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- PDB-8cwp: X-ray crystal structure of NTHi Protein D bound to a putative gly... -

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Basic information

Entry
Database: PDB / ID: 8cwp
TitleX-ray crystal structure of NTHi Protein D bound to a putative glycerol moiety
ComponentsGlycerophosphoryl diester phosphodiesteraseGlycerophosphodiester phosphodiesterase
KeywordsHYDROLASE / NTHi / otitis media / outer membrane protein / phosphodiesterase / lipo-glycerophosphodiesterase / sn-glycero-3-phosphocholine / choline / sn-glycerol 3-phosphate
Function / homologyGlycerophosphodiester phosphodiesterase domain / Glycerophosphoryl diester phosphodiesterase family / GP-PDE domain profile. / PLC-like phosphodiesterase, TIM beta/alpha-barrel domain superfamily / phosphoric diester hydrolase activity / lipid metabolic process / Glycerophosphoryl diester phosphodiesterase
Function and homology information
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsJones, S.P. / Cook, K.H. / Holmquist, M.L. / Almekinder, L. / DeLaney, A. / Labbe, N. / Perdue, J. / Jackson, N. / Charles, R. / Pichichero, M. ...Jones, S.P. / Cook, K.H. / Holmquist, M.L. / Almekinder, L. / DeLaney, A. / Labbe, N. / Perdue, J. / Jackson, N. / Charles, R. / Pichichero, M. / Kaur, R. / Michel, L. / Gleghorn, M.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Deafness and Other Communication Disorders (NIH/NIDCD)R21 AI153936-01 United States
CitationJournal: Proteins / Year: 2023
Title: Vaccine target and carrier molecule nontypeable Haemophilus influenzae protein D dimerizes like the close Escherichia coli GlpQ homolog but unlike other known homolog dimers.
Authors: Jones, S.P. / Cook, K.H. / Holmquist, M.L. / Almekinder, L.J. / Delaney, A.M. / Charles, R. / Labbe, N. / Perdue, J. / Jackson, N. / Pichichero, M.E. / Kaur, R. / Michel, L.V. / Gleghorn, M.L.
History
DepositionMay 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 11, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3943
Polymers41,2791
Non-polymers1152
Water8,233457
1
A: Glycerophosphoryl diester phosphodiesterase
hetero molecules

A: Glycerophosphoryl diester phosphodiesterase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,7886
Polymers82,5582
Non-polymers2304
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area3180 Å2
ΔGint-43 kcal/mol
Surface area26860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.090, 73.090, 162.859
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-622-

HOH

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Components

#1: Protein Glycerophosphoryl diester phosphodiesterase / Glycerophosphodiester phosphodiesterase


Mass: 41278.863 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: glpQ, CHBNIII1_03270 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A8D4QYM6
#2: Chemical ChemComp-NA / SODIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 457 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.73 Å3/Da / Density % sol: 55 %
Description: The crystals were approximately 3 millimeters x 120 micrometers (Visually appeared thinner in the third dimension).
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 20% w/v PEG3000, 0.1 M Sodium Citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Ambient temp details: Cryostream (Exact temperature unknown)
Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97927 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97927 Å / Relative weight: 1
ReflectionResolution: 1.8→28 Å / Num. obs: 41845 / % possible obs: 99.7 % / Redundancy: 14.5 % / Biso Wilson estimate: 37.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 13.6 % / Rmerge(I) obs: 2.6 / Mean I/σ(I) obs: 0.98 / Num. unique obs: 2934 / CC1/2: 0.394 / % possible all: 96

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
pointlessdata scaling
Aimlessdata scaling
PHENIX1.19.2_4158phasing
PHENIX1.19.2_4158model building
Coot0.9.6model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YDY

1ydy


Resolution: 1.8→28 Å / SU ML: 0.2342 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.878
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1875 2000 4.79 %
Rwork0.1545 39750 -
obs0.1561 41750 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.24 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2696 0 7 457 3160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01132781
X-RAY DIFFRACTIONf_angle_d1.05933758
X-RAY DIFFRACTIONf_chiral_restr0.0614393
X-RAY DIFFRACTIONf_plane_restr0.0091478
X-RAY DIFFRACTIONf_dihedral_angle_d13.47841032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.840.39691360.33862678X-RAY DIFFRACTION95.49
1.84-1.890.35221400.29862786X-RAY DIFFRACTION100
1.89-1.950.30591410.24282800X-RAY DIFFRACTION100
1.95-2.010.21461390.20472793X-RAY DIFFRACTION100
2.01-2.080.22331420.17512813X-RAY DIFFRACTION100
2.08-2.170.20981410.16742804X-RAY DIFFRACTION100
2.17-2.270.21261410.15872817X-RAY DIFFRACTION100
2.27-2.390.19361420.15072810X-RAY DIFFRACTION100
2.39-2.530.21861430.14242844X-RAY DIFFRACTION100
2.53-2.730.17341430.14892837X-RAY DIFFRACTION100
2.73-30.19281440.15332861X-RAY DIFFRACTION100
3.01-3.440.16451460.14162889X-RAY DIFFRACTION100
3.44-4.330.13331470.12492926X-RAY DIFFRACTION100
4.33-280.20211550.15913092X-RAY DIFFRACTION99.94
Refinement TLS params.Method: refined / Origin x: -0.855320487543 Å / Origin y: -10.7265812324 Å / Origin z: -22.8939257229 Å
111213212223313233
T0.245451909361 Å20.048955559186 Å20.0101852216707 Å2-0.272508633625 Å20.0324100421408 Å2--0.241732643669 Å2
L1.51846979541 °20.351530544597 °2-0.899821423267 °2-1.34557621274 °2-0.558833796386 °2--2.3954818541 °2
S-0.030296464887 Å °-0.333583344843 Å °-0.129603534708 Å °0.0849960441068 Å °-0.0695391881414 Å °-0.0325511649031 Å °0.291998608754 Å °0.356588074216 Å °0.0407975114415 Å °
Refinement TLS groupSelection details: all

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