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- PDB-1gk2: Histidine Ammonia-Lyase (HAL) Mutant F329G from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 1gk2
TitleHistidine Ammonia-Lyase (HAL) Mutant F329G from Pseudomonas putida
ComponentsHISTIDINE AMMONIA-LYASE
KeywordsLYASE / 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: 1.9 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: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / 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
B: HISTIDINE AMMONIA-LYASE
C: HISTIDINE AMMONIA-LYASE
D: HISTIDINE AMMONIA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,01312
Polymers214,2614
Non-polymers7538
Water20,9511163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area27240 Å2
ΔGint-200.4 kcal/mol
Surface area55810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.966, 130.561, 115.835
Angle α, β, γ (deg.)90.00, 91.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999619, -0.00921, 0.02601), (0.009986, -0.999504, 0.029883), (0.025722, 0.030131, 0.999215)38.8063, -1.0084, -0.5123
2given(0.973273, -0.228978, -0.017545), (-0.228881, -0.973426, 0.007412), (-0.018776, -0.003198, -0.999819)1.0614, 4.3502, 58.5465
3given(-0.973921, 0.226861, -0.003334), (0.226829, 0.973249, -0.036532), (-0.005043, -0.036336, -0.999327)39.2049, -3.47, 58.2918

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Components

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


Mass: 53565.133 Da / Num. of mol.: 4 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1163 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN A, B, C, D ENGINEERED MUTATION CYS273ALA, PHE329GLY MUTANT F329G IS UNABLE TO FORM THE ...CHAIN A, B, C, D ENGINEERED MUTATION CYS273ALA, PHE329GLY MUTANT F329G 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: 2.75 Å3/Da / Density % sol: 55.29 %
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: 1.9→25 Å / Num. obs: 138987 / % possible obs: 77 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.045 / Net I/σ(I): 12.6
Reflection shell
*PLUS
% possible obs: 51 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 6.4

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Processing

Software
NameClassification
SHELXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1.9→25 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: RESIDUES 271-276 NOT VISIBLE IN ELECTRON DENSITY
RfactorNum. reflection% reflection
Rfree0.226 --
obs0.17 -77 %
all-138987 -
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15028 0 44 1163 16235
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.018
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 obs: 0.17 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS

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