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- PDB-1b8f: Histidine ammonia-lyase (HAL) from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 1b8f
TitleHistidine ammonia-lyase (HAL) from Pseudomonas putida
ComponentsHistidine ammonia-lyase
KeywordsLYASE / AMMONIA-LYASE / HISTIDINE DEGRADATION
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/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal ...Histidine ammonia-lyase / Phenylalanine/histidine ammonia-lyases, active site / Phenylalanine and histidine ammonia-lyases signature. / Aromatic amino acid lyase / Aromatic amino acid lyase / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Histidine ammonia-lyase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsSchwede, T.F. / Schulz, G.E.
Citation
Journal: Biochemistry / Year: 1999
Title: Crystal structure of histidine ammonia-lyase revealing a novel polypeptide modification as the catalytic electrophile.
Authors: Schwede, T.F. / Retey, J. / Schulz, G.E.
#1: Journal: Protein Eng. / Year: 1999
Title: Homogenization and crystallization of histidine ammonia-lyase by exchange of a surface cysteine residue.
Authors: Schwede, T.F. / Badeker, M. / Langer, M. / Retey, J. / Schulz, G.E.
History
DepositionJan 31, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0May 6, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Sep 14, 2011Group: Structure summary
Revision 1.4Oct 30, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_validate_main_chain_plane / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 20, 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: Histidine ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8073
Polymers53,6191
Non-polymers1882
Water3,783210
1
A: Histidine ammonia-lyase
hetero molecules

A: Histidine ammonia-lyase
hetero molecules

A: Histidine ammonia-lyase
hetero molecules

A: Histidine ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,23012
Polymers214,4774
Non-polymers7538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area27650 Å2
ΔGint-209 kcal/mol
Surface area56370 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)79.267, 116.788, 129.532
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Histidine ammonia-lyase / E.C.4.3.1.3 / HAL / Histidase


Mass: 53619.223 Da / Num. of mol.: 1 / Mutation: C273A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Cellular location: CYTOPLASM / Gene: hutH / Plasmid: PT7-7H / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P21310, histidine ammonia-lyase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 8.1
Details: CRYSTALLIZED FROM 2.0 M (NH4)2SO4, 1 % GLYCEROL, 2 % PEG 400, 0.1 M HEPES AT pH 8.1. 20 % (V/V) GLYCEROL WERE USED AS CRYOPROTECTANT
Components of the solutions
IDNameCrystal-IDSol-ID
1(NH4)2SO411
2glycerol11
3peg 40011
4HEPES11
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 mg/mlprotein1drop
22.0 Mammonium sulfate1reservoir
31 %glycerol1reservoir
42 %PEG4001reservoir
50.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Feb 15, 1998
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→39 Å / Num. obs: 28972 / % possible obs: 83 % / Redundancy: 2.9 % / Biso Wilson estimate: 15.8 Å2 / Rsym value: 8.2 / Net I/σ(I): 7.9
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 3 / Rsym value: 18.2 / % possible all: 66
Reflection
*PLUS
Num. measured all: 82830 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 66 % / Rmerge(I) obs: 0.182

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
XDSdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HISTIDASE IN SPACE GROUP P21 (NOT DEPOSITED)

Resolution: 2.1→39 Å / SU B: 5.17 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.263 1485 5 %
Rwork0.187 --
obs0.197 28972 83 %
all-28972 -
Displacement parametersBiso mean: 22.9 Å2
Refinement stepCycle: LAST / Resolution: 2.1→39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 11 210 3983
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0140.025
X-RAY DIFFRACTIONp_angle_d0.0240.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0580.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.392
X-RAY DIFFRACTIONp_mcangle_it2.053
X-RAY DIFFRACTIONp_scbond_it1.612
X-RAY DIFFRACTIONp_scangle_it2.33
X-RAY DIFFRACTIONp_plane_restr0.02230.03
X-RAY DIFFRACTIONp_chiral_restr0.1190.15
X-RAY DIFFRACTIONp_singtor_nbd0.180.3
X-RAY DIFFRACTIONp_multtor_nbd0.2650.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1430.3
X-RAY DIFFRACTIONp_planar_tor8.330
X-RAY DIFFRACTIONp_staggered_tor19.515
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor37.420
X-RAY DIFFRACTIONp_special_tor1.5
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 39 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_plane_restr0.0220.03
X-RAY DIFFRACTIONp_mcbond_it1.392
X-RAY DIFFRACTIONp_scbond_it1.612
X-RAY DIFFRACTIONp_mcangle_it2.053
X-RAY DIFFRACTIONp_scangle_it2.33

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