyase
KeywordsLYASE / histidine ammonia-lyase / protection domain absence
Function / homology
Function and homology information


histidine ammonia-lyase / histidine ammonia-lyase activity / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate / cytoplasm
Similarity search - Function
Histidine ammonia-lyase / Phenylalanine/histidine ammonia-lyases, active site / Phenylalanine and histidine ammonia-lyases signature. / Aromatic amino acid lyase / Aromatic amino acid lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
Similarity search - Domain/homology
Histidine ammonia-lyase
Similarity search - Component
Biological speciesTrypanosoma cruzi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMiranda, R.R. / Silva, M. / Barison, M.J. / Silber, A.M. / Iulek, J.
Funding supportBelize, 1items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development573607/2008-7 and 08/57910-0Belize
CitationJournal: Biochimie / Year: 2020
Title: Crystal structure of histidine ammonia-lyase from Trypanosoma cruzi.
Authors: Miranda, R.R. / Silva, M. / Barison, M.J. / Silber, A.M. / Iulek, J.
History
DepositionDec 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 15, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histidine ammonia-lyase
B: Histidine ammonia-lyase
C: Histidine ammonia-lyase
D: Histidine ammonia-lyase


Theoretical massNumber of molelcules
Total (without water)235,9804
Polymers235,9804
Non-polymers00
Water11,746652
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27310 Å2
ΔGint-158 kcal/mol
Surface area56040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.812, 144.555, 173.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42
13
23
33
14
24
34
15
25
35
16
26
17
27
18
28

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and ( resseq 2:4 or resseq 6:17 or...
211chain B and ( resseq 2:4 or resseq 6:17 or...
311chain C and ( resseq 2:4 or resseq 6:17 or...
411chain D and ( resseq 2:4 or resseq 6:17 or...
112chain A and ( resid 18 or resid 25 or...
212chain B and ( resid 18 or resid 25 or...
312chain C and ( resid 18 or resid 25 or...
412chain D and ( resid 18 or resid 25 or...
113chain B and ( ( name ca or name cb or name sg ) and resseq 315:315 )
213chain C and ( ( name ca or name cb or name sg ) and resseq 315:315 )
313chain D and ( ( name ca or name cb or name sg ) and resseq 315:315 )
114chain A and ( resseq 43:43 or resseq 47:47 or resseq 184:184 )
214chain C and ( resseq 43:43 or resseq 47:47 or resseq 184:184 )
314chain D and ( resseq 43:43 or resseq 47:47 or resseq 184:184 )
115chain A and ( resseq 46:46 )
215chain B and ( resseq 46:46 )
315chain D and ( resseq 46:46 )
116chain C and ( resseq 56:56 )
216chain D and ( resseq 56:56 )
117chain A and ( resseq 368:368 )
217chain C and ( resseq 368:368 )
118chain B and ( resseq 483:484 )
218chain C and ( resseq 483:484 )

NCS ensembles :
ID
1
2
3
4
5
6
7
8

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Components

#1: Protein
Histidine ammonia-lyase


Mass: 58994.906 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma cruzi (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: Q4E133, histidine ammonia-lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.49 Å3/Da / Density % sol: 50.65 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 1 mol L-1 succinic acid, 1% (w/v) PEG mme 2.000 and 0.1 mol L-1 HEPES buffer pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 24, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.55→111.13 Å / Num. obs: 72424 / % possible obs: 99.3 % / Redundancy: 6 % / CC1/2: 0.991 / Net I/σ(I): 11.9
Reflection shellResolution: 2.55→2.63 Å / Num. unique obs: 6307 / CC1/2: 0.732

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GKM

1gkm


Resolution: 2.55→32.314 Å / Cross valid method: FREE R-VALUE / σ(F): 1.34
RfactorNum. reflection% reflection
Rfree0.2166 2004 2.77 %
Rwork0.1794 --
obs0.1805 72347 99.41 %
Refinement stepCycle: LAST / Resolution: 2.55→32.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14995 0 0 652 15647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315290
X-RAY DIFFRACTIONf_dihedral_angle_d13.2135488
X-RAY DIFFRACTIONf_plane_restr0.0032699
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2960X-RAY DIFFRACTIONPOSITIONAL
12B2960X-RAY DIFFRACTIONPOSITIONAL0.001
13C2959X-RAY DIFFRACTIONPOSITIONAL0.001
14D2948X-RAY DIFFRACTIONPOSITIONAL0.001
21A125X-RAY DIFFRACTIONPOSITIONAL
22B125X-RAY DIFFRACTIONPOSITIONAL0.002
23C125X-RAY DIFFRACTIONPOSITIONAL0.002
24D125X-RAY DIFFRACTIONPOSITIONAL0.002
31B3X-RAY DIFFRACTIONPOSITIONAL
32C3X-RAY DIFFRACTIONPOSITIONAL0.002
33D3X-RAY DIFFRACTIONPOSITIONAL0.001
41A21X-RAY DIFFRACTIONPOSITIONAL
42C21X-RAY DIFFRACTIONPOSITIONAL0.002
43D21X-RAY DIFFRACTIONPOSITIONAL0.002
51A8X-RAY DIFFRACTIONPOSITIONAL
52B8X-RAY DIFFRACTIONPOSITIONAL0.001
53D8X-RAY DIFFRACTIONPOSITIONAL0.001
61C8X-RAY DIFFRACTIONPOSITIONAL
62D8X-RAY DIFFRACTIONPOSITIONAL0.001
71A8X-RAY DIFFRACTIONPOSITIONAL
72C8X-RAY DIFFRACTIONPOSITIONAL0.001
81B10X-RAY DIFFRACTIONPOSITIONAL
82C10X-RAY DIFFRACTIONPOSITIONAL0.001
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9760.11850.10080.57660.08450.64320.0195-0.05380.00070.0663-0.02420.0590.03820.00420.00440.1725-0.00490.00120.1936-0.01820.16372.374674.168789.1552
21.01120.17460.17830.669-0.00260.5244-0.00690.0277-0.0708-0.0465-0.00570.03830.16910.02720.01350.26030.0428-0.02510.2283-0.04190.2167-0.475152.384965.7051
30.6447-0.2032-0.10650.59470.01460.57160.00080.02430.05660.0093-0.02550.0323-0.07330.01790.02720.176-0.0117-0.01930.1896-0.00950.1868-1.118297.997367.2565
40.7756-0.1819-0.04250.5353-0.1360.63260.00390.1035-0.0126-0.1091-0.01630.07520.05330.0020.02270.23080.0212-0.05810.2814-0.03670.198-3.464376.348943.698
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resseq 1:700
2X-RAY DIFFRACTION2chain B and resseq 1:700
3X-RAY DIFFRACTION3chain C and resseq 1:700
4X-RAY DIFFRACTION4chain D and resseq 1:700

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