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- PDB-8uwq: Crystal structure of BT1282 GH18-like from Bacteroides thetaiotao... -

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Basic information

Entry
Database: PDB / ID: 8uwq
TitleCrystal structure of BT1282 GH18-like from Bacteroides thetaiotaomicron VPI-5482
ComponentsBT1282
KeywordsSUGAR BINDING PROTEIN / GH18-like family / Lipoprotein / inactive ENGase / Bacteroides thetaiotaomicron
Function / homologyGlycoside hydrolase family 18, BT1044-like / Glycoside hydrolase family 18, BT1044-like / Prokaryotic membrane lipoprotein lipid attachment site profile. / Lipoprotein
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.36 Å
AuthorsSastre, D.E. / Sultana, N. / Navarro, M.V.A.S. / Sundberg, E.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R01GM148075-01A1 United States
CitationJournal: To Be Published
Title: Crystal structure of BT1282 GH18-like from Bacteroides thetaiotaomicron VPI-5482
Authors: Sastre, D.E. / Sultana, N. / Navarro, M.V.A.S. / Sundberg, E.J.
History
DepositionNov 7, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BT1282
B: BT1282
C: BT1282
D: BT1282


Theoretical massNumber of molelcules
Total (without water)129,6214
Polymers129,6214
Non-polymers00
Water6,630368
1
A: BT1282


Theoretical massNumber of molelcules
Total (without water)32,4051
Polymers32,4051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BT1282


Theoretical massNumber of molelcules
Total (without water)32,4051
Polymers32,4051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: BT1282


Theoretical massNumber of molelcules
Total (without water)32,4051
Polymers32,4051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: BT1282


Theoretical massNumber of molelcules
Total (without water)32,4051
Polymers32,4051
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)188.936, 75.995, 112.160
Angle α, β, γ (deg.)90.00, 121.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
BT1282


Mass: 32405.254 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_1282 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8A892
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350 (Index D6)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→27.3 Å / Num. obs: 54723 / % possible obs: 98.8 % / Redundancy: 6.7 % / CC1/2: 0.992 / CC star: 0.998 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.054 / Rrim(I) all: 0.141 / Χ2: 0.409 / Net I/σ(I): 12.25
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.611 / Mean I/σ(I) obs: 2.18 / Num. unique obs: 2718 / CC1/2: 0.867 / CC star: 0.964 / Rpim(I) all: 0.266 / Rrim(I) all: 0.668 / Χ2: 0.273 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.36→27.13 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 20.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 2003 3.66 %
Rwork0.1735 --
obs0.1748 54693 97.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.36→27.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8520 0 0 368 8888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098706
X-RAY DIFFRACTIONf_angle_d1.02111834
X-RAY DIFFRACTIONf_dihedral_angle_d11.9141198
X-RAY DIFFRACTIONf_chiral_restr0.0571390
X-RAY DIFFRACTIONf_plane_restr0.0071556
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.36-2.420.27421280.20973321X-RAY DIFFRACTION87
2.42-2.490.2521410.20563789X-RAY DIFFRACTION99
2.49-2.560.24631420.21113787X-RAY DIFFRACTION99
2.56-2.640.26091390.20373805X-RAY DIFFRACTION99
2.64-2.740.24351550.19063822X-RAY DIFFRACTION99
2.74-2.850.21491470.18673784X-RAY DIFFRACTION99
2.85-2.980.24241310.1743588X-RAY DIFFRACTION94
2.98-3.130.24141510.18123776X-RAY DIFFRACTION98
3.13-3.330.23811400.18533821X-RAY DIFFRACTION99
3.33-3.580.18531450.16843820X-RAY DIFFRACTION100
3.58-3.940.18861470.15663830X-RAY DIFFRACTION100
3.94-4.510.15221480.14173882X-RAY DIFFRACTION100
4.51-5.680.19371430.16633782X-RAY DIFFRACTION98
5.68-27.130.19791460.17643883X-RAY DIFFRACTION98

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