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- PDB-6dk2: Bacteroidetes AC2a SusD-like -

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Basic information

Entry
Database: PDB / ID: 6dk2
TitleBacteroidetes AC2a SusD-like
ComponentsSusDLunca, Bihor
KeywordsSUGAR BINDING PROTEIN / SusD-like / cellulose / rumen / Bacteroidetes
Function / homologySusD-like 2 / Starch-binding associating with outer membrane / Tetratricopeptide-like helical domain superfamily / SusD
Function and homology information
Biological speciesBacteroidetes bacterium AC2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.02 Å
AuthorsKoropatkin, N.M.
CitationJournal: To Be Published
Title: To Be Published
Authors: Koropatkin, N.M. / Bahr, C.M.E. / Pope, P.B. / Naas, A.E.
History
DepositionMay 28, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SusD
B: SusD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,46846
Polymers119,3152
Non-polymers3,15444
Water17,727984
1
A: SusD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,64129
Polymers59,6571
Non-polymers1,98328
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SusD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,82817
Polymers59,6571
Non-polymers1,17016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)101.703, 140.269, 186.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SusD / Lunca, Bihor


Mass: 59657.348 Da / Num. of mol.: 2 / Fragment: UNP residues 33-560
Source method: isolated from a genetically manipulated source
Details: metagenomic data set
Source: (gene. exp.) Bacteroidetes bacterium AC2a (bacteria)
Plasmid: PETite Nhis / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: A0A076ML24
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 984 / Source method: isolated from a natural source / Formula: H2O

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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

Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 1.5 M ammonium sulphate, 50 mM Tris-HCl pH 7.5 / Temp details: cold room

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 15, 2015
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.02→56.93 Å / Num. obs: 172008 / % possible obs: 99.71 % / Redundancy: 6.2 % / Biso Wilson estimate: 35.74 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.093 / Net I/σ(I): 11.13
Reflection shellResolution: 2.02→2.094 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.521 / Mean I/σ(I) obs: 2.27 / Num. unique obs: 17235 / CC1/2: 0.914 / % possible all: 99.99

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.47 Å93.35 Å
Translation2.47 Å93.35 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
xia2data scaling
PHASER2.5.6phasing
PDB_EXTRACT3.24data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5J5U

5j5u


Resolution: 2.02→56.93 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.964 / SU B: 5.489 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.108 / ESU R Free: 0.087
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1761 8392 4.9 %RANDOM
Rwork0.1516 ---
obs0.1528 163616 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 130.54 Å2 / Biso mean: 43.579 Å2 / Biso min: 23.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.98 Å20 Å20 Å2
2---0.45 Å20 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 2.02→56.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8220 0 184 984 9388
Biso mean--77.9 50.91 -
Num. residues----1031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0148617
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177328
X-RAY DIFFRACTIONr_angle_refined_deg0.9211.6711696
X-RAY DIFFRACTIONr_angle_other_deg0.8341.66117129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85151035
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.05822.597489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.013151284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3591552
X-RAY DIFFRACTIONr_chiral_restr0.0470.21100
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029768
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021716
X-RAY DIFFRACTIONr_rigid_bond_restr0.704315945
X-RAY DIFFRACTIONr_sphericity_free31.5145505
X-RAY DIFFRACTIONr_sphericity_bonded16.714516238
LS refinement shellResolution: 2.022→2.074 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 630 -
Rwork0.22 12114 -
all-12744 -
obs--99.88 %
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)
11.8762-0.33250.45350.7834-0.30890.91240.0332-0.23280.06470.1594-0.02640.0173-0.0420.0147-0.00680.0450.00150.01690.10420.01740.01647.5957-39.596821.2162
20.86930.0570.08021.17410.51811.7572-0.0877-0.001-0.150.1044-0.070.0240.1070.02710.15780.0701-0.05920.07490.187-0.12890.1563-27.1678-16.743143.3293
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 560
2X-RAY DIFFRACTION2B36 - 560

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