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- PDB-1pya: REFINED STRUCTURE OF THE PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLA... -

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Entry
Database: PDB / ID: 1pya
TitleREFINED STRUCTURE OF THE PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE FROM LACTOBACILLUS 30A
Components(PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)) x 2
KeywordsCARBOXY-LYASE
Function / homology
Function and homology information


histidine decarboxylase / histidine decarboxylase activity / L-histidine metabolic process
Similarity search - Function
Pyruvoyl-Dependent Histidine Decarboxylas; Chain A / Pyruvoyl-Dependent Histidine Decarboxylas, subunit A / Histidine decarboxylase proenzyme / Histidine decarboxylase proenzyme, N-terminal / Histidine carboxylase PI chain / Pyruvoyl-Dependent Histidine Decarboxylase, subunit B / Pyruvoyl-dependent histidine/arginine decarboxylase / Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain / Pyruvoyl-Dependent Histidine Decarboxylase; Chain B / 3-Layer(bba) Sandwich ...Pyruvoyl-Dependent Histidine Decarboxylas; Chain A / Pyruvoyl-Dependent Histidine Decarboxylas, subunit A / Histidine decarboxylase proenzyme / Histidine decarboxylase proenzyme, N-terminal / Histidine carboxylase PI chain / Pyruvoyl-Dependent Histidine Decarboxylase, subunit B / Pyruvoyl-dependent histidine/arginine decarboxylase / Pyruvoyl-dependent histidine/arginine decarboxylase, 3-layer sandwich domain / Pyruvoyl-Dependent Histidine Decarboxylase; Chain B / 3-Layer(bba) Sandwich / Few Secondary Structures / Irregular / Alpha Beta
Similarity search - Domain/homology
Histidine decarboxylase proenzyme
Similarity search - Component
Biological speciesLactobacillus sp. 30A (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsGallagher, T. / Rozwarski, D.A. / Ernst, S.R. / Hackert, M.L.
Citation
Journal: J.Mol.Biol. / Year: 1993
Title: Refined structure of the pyruvoyl-dependent histidine decarboxylase from Lactobacillus 30a.
Authors: Gallagher, T. / Rozwarski, D.A. / Ernst, S.R. / Hackert, M.L.
#1: Journal: J.Biol.Chem. / Year: 1989
Title: Pyruvoyl-Dependent Histidine Decarboxylase: Active Site Structure and Mechanistic Analysis
Authors: Gallagher, T. / Snell, E.E. / Hackert, M.L.
#2: Journal: J.Mol.Biol. / Year: 1985
Title: Structure Determination of Histidine Decarboxylase from Lactobacillus 30A at 3.0 Angstroms Resolution
Authors: Parks, E.H. / Ernst, S.R. / Hamlin, R. / Xuong, N.H. / Hackert, M.L.
#3: Journal: Acta Crystallogr.,Sect.B / Year: 1983
Title: The Molecular Symmetry of Histidine Decarboxylase and Prohistidine Decarboxylase by Rotation Function Analysis
Authors: Parks, E.H. / Clinger, K. / Hackert, M.L.
#4: Journal: J.Biol.Chem. / Year: 1981
Title: Crystallization and Subunit Structure of Histidine Decarboxylase from Lactobacillus 30A
Authors: Hackert, M.L. / Meador, W.E. / Oliver, R.M. / Salmon, J.B. / Rescei, P.A. / Snell, E.E.
History
DepositionDec 18, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
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_struct_sheet_hbond / struct_conn
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 / _pdbx_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id
Revision 2.1Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX ISOLATED TURNS OF A 3-10 HELIX OCCUR AT RESIDUES 98 - 102 AND 266 - 270.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)
B: PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)
C: PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)
D: PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)
E: PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)
F: PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)


Theoretical massNumber of molelcules
Total (without water)102,4096
Polymers102,4096
Non-polymers00
Water8,485471
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29310 Å2
ΔGint-135 kcal/mol
Surface area31250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.700, 221.700, 107.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.47771, -0.503811, -0.7197), (0.515178, -0.502924, 0.694017), (-0.711608, -0.702312, 0.019301)113.89865, 110.27171, 156.94324
2given(0.47771, 0.515178, -0.711608), (-0.503811, -0.502924, -0.702312), (-0.7197, 0.694017, 0.019301)0.46197, 223.06477, 2.41324
DetailsTWO TRIMERS RELATED BY A CRYSTALLOGRAPHIC TWO-FOLD SYMMETRY AXIS GENERATE THE HEXAMER. THE TRANSFORMATION PRESENTED AS *MTRIX 1* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *B* WHEN APPLIED TO CHAINS *C* AND *D*, RESPECTIVELY. THE TRANSFORMATION PRESENTED AS *MTRIX 2* BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAINS *A* AND *B* WHEN APPLIED TO CHAINS *E* AND *F*, RESPECTIVELY.

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Components

#1: Protein PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)


Mass: 8850.832 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus sp. 30A (bacteria) / Strain: 30a / References: UniProt: P00862, histidine decarboxylase
#2: Protein PYRUVOYL-DEPENDENT HISTIDINE DECARBOXYLASE (L-HISTIDINE CARBOXYLASE)


Mass: 25285.375 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus sp. 30A (bacteria) / Strain: 30a / References: UniProt: P00862, histidine decarboxylase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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

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Sample preparation

CrystalDensity Matthews: 3.21 Å3/Da / Density % sol: 61.71 %
Crystal grow
*PLUS
pH: 4.8 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-15 mg/mlprotein1drop
20.20 Mammonium acetate1drop
345 %satammonium sulfate1reservoir
40.20 Mammonium acetate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementRfactor Rwork: 0.15 / Rfactor obs: 0.15 / Highest resolution: 2.5 Å
Details: THE SEGMENT NUMBERS ARE AS FOLLOWS: (1,3,5 = BETA SUBUNITS) (2,4,6 = ALPHA SUBUNITS), (7,8,9 = PVL MOIETIES WITH 7-2 REPRESENTING THE PVL GROUP COVALENTLY ATTACHED TO THE BEGINNING OF AN ...Details: THE SEGMENT NUMBERS ARE AS FOLLOWS: (1,3,5 = BETA SUBUNITS) (2,4,6 = ALPHA SUBUNITS), (7,8,9 = PVL MOIETIES WITH 7-2 REPRESENTING THE PVL GROUP COVALENTLY ATTACHED TO THE BEGINNING OF AN ALPHA SUBUNIT OR SEGMENT 2). THE SEGMENT NUMBERS FOR THE THREE *AB* SUBUNITS ARE: 1, 7 - 2; 3, 8 - 4; AND 5, 9 - 6.
Refinement stepCycle: LAST / Highest resolution: 2.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8727 0 0 1413 10140
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 5 Å / Num. reflection obs: 39926 / Rfactor obs: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_d3
X-RAY DIFFRACTIONx_dihedral_angle_d26.3
X-RAY DIFFRACTIONx_dihedral_angle_deg1.3

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