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- PDB-7eru: Crystal structure of L-histidine decarboxylase (C57S mutant) from... -

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Basic information

Entry
Database: PDB / ID: 7eru
TitleCrystal structure of L-histidine decarboxylase (C57S mutant) from Photobacterium phosphoreum
ComponentsHistidine decarboxylase
KeywordsLYASE / decarboxylase
Function / homology
Function and homology information


histidine decarboxylase / histidine decarboxylase activity / carboxylic acid metabolic process / pyridoxal phosphate binding
Similarity search - Function
Histidine decarboxylase, bacteria / : / Pyridoxal-phosphate binding site / DDC / GAD / HDC / TyrDC pyridoxal-phosphate attachment site. / Pyridoxal phosphate-dependent decarboxylase / Pyridoxal-dependent decarboxylase conserved domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Histidine decarboxylase
Similarity search - Component
Biological speciesPhotobacterium phosphoreum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsOda, Y. / Nakata, K. / Yamaguchi, H. / Kashiwagi, T. / Miyano, H. / Mizukoshi, T.
CitationJournal: J.Biochem. / Year: 2022
Title: Structural insights into the enhanced thermostability of cysteine substitution mutants of L-histidine decarboxylase from Photobacterium phosphoreum.
Authors: Oda, Y. / Nakata, K. / Miyano, H. / Mizukoshi, T. / Yamaguchi, H. / Kashiwagi, T.
History
DepositionMay 7, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine decarboxylase


Theoretical massNumber of molelcules
Total (without water)42,1911
Polymers42,1911
Non-polymers00
Water00
1
A: Histidine decarboxylase

A: Histidine decarboxylase


Theoretical massNumber of molelcules
Total (without water)84,3812
Polymers84,3812
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area9470 Å2
ΔGint-67 kcal/mol
Surface area26650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.434, 111.434, 126.642
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Histidine decarboxylase / HDC


Mass: 42190.547 Da / Num. of mol.: 1 / Mutation: C57S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Photobacterium phosphoreum (bacteria) / Gene: hdc / Production host: Escherichia coli (E. coli) / References: UniProt: Q1JU62, histidine decarboxylase
Has ligand of interestY

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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: 2.71 Å3/Da / Density % sol: 54.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: PEG1000, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Mar 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.85→100 Å / Num. obs: 11390 / % possible obs: 99.9 % / Redundancy: 18.7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 27.7
Reflection shellResolution: 2.85→2.93 Å / Num. unique obs: 11390 / CC1/2: 0.949

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-20002.3.10data scaling
HKL-20002.3.10data collection
MOLREP11.0.05phasing
HKL-20002.3.10data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3F9T

3f9t


Resolution: 2.85→45.13 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.893 / SU B: 14.1 / SU ML: 0.276 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.377 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2481 567 5 %RANDOM
Rwork0.1862 ---
obs0.1893 10789 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 202.56 Å2 / Biso mean: 57.263 Å2 / Biso min: 23.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.39 Å2-0.2 Å2-0 Å2
2---0.39 Å20 Å2
3---1.27 Å2
Refinement stepCycle: final / Resolution: 2.85→45.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2965 0 0 0 2965
Num. residues----373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133036
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172788
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.634114
X-RAY DIFFRACTIONr_angle_other_deg1.2221.5836434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6145372
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68323.526156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.84815506
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7161512
X-RAY DIFFRACTIONr_chiral_restr0.0640.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023455
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02696
LS refinement shellResolution: 2.85→2.924 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 49 -
Rwork0.231 766 -
all-815 -
obs--100 %

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