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- PDB-6a0n: The crystal structure of apo-Lpg2622 -

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Basic information

Entry
Database: PDB / ID: 6a0n
TitleThe crystal structure of apo-Lpg2622
ComponentsLpg2622
KeywordsHYDROLASE / Cysteine proteases
Function / homologyPapain-like cysteine peptidase superfamily / Cysteine protease
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsGong, X. / Ge, H.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31270770 China
National Natural Science Foundation of China31400641 China
CitationJournal: FEBS Lett. / Year: 2018
Title: Structural characterization of the hypothetical protein Lpg2622, a new member of the C1 family peptidases from Legionella pneumophila
Authors: Gong, X. / Zhao, X. / Zhang, W. / Wang, J. / Chen, X. / Hameed, M.F. / Zhang, N. / Ge, H.
History
DepositionJun 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lpg2622
B: Lpg2622


Theoretical massNumber of molelcules
Total (without water)76,1642
Polymers76,1642
Non-polymers00
Water3,045169
1
A: Lpg2622

A: Lpg2622


Theoretical massNumber of molelcules
Total (without water)76,1642
Polymers76,1642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2080 Å2
ΔGint-11 kcal/mol
Surface area26480 Å2
MethodPISA
2
B: Lpg2622

B: Lpg2622


Theoretical massNumber of molelcules
Total (without water)76,1642
Polymers76,1642
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_553-x+y,y,-z-3/21
Buried area2070 Å2
ΔGint-11 kcal/mol
Surface area25540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)178.628, 178.628, 113.227
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-497-

HOH

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Components

#1: Protein Lpg2622


Mass: 38081.855 Da / Num. of mol.: 2 / Fragment: UNP residues 20-353
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
Strain: Philadelphia 1 / Gene: lpg2622 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5ZS97
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.06 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 0.4M Sodium acetate trihydrate, pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 59115 / % possible obs: 100 % / Redundancy: 16.9 % / Net I/σ(I): 24.8
Reflection shellResolution: 2.1→2.14 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.481 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.154 / ESU R Free: 0.148 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23255 3154 5.1 %RANDOM
Rwork0.19538 ---
obs0.19726 59115 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.646 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20.35 Å20 Å2
2--0.7 Å20 Å2
3----2.26 Å2
Refinement stepCycle: 1 / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5057 0 0 169 5226
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0195161
X-RAY DIFFRACTIONr_bond_other_d0.0050.024833
X-RAY DIFFRACTIONr_angle_refined_deg1.8521.9626987
X-RAY DIFFRACTIONr_angle_other_deg0.875311155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1835644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6825.593236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.02315886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7811514
X-RAY DIFFRACTIONr_chiral_restr0.1120.2765
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021133
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6743.7952591
X-RAY DIFFRACTIONr_mcbond_other3.673.7942590
X-RAY DIFFRACTIONr_mcangle_it5.0285.6673230
X-RAY DIFFRACTIONr_mcangle_other5.0275.6683231
X-RAY DIFFRACTIONr_scbond_it4.6014.2832566
X-RAY DIFFRACTIONr_scbond_other4.64.2842567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7876.2313757
X-RAY DIFFRACTIONr_long_range_B_refined8.58130.6465992
X-RAY DIFFRACTIONr_long_range_B_other8.59130.6475947
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.099→2.153 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 223 -
Rwork0.263 4259 -
obs--98.66 %

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