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- PDB-6a0q: The crystal structure of Lpg2622_E64 complex -

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Basic information

Entry
Database: PDB / ID: 6a0q
TitleThe crystal structure of Lpg2622_E64 complex
ComponentsLpg2622
KeywordsHYDROLASE / Cysteine protease
Function / homologyPapain-like cysteine peptidase superfamily / Chem-E64 / Uncharacterized protein
Function and homology information
Biological speciesLegionella pneumophila subsp. pneumophila str. Philadelphia 1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 6, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lpg2622
B: Lpg2622
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,5243
Polymers76,1642
Non-polymers3601
Water2,216123
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 area2060 Å2
ΔGint-13 kcal/mol
Surface area26730 Å2
MethodPISA
2
B: Lpg2622
hetero molecules

B: Lpg2622
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,8854
Polymers76,1642
Non-polymers7212
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+3/21
Buried area3480 Å2
ΔGint-9 kcal/mol
Surface area25480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.938, 179.938, 113.041
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-470-

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: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N5O5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.47 Å3/Da / Density % sol: 64.53 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: 0.4 M 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: Dec 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 54772 / % possible obs: 100 % / Redundancy: 21.7 % / Net I/σ(I): 27.2
Reflection shellResolution: 2.2→2.24 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24086 2777 5.1 %RANDOM
Rwork0.20457 ---
obs0.20639 51971 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.083 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.23 Å20 Å2
2--0.46 Å20 Å2
3----1.51 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4997 0 25 123 5145
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195121
X-RAY DIFFRACTIONr_bond_other_d00.024808
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9676923
X-RAY DIFFRACTIONr_angle_other_deg3.753311091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5275632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.32725.574235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.92815880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0111514
X-RAY DIFFRACTIONr_chiral_restr0.1490.2758
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025817
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021132
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_it4.0553.9572549
X-RAY DIFFRACTIONr_mcbond_other4.0553.9562548
X-RAY DIFFRACTIONr_mcangle_it5.8345.8953174
X-RAY DIFFRACTIONr_mcangle_other5.8345.8973175
X-RAY DIFFRACTIONr_scbond_it5.0384.5782571
X-RAY DIFFRACTIONr_scbond_other5.0374.5792572
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.7426.6173749
X-RAY DIFFRACTIONr_long_range_B_refined10.833.0465980
X-RAY DIFFRACTIONr_long_range_B_other10.81433.0725950
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 208 -
Rwork0.295 3737 -
obs--98.35 %

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