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- PDB-8uwv: Crystal structure of BT3984 SusD-like from Bacteroides thetaiotao... -

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Basic information

Entry
Database: PDB / ID: 8uwv
TitleCrystal structure of BT3984 SusD-like from Bacteroides thetaiotaomicron VPI-5482 at 1.1 A resolution (Space group P21)
ComponentsBT3984 SusD-like
KeywordsSUGAR BINDING PROTEIN / SusD-like / High-mannose N-glycan PUL / Bacteroides thetaiotaomicron
Function / homologySusD-like / Susd and RagB outer membrane lipoprotein / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / metal ion binding / SusD homolog
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsSastre, D.E. / 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 BT3984 SusD-like from Bacteroides thetaiotaomicron VPI-5482 at 1.1 A resolution (Space group P21)
Authors: Sastre, D.E. / Navarro, M.V.A.S. / Sundberg, E.J.
History
DepositionNov 8, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BT3984 SusD-like
B: BT3984 SusD-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,6443
Polymers113,6202
Non-polymers241
Water28,3201572
1
A: BT3984 SusD-like
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8342
Polymers56,8101
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BT3984 SusD-like


Theoretical massNumber of molelcules
Total (without water)56,8101
Polymers56,8101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.370, 82.592, 100.265
Angle α, β, γ (deg.)90.00, 98.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BT3984 SusD-like


Mass: 56809.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_3984 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8A0N7
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1572 / 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: 2.03 Å3/Da / Density % sol: 39.4 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Magnesium chloride hexahydrate, 0.1 M BIS-TRIS pH 6.5, 25% w/v Polyethylene glycol 3,350 (INDEX G-11)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 0.97718 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97718 Å / Relative weight: 1
ReflectionResolution: 1.08→46.18 Å / Num. obs: 355545 / % possible obs: 91.5 % / Redundancy: 2.5 % / Biso Wilson estimate: 9.03 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.0476 / Net I/σ(I): 19.05
Reflection shellResolution: 1.08→1.119 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.63 / Num. unique obs: 15911 / CC1/2: 0.943 / Rrim(I) all: 0.254 / % possible all: 41.19

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.08→46.18 Å / SU ML: 0.06 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 12.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.139 17777 5 %
Rwork0.1209 --
obs0.1218 355499 91.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.08→46.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7742 0 1 1572 9315
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0168013
X-RAY DIFFRACTIONf_angle_d1.77710936
X-RAY DIFFRACTIONf_dihedral_angle_d7.8831098
X-RAY DIFFRACTIONf_chiral_restr0.1071169
X-RAY DIFFRACTIONf_plane_restr0.0131450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.090.23761120.21652113X-RAY DIFFRACTION17
1.09-1.10.22552700.18545136X-RAY DIFFRACTION42
1.1-1.120.18353770.15477157X-RAY DIFFRACTION58
1.12-1.130.17054430.14048429X-RAY DIFFRACTION69
1.13-1.150.15135040.12779576X-RAY DIFFRACTION78
1.15-1.160.15245680.122110802X-RAY DIFFRACTION88
1.16-1.180.14136300.121111975X-RAY DIFFRACTION97
1.18-1.20.13296320.115711997X-RAY DIFFRACTION98
1.2-1.210.14016390.11512141X-RAY DIFFRACTION99
1.21-1.230.13366450.116612263X-RAY DIFFRACTION100
1.23-1.260.14266460.112212270X-RAY DIFFRACTION100
1.26-1.280.14336470.116312300X-RAY DIFFRACTION100
1.28-1.30.13636470.115612284X-RAY DIFFRACTION100
1.3-1.330.146450.112712261X-RAY DIFFRACTION100
1.33-1.360.13576460.111912265X-RAY DIFFRACTION100
1.36-1.390.14256460.112612280X-RAY DIFFRACTION100
1.39-1.430.13556470.11112296X-RAY DIFFRACTION100
1.43-1.460.13876450.110212251X-RAY DIFFRACTION100
1.46-1.510.13246480.10912306X-RAY DIFFRACTION100
1.51-1.560.12556490.108612343X-RAY DIFFRACTION100
1.56-1.610.13616480.108912305X-RAY DIFFRACTION100
1.61-1.680.12686460.110512270X-RAY DIFFRACTION100
1.68-1.750.13466470.111412304X-RAY DIFFRACTION100
1.75-1.840.13196450.113112259X-RAY DIFFRACTION100
1.84-1.960.12456490.115912328X-RAY DIFFRACTION100
1.96-2.110.12866480.115212300X-RAY DIFFRACTION100
2.11-2.320.12516490.1112342X-RAY DIFFRACTION100
2.32-2.660.13446490.120412332X-RAY DIFFRACTION100
2.66-3.350.14626500.128912355X-RAY DIFFRACTION100
3.35-46.180.15416600.143112528X-RAY DIFFRACTION100

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