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- PDB-7tqr: Crystal Structure of histidine ammonia lyase from Thermoplasma ac... -

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Basic information

Entry
Database: PDB / ID: 7tqr
TitleCrystal Structure of histidine ammonia lyase from Thermoplasma acidophilum
ComponentsProbable histidine ammonia-lyase
KeywordsLYASE / histidine ammonia lyase / acid stress
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
Probable histidine ammonia-lyase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsWu, K. / Dulchavsky, M. / Bardwell, J.C.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Mater Adv / Year: 2022
Title: Microreactor equipped with naturally acid-resistant histidine ammonia lyase from an extremophile.
Authors: Ade, C. / Marcelino, T.F. / Dulchavsky, M. / Wu, K. / Bardwell, J.C.A. / Stadler, B.
History
DepositionJan 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Probable histidine ammonia-lyase


Theoretical massNumber of molelcules
Total (without water)54,2591
Polymers54,2591
Non-polymers00
Water2,090116
1
A: Probable histidine ammonia-lyase

A: Probable histidine ammonia-lyase

A: Probable histidine ammonia-lyase

A: Probable histidine ammonia-lyase


Theoretical massNumber of molelcules
Total (without water)217,0354
Polymers217,0354
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation10_665-y+1,-x+1,-z1
Buried area24470 Å2
ΔGint-133 kcal/mol
Surface area54780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.990, 168.990, 67.751
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622
Space group name HallP62
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: x-y,-y,-z
#7: -x,-x+y,-z
#8: -x,-y,z
#9: y,x,-z
#10: -y,-x,-z
#11: -x+y,y,-z
#12: x,x-y,-z
Components on special symmetry positions
IDModelComponents
11A-591-

HOH

21A-610-

HOH

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Components

#1: Protein Probable histidine ammonia-lyase / Histidase


Mass: 54258.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: hutH, Ta0242 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HLI6, histidine ammonia-lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 50 mM sodium cacodylate pH 7.0, 50 mM lithium chloride, 12 mM spermine tetrahydrochloride, 52 mM strontium chloride, and 30% v/v (+/-)-2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.978 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.1→61.48 Å / Num. obs: 33715 / % possible obs: 100 % / Redundancy: 18.1 % / Biso Wilson estimate: 30.67 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.7
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 2714 / CC1/2: 0.961

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GK3

1gk3


Resolution: 2.1→52.86 Å / SU ML: 0.1558 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.4677
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1827 1648 4.89 %
Rwork0.1479 32045 -
obs0.1496 33693 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.51 Å2
Refinement stepCycle: LAST / Resolution: 2.1→52.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3685 0 0 116 3801
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143753
X-RAY DIFFRACTIONf_angle_d1.45165088
X-RAY DIFFRACTIONf_chiral_restr0.0726587
X-RAY DIFFRACTIONf_plane_restr0.0115664
X-RAY DIFFRACTIONf_dihedral_angle_d6.601527
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.21861370.1752621X-RAY DIFFRACTION99.93
2.16-2.230.22351360.16022614X-RAY DIFFRACTION100
2.23-2.310.17661280.14072637X-RAY DIFFRACTION100
2.31-2.40.20131260.15062642X-RAY DIFFRACTION99.86
2.4-2.510.18151480.14852622X-RAY DIFFRACTION99.93
2.51-2.650.20411340.14432641X-RAY DIFFRACTION99.82
2.65-2.810.17611470.14022639X-RAY DIFFRACTION100
2.81-3.030.17511510.14372640X-RAY DIFFRACTION99.96
3.03-3.330.19471330.14482673X-RAY DIFFRACTION99.89
3.33-3.820.16261390.13722689X-RAY DIFFRACTION99.96
3.82-4.810.17351460.13722743X-RAY DIFFRACTION100
4.81-52.860.18451230.16712884X-RAY DIFFRACTION98.75
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)
11.12844099558-0.3801994583850.1985998895381.48867441906-0.1802074490611.46661269739-0.125936170665-0.05028574931140.1139687440050.2254586311890.05354098328440.10394045844-0.428757129523-0.2128934797470.06869590521530.4620135146650.217828721051-0.0105471179090.3374276865810.02299947295280.29907985754929.2668739026101.31650934318.8466402655
20.3954761477820.3084888896560.004544884085820.997683209519-0.0166336178330.82673141236-0.06558433418560.05588383959070.01578896028350.1936887312070.03911976679080.124823132290.0822163626504-0.2125423327340.02955798994780.2722302357210.1145706902590.06318828999180.345620200599-0.001244842745120.2383240078526.311485772767.494257129913.8077401487
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 0 through 196 )0 - 1961 - 184
22chain 'A' and (resid 197 through 496 )197 - 496185 - 484

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