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- PDB-1gk3: Histidine Ammonia-Lyase (HAL) Mutant D145A from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 1gk3
TitleHistidine Ammonia-Lyase (HAL) Mutant D145A 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 / OTHER / Resolution: 2.25 Å
AuthorsBaedeker, M. / Schulz, G.E.
Citation
Journal: Structure / Year: 2002
Title: Autocatalytic Peptide Cyclization During Chain Folding of Histidine Ammonia-Lyase.
Authors: Baedeker, M. / Schulz, G.E.
#1: 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.
#2: Journal: Protein Eng. / Year: 1999
Title: Homogenization and Crystallization of Histidine Ammonia-Lyase by Exchange of a Surface Cysteine Residue
Authors: Schwede, T.F. / Baedeker, M. / Langer, M. / Retey, J. / Schulz, G.E.
History
DepositionAug 7, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jun 20, 2018Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: citation / pdbx_unobs_or_zero_occ_residues / struct
Item: _citation.page_last / _struct.title
Revision 1.3May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_unobs_or_zero_occ_residues / 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 / _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: HISTIDINE AMMONIA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7993
Polymers53,6111
Non-polymers1882
Water3,315184
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)215,19812
Polymers214,4454
Non-polymers7538
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation2_555-x,-y,z1
Buried area27360 Å2
ΔGint-213.3 kcal/mol
Surface area55480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.815, 117.105, 130.072
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2059-

HOH

21A-2127-

HOH

31A-2144-

HOH

41A-2145-

HOH

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Components

#1: Protein HISTIDINE AMMONIA-LYASE / HISTIDASE / HAL


Mass: 53611.246 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: THIS MUTANT DOES NOT CONTAIN A 4-METHYLIDENE-IMIDAZOLE-5-ONE GROUP.
Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Plasmid: PT7-7H / 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.: 184 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A ENGINEERED MUTATION CYS273ALA, ASP145ALA MUTANT D145A IS UNABLE TO FORM THE CATALYTICALLY ...CHAIN A ENGINEERED MUTATION CYS273ALA, ASP145ALA MUTANT D145A IS UNABLE TO FORM THE CATALYTICALLY ESSENTIAL ELECTROPHILE MIO

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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: 58.06 %
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
Crystal grow
*PLUS
pH: 3.85 / Method: vapor diffusion, hanging drop / Details: Schwede, T.F., (1999) Protein Eng., 12, 151.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
112 mg/mlprotein1drop
21.6 Msodium potassium phosphate1reservoir
30.1 MHEPES1reservoir
41.5 mMEDTA1reservoir
53 %dioxane1reservoirpH3.85

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUB200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→21 Å / Num. obs: 26022 / % possible obs: 91 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 2.4
Reflection shell
*PLUS
% possible obs: 95 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 1.4

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Processing

Software
NameClassification
SHELXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.25→21 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: RESIDUES 272-275 AND 363-374 NOT VISIBLE IN ELECTRON DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.28 -5 %RANDOM
obs0.221 -91 %-
all-26022 --
Refinement stepCycle: LAST / Resolution: 2.25→21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3761 0 11 184 3956
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.016
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes
X-RAY DIFFRACTIONs_zero_chiral_vol
X-RAY DIFFRACTIONs_non_zero_chiral_vol
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt
X-RAY DIFFRACTIONs_similar_adp_cmpnt
X-RAY DIFFRACTIONs_approx_iso_adps
Software
*PLUS
Name: SHELX / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.28 / Rfactor Rwork: 0.221
Solvent computation
*PLUS
Displacement parameters
*PLUS

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