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- PDB-5t8b: Crystal structure of lpg1496 under 350 MPa -

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Basic information

Entry
Database: PDB / ID: 5t8b
TitleCrystal structure of lpg1496 under 350 MPa
Componentslpg1496
KeywordsUNKNOWN FUNCTION / lpg1496 / high-pressure cryocooling
Function / homology:
Function and homology information
Biological speciesLegionella pneumophila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 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 350 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 1.1Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 23, 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

Downloads & links

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Assembly

Deposited unit
A: lpg1496


Theoretical massNumber of molelcules
Total (without water)34,2991
Polymers34,2991
Non-polymers00
Water7,710428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.618, 75.618, 99.991
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-893-

HOH

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Components

#1: Protein lpg1496


Mass: 34299.465 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.: 428 / 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: 2.12 Å3/Da / Density % sol: 41.89 %
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 / Temp details: ROOM TEMPERATURE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 47082 / % possible obs: 99.8 % / Redundancy: 24 % / Net I/σ(I): 40.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 14 % / Rmerge(I) obs: 0.966 / Mean I/σ(I) obs: 2 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→41.704 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.62
RfactorNum. reflection% reflection
Rfree0.1962 3769 4.25 %
Rwork0.1702 --
obs0.1713 88625 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→41.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 0 428 2746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062392
X-RAY DIFFRACTIONf_angle_d0.8293241
X-RAY DIFFRACTIONf_dihedral_angle_d111428
X-RAY DIFFRACTIONf_chiral_restr0.047340
X-RAY DIFFRACTIONf_plane_restr0.005419
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5190.2941310.26343059X-RAY DIFFRACTION97
1.519-1.5390.3031380.24943135X-RAY DIFFRACTION98
1.539-1.56010.24461390.22253157X-RAY DIFFRACTION100
1.5601-1.58240.23071400.21163122X-RAY DIFFRACTION100
1.5824-1.6060.21091390.20623169X-RAY DIFFRACTION100
1.606-1.63110.23171410.20663144X-RAY DIFFRACTION100
1.6311-1.65780.22081390.19493135X-RAY DIFFRACTION100
1.6578-1.68640.23371410.18843114X-RAY DIFFRACTION100
1.6864-1.71710.19651420.19953187X-RAY DIFFRACTION100
1.7171-1.75010.21941360.19593117X-RAY DIFFRACTION100
1.7501-1.78580.20461390.18233186X-RAY DIFFRACTION100
1.7858-1.82470.23791420.18853125X-RAY DIFFRACTION100
1.8247-1.86710.25571380.19043140X-RAY DIFFRACTION100
1.8671-1.91380.20081410.17823140X-RAY DIFFRACTION100
1.9138-1.96550.20521420.1783163X-RAY DIFFRACTION100
1.9655-2.02340.20511380.17283145X-RAY DIFFRACTION100
2.0234-2.08870.20791410.17353170X-RAY DIFFRACTION100
2.0887-2.16330.18471410.16433143X-RAY DIFFRACTION100
2.1633-2.24990.17981330.16823136X-RAY DIFFRACTION100
2.2499-2.35230.18951400.16753141X-RAY DIFFRACTION100
2.3523-2.47630.19091430.16883119X-RAY DIFFRACTION100
2.4763-2.63150.21571410.17733157X-RAY DIFFRACTION100
2.6315-2.83460.20451410.17543137X-RAY DIFFRACTION100
2.8346-3.11980.18071440.17483162X-RAY DIFFRACTION100
3.1198-3.5710.1951390.15593157X-RAY DIFFRACTION100
3.571-4.49820.16111350.12983130X-RAY DIFFRACTION100
4.4982-41.72060.17131450.15843166X-RAY DIFFRACTION100

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