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- PDB-1gkm: HISTIDINE AMMONIA-LYASE (HAL) FROM PSEUDOMONAS PUTIDA INHIBITED W... -

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Entry
Database: PDB / ID: 1gkm
TitleHISTIDINE AMMONIA-LYASE (HAL) FROM PSEUDOMONAS PUTIDA INHIBITED WITH L-CYSTEINE
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
CYSTEINE / Histidine ammonia-lyase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 1 Å
AuthorsBaedeker, M. / Schulz, G.E.
Citation
Journal: Eur.J.Biochem. / Year: 2002
Title: Structures of Two Histidine Ammonia-Lyase Modifications and Implications for the Catalytic Mechanism
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 16, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 5, 2002Provider: repository / Type: Initial release
Revision 1.1Sep 7, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Other / Category: pdbx_database_status / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_sf / _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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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 3.0Jun 26, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / database_PDB_caveat / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_oper_list / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_chiral / pdbx_validate_close_contact / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _chem_comp_atom.atom_id / _chem_comp_atom.comp_id / _chem_comp_atom.pdbx_aromatic_flag / _chem_comp_atom.pdbx_stereo_config / _chem_comp_atom.type_symbol / _entity_name_com.name / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_strand_id / _entity_poly_seq.mon_id / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_distant_solvent_atoms.auth_asym_id / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_distant_solvent_atoms.neighbor_macromolecule_distance / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_special_symmetry.auth_asym_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_1 / _pdbx_validate_rmsd_angle.auth_asym_id_2 / _pdbx_validate_rmsd_angle.auth_asym_id_3 / _pdbx_validate_rmsd_angle.auth_seq_id_1 / _pdbx_validate_rmsd_angle.auth_seq_id_2 / _pdbx_validate_rmsd_angle.auth_seq_id_3 / _pdbx_validate_rmsd_bond.auth_asym_id_1 / _pdbx_validate_rmsd_bond.auth_asym_id_2 / _pdbx_validate_rmsd_bond.auth_seq_id_1 / _pdbx_validate_rmsd_bond.auth_seq_id_2 / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.pdbx_strand_id / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_pdb_strand_id / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Histidine ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9454
Polymers53,6351
Non-polymers3093
Water9,818545
1
B: Histidine ammonia-lyase
hetero molecules

B: Histidine ammonia-lyase
hetero molecules

B: Histidine ammonia-lyase
hetero molecules

B: Histidine ammonia-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,77816
Polymers214,5414
Non-polymers1,23712
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 area27700 Å2
ΔGint-205 kcal/mol
Surface area55480 Å2
MethodPISA
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
Components on special symmetry positions
IDModelComponents
11B-1158-

HOH

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Components

#1: Protein Histidine ammonia-lyase / Histidase


Mass: 53635.223 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: ALA 142, SER 143 AND GLY 144 ARE FORMING AN 4-METHYLIDENE-IMIDAZOLE-5-ONE GROUP(MDO). THE CARBONYL CARBON OF ALA 142 IS BONDED TO THE NITROGEN OF GLY 144. THE CARBONYL OXYGEN OF ALA 142 IS ...Details: ALA 142, SER 143 AND GLY 144 ARE FORMING AN 4-METHYLIDENE-IMIDAZOLE-5-ONE GROUP(MDO). THE CARBONYL CARBON OF ALA 142 IS BONDED TO THE NITROGEN OF GLY 144. THE CARBONYL OXYGEN OF ALA 142 IS DELETED. THE SIDE CHAIN OF SER 143 IS DEHYDRATED.
Source: (gene. exp.) Pseudomonas putida (bacteria) / Gene: hutH / Plasmid: PT7-7H / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P21310, histidine ammonia-lyase
#2: Chemical ChemComp-CYS / CYSTEINE


Type: L-peptide linking / Mass: 121.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO2S
#3: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 545 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE 3 RESIDUES ALA 142, SER 143 AND GLY 144 ARE LINKED TO GIVE THE MIO 4-METHYLIDENE-IMIDAZOLE-5- ...THE 3 RESIDUES ALA 142, SER 143 AND GLY 144 ARE LINKED TO GIVE THE MIO 4-METHYLIDENE-IMIDAZOLE-5-ONE SPECIES (MDO): {2-[(1S)-1-AMINOETHYL]-5-HYDROXY-4-METHYL-1H-IMIDAZOL -1-YL}ACETIC ACID THE CARBONYL CARBON OF ALA 142 IS BONDED TO THE NITROGEN OF GLY 144. THE CARBONYL OXYGEN OF ALA 142 IS DELETED. THE SIDE CHAIN O F SER 143 IS DEHYDRATED. HAL WAS INACTIVATED WITH L-CYSTEINE, WHICH IS COVALENTLY BOUND TO SER 143-CB (MDO CB2).
Nonpolymer detailsCYS A1510 IS COVALENTLY ATTACHED TO THE CB2 OF MDO142 O A1511 IS COVALENTLY ATTACHED TO THE CB2 OF ...CYS A1510 IS COVALENTLY ATTACHED TO THE CB2 OF MDO142 O A1511 IS COVALENTLY ATTACHED TO THE CB2 OF MDO142 CYS A1510 AND OXO A1511 ARE TWO DIFFERENT MODIFICATIONS WITH 50% AND 50% OCCUPANCY RESPECTIVELY. THE OXO MODIFICATION APPEARS TO BE ASSOCIATED WITH THE SULFATE A1512

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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 %
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. 25 % (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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.909
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.909 Å / Relative weight: 1
ReflectionResolution: 1→40 Å / Num. obs: 301145 / % possible obs: 96 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.035 / Net I/σ(I): 11.3
Reflection shellResolution: 1→1.06 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.9 / % possible all: 91
Reflection
*PLUS
Lowest resolution: 40 Å / % possible obs: 96 %
Reflection shell
*PLUS
% possible obs: 91 %

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Processing

Software
NameClassification
SHELXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 1→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.135 --
obs0.119 -96 %
all-301145 -
Refine analyzeNum. disordered residues: 11
Refinement stepCycle: LAST / Resolution: 1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3762 0 19 545 4326
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.037
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
Refinement
*PLUS
Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.119
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.22 / Rfactor Rwork: 0.199 / Rfactor obs: 0.199

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