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- PDB-7erv: Crystal structure of L-histidine decarboxylase (C57S/C101V/C282V ... -

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Basic information

Entry
Database: PDB / ID: 7erv
TitleCrystal structure of L-histidine decarboxylase (C57S/C101V/C282V 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
IMIDAZOLE / Histidine decarboxylase
Similarity search - Component
Biological speciesPhotobacterium phosphoreum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3662
Polymers42,2971
Non-polymers691
Water1,946108
1
A: Histidine decarboxylase
hetero molecules

A: Histidine decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,7314
Polymers84,5932
Non-polymers1382
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area10090 Å2
ΔGint-60 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.166, 114.166, 151.191
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: 42296.625 Da / Num. of mol.: 1 / Mutation: C57S/C101V/C282V
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
#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
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: 3.39 Å3/Da / Density % sol: 63.7 %
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: May 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.5→37.81 Å / Num. obs: 20646 / % possible obs: 99.3 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 19.3
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 20646 / CC1/2: 0.968

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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: 2.5→37.81 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.904 / SU B: 7.078 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.307 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2389 1060 5.1 %RANDOM
Rwork0.1837 ---
obs0.1865 19546 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 116.69 Å2 / Biso mean: 31.858 Å2 / Biso min: 9.17 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å2-0.6 Å2-0 Å2
2---1.21 Å2-0 Å2
3---3.91 Å2
Refinement stepCycle: final / Resolution: 2.5→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2975 0 5 108 3088
Biso mean--66.39 26.29 -
Num. residues----374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133051
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172809
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.6294134
X-RAY DIFFRACTIONr_angle_other_deg1.2991.5836477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2215373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.42623.567157
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40215507
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9791512
X-RAY DIFFRACTIONr_chiral_restr0.0760.2400
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023483
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02704
LS refinement shellResolution: 2.501→2.566 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 90 -
Rwork0.217 1418 -
all-1508 -
obs--100 %

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