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- PDB-5dip: Crystal structure of lpg0406 in reduced form from Legionella pneu... -

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Basic information

Entry
Database: PDB / ID: 5dip
TitleCrystal structure of lpg0406 in reduced form from Legionella pneumophila
ComponentsAlkyl hydroperoxide reductase AhpD
KeywordsOXIDOREDUCTASE / alkylhydroperoxidase
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
Alkylhydroperoxidase AhpD core / AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
: / Carboxymuconolactone decarboxylase-like domain-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.097 Å
AuthorsChen, X. / Gong, X. / Zhang, N. / Ge, H.
Funding support China, 2items
OrganizationGrant numberCountry
the National Natural Science Foundation of China31270770 China
the National Natural Science Foundation of China31400641 China
CitationJournal: Protein Sci. / Year: 2015
Title: Structure of lpg0406, a carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response from Legionella pneumophila
Authors: Chen, X. / Hu, Y. / Yang, B. / Gong, X. / Zhang, N. / Niu, L. / Wu, Y. / Ge, H.
History
DepositionSep 1, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alkyl hydroperoxide reductase AhpD
B: Alkyl hydroperoxide reductase AhpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8166
Polymers26,6552
Non-polymers1614
Water3,783210
1
A: Alkyl hydroperoxide reductase AhpD
B: Alkyl hydroperoxide reductase AhpD
hetero molecules

A: Alkyl hydroperoxide reductase AhpD
B: Alkyl hydroperoxide reductase AhpD
hetero molecules

A: Alkyl hydroperoxide reductase AhpD
B: Alkyl hydroperoxide reductase AhpD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,44818
Polymers79,9656
Non-polymers48312
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area21940 Å2
ΔGint-321 kcal/mol
Surface area23430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.712, 145.712, 145.712
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11B-394-

HOH

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Components

#1: Protein Alkyl hydroperoxide reductase AhpD / alkylhydroperoxidase


Mass: 13327.461 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Gene: lptwr_00386, lpymg_00422 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta
References: UniProt: A0A0C9P2U2, UniProt: Q5ZYG6*PLUS, peroxiredoxin
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O

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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: 4.84 Å3/Da / Density % sol: 74 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 4.5 / Details: 0.1 M sodium acetate, 22% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97861 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.097→50 Å / Num. obs: 30286 / % possible obs: 100 % / Redundancy: 20 % / Net I/σ(I): 29.1

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Processing

SoftwareName: PHENIX / Version: 1.8.4_1496 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DIK

5dik


Resolution: 2.097→28.576 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.4 / Phase error: 13.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.158 1528 5.05 %
Rwork0.1342 --
obs0.1354 30247 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.097→28.576 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 9 210 1915
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071806
X-RAY DIFFRACTIONf_angle_d1.1232441
X-RAY DIFFRACTIONf_dihedral_angle_d14.296700
X-RAY DIFFRACTIONf_chiral_restr0.049284
X-RAY DIFFRACTIONf_plane_restr0.005308
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0975-2.16520.16991370.13612629X-RAY DIFFRACTION100
2.1652-2.24250.16691360.13372609X-RAY DIFFRACTION100
2.2425-2.33230.1531330.13012562X-RAY DIFFRACTION100
2.3323-2.43840.1751470.14492573X-RAY DIFFRACTION100
2.4384-2.56690.15641250.14562611X-RAY DIFFRACTION100
2.5669-2.72760.17391450.15032585X-RAY DIFFRACTION100
2.7276-2.9380.17981410.15812601X-RAY DIFFRACTION100
2.938-3.23330.18161480.15322594X-RAY DIFFRACTION100
3.2333-3.70030.14651420.12982599X-RAY DIFFRACTION100
3.7003-4.65870.13181340.10922648X-RAY DIFFRACTION100
4.6587-28.57910.14991400.12772708X-RAY DIFFRACTION100

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