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- PDB-5t8c: Crystal structure of lpg1496 under 300 MPa -

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Basic information

Entry
Database: PDB / ID: 5t8c
TitleCrystal structure of lpg1496 under 300 MPa
Componentslpg1496
KeywordsUNKNOWN FUNCTION / lpg1496 / high-pressure cryocooling
Function / homology:
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.481 Å
AuthorsHuang, Q. / Szebenyi, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
Citation
Journal: To Be Published
Title: Crystal structure of lpg1496 under 300 MPa
Authors: Huang, Q. / Szebenyi, D.
#1: Journal: J Appl Crystallogr / Year: 2016
Title: Reduction of lattice disorder in protein crystals by high-pressure cryocooling.
Authors: Huang, Q. / Gruner, S.M. / Kim, C.U. / Mao, Y. / Wu, X. / Szebenyi, D.M.
History
DepositionSep 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: lpg1496


Theoretical massNumber of molelcules
Total (without water)33,9241
Polymers33,9241
Non-polymers00
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.016, 75.016, 99.191
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11A-830-

HOH

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Components

#1: Protein lpg1496


Mass: 33924.309 Da / Num. of mol.: 1 / Fragment: UNP residues 298-598
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila (bacteria) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G8UY02
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.4 / Details: 12% PEG6000, 0.2M MgCl2, 0.1M Tris-HCl, pH8.4 / PH range: 8.0-8.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.6326 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: May 29, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6326 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 47739 / % possible obs: 99.9 % / Redundancy: 13.7 % / Net I/σ(I): 48.7
Reflection shellResolution: 1.48→1.51 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 4.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5T8B

5t8b


Resolution: 1.481→33.548 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.09
RfactorNum. reflection% reflection
Rfree0.1896 1999 4.19 %
Rwork0.1588 --
obs0.1601 47655 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.481→33.548 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 0 350 2664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062416
X-RAY DIFFRACTIONf_angle_d0.843285
X-RAY DIFFRACTIONf_dihedral_angle_d14.12894
X-RAY DIFFRACTIONf_chiral_restr0.072347
X-RAY DIFFRACTIONf_plane_restr0.005425
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4813-1.51830.22641400.15283210X-RAY DIFFRACTION100
1.5183-1.55940.19251410.14353215X-RAY DIFFRACTION100
1.5594-1.60520.20671400.14463198X-RAY DIFFRACTION100
1.6052-1.6570.19091420.14743234X-RAY DIFFRACTION100
1.657-1.71630.19161400.15723204X-RAY DIFFRACTION100
1.7163-1.7850.24191420.16533242X-RAY DIFFRACTION100
1.785-1.86620.19631410.16123203X-RAY DIFFRACTION100
1.8662-1.96460.21241420.15743257X-RAY DIFFRACTION100
1.9646-2.08770.21191410.15333239X-RAY DIFFRACTION100
2.0877-2.24880.18051430.1563256X-RAY DIFFRACTION100
2.2488-2.47510.18511440.16353283X-RAY DIFFRACTION100
2.4751-2.83310.1931450.1693296X-RAY DIFFRACTION100
2.8331-3.56870.19981460.16133349X-RAY DIFFRACTION100
3.5687-33.55680.15971520.15743470X-RAY DIFFRACTION99

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