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- PDB-5fq3: Crystal structure of the lipoprotein BT2262 from Bacteroides thet... -

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Basic information

Entry
Database: PDB / ID: 5fq3
TitleCrystal structure of the lipoprotein BT2262 from Bacteroides thetaiotaomicron
ComponentsBT_2262
KeywordsMEMBRANE PROTEIN / OUTER MEMBRANE LIPOPROTEIN
Function / homologyDomain of unknown function DUF5012 / BT_2262-like, C-terminal domain / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like fold / DUF5012 domain-containing protein
Function and homology information
Biological speciesBACTEROIDES THETAIOTAOMICRON (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGlenwright, A.J. / Pothula, K.R. / Chorev, D.S. / Basle, A. / Robinson, C.V. / Kleinekathoefer, U. / Bolam, D.N. / van den Berg, B.
CitationJournal: Nature / Year: 2017
Title: Structural basis for nutrient acquisition by dominant members of the human gut microbiota.
Authors: Glenwright, A.J. / Pothula, K.R. / Bhamidimarri, S.P. / Chorev, D.S. / Basle, A. / Firbank, S.J. / Zheng, H. / Robinson, C.V. / Winterhalter, M. / Kleinekathofer, U. / Bolam, D.N. / van den Berg, B.
History
DepositionDec 4, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2017Group: Database references
Revision 1.2Jan 25, 2017Group: Database references
Revision 1.3Feb 1, 2017Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BT_2262
B: BT_2262
C: BT_2262
D: BT_2262


Theoretical massNumber of molelcules
Total (without water)94,0604
Polymers94,0604
Non-polymers00
Water00
1
A: BT_2262


Theoretical massNumber of molelcules
Total (without water)23,5151
Polymers23,5151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: BT_2262


Theoretical massNumber of molelcules
Total (without water)23,5151
Polymers23,5151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: BT_2262


Theoretical massNumber of molelcules
Total (without water)23,5151
Polymers23,5151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
D: BT_2262


Theoretical massNumber of molelcules
Total (without water)23,5151
Polymers23,5151
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)167.320, 167.320, 100.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
BT_2262


Mass: 23515.039 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 20-230
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL CYSTEINE RESIDUE REMOVED
Source: (gene. exp.) BACTEROIDES THETAIOTAOMICRON (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8A5H7

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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: 3.8 Å3/Da / Density % sol: 67 % / Description: NONE
Crystal growDetails: 2 M AMMONIUM SULPHATE 0.1 M SODIUM HEPES PH 7.5 2% W/W PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.1→48.75 Å / Num. obs: 26439 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 14.7 % / Biso Wilson estimate: 85.57 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 15.3
Reflection shellResolution: 3.1→3.31 Å / Redundancy: 14.8 % / Rmerge(I) obs: 1.5 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N-TERMINAL DOMAIN FROM COMPLEX STRUCTURE

Resolution: 3.1→48.749 Å / SU ML: 0.43 / σ(F): 1.34 / Phase error: 27.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2602 1999 7.6 %
Rwork0.1994 --
obs0.204 26387 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 86.2 Å2
Refinement stepCycle: LAST / Resolution: 3.1→48.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6180 0 0 0 6180
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.016332
X-RAY DIFFRACTIONf_angle_d1.3728624
X-RAY DIFFRACTIONf_dihedral_angle_d11.9143664
X-RAY DIFFRACTIONf_chiral_restr0.076940
X-RAY DIFFRACTIONf_plane_restr0.0081120
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.17750.35651470.30281684X-RAY DIFFRACTION100
3.1775-3.26340.40361400.28421712X-RAY DIFFRACTION100
3.2634-3.35940.31921420.27221717X-RAY DIFFRACTION100
3.3594-3.46780.351380.26651710X-RAY DIFFRACTION100
3.4678-3.59180.31941550.2351697X-RAY DIFFRACTION100
3.5918-3.73550.3231370.24321723X-RAY DIFFRACTION100
3.7355-3.90550.29361620.2231715X-RAY DIFFRACTION100
3.9055-4.11130.27441330.19011716X-RAY DIFFRACTION100
4.1113-4.36870.21141370.16481757X-RAY DIFFRACTION100
4.3687-4.70570.20741490.14641719X-RAY DIFFRACTION100
4.7057-5.17880.20631240.14971778X-RAY DIFFRACTION100
5.1788-5.92710.23721480.1791766X-RAY DIFFRACTION100
5.9271-7.46320.26671350.21461797X-RAY DIFFRACTION100
7.4632-48.75480.22261520.19521897X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.16721.24071.21422.34380.67152.27250.1482-0.26830.34970.2126-0.29410.36-0.1423-0.1980.13690.6165-0.11610.29420.4256-0.13240.7531170.6772138.9552110.5978
23.9312-1.6250.19664.12161.45042.95120.11150.1572-0.0940.39630.2259-0.21630.2280.2801-0.31520.5621-0.03820.04760.3411-0.05480.4642191.0436118.263496.2124
34.01722.05720.18182.5183-0.28461.69120.04650.4840.4167-0.26920.21380.20290.1056-0.0497-0.27970.49090.06010.06440.52290.11020.4639147.1314120.761981.4183
42.9102-0.3099-0.42911.73320.69051.57380.3650.9341.0815-0.3401-0.08760.3232-0.5093-0.4445-0.25350.74020.09650.25030.90150.38570.9305169.5938139.638867.4801
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN 'A' AND RESID 14 THROUGH 212)
2X-RAY DIFFRACTION2(CHAIN 'B' AND RESID 14 THROUGH 212)
3X-RAY DIFFRACTION3(CHAIN 'C' AND RESID 14 THROUGH 212)
4X-RAY DIFFRACTION4(CHAIN 'D' AND RESID 14 THROUGH 212)

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