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- PDB-8bou: Crystal structure of Blautia producta GH94 -

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Basic information

Entry
Database: PDB / ID: 8bou
TitleCrystal structure of Blautia producta GH94
ComponentsN,N'-diacetylchitobiose phosphorylase
KeywordsHYDROLASE / Glycoside Hydrolase Family 94
Function / homology
Function and homology information


macromolecule modification / : / glycosyltransferase activity / methyltransferase activity / methylation / carbohydrate binding / nucleic acid binding / carbohydrate metabolic process
Similarity search - Function
N,N'-diacetylchitobiose phosphorylase, N-terminal / Putative carbohydrate binding domain / Putative carbohydrate binding domain / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site ...N,N'-diacetylchitobiose phosphorylase, N-terminal / Putative carbohydrate binding domain / Putative carbohydrate binding domain / Glycosyl hydrolase 94 / Glycosyltransferase family 36 / Glycosyl hydrolase 36, catalytic domain / Glycosyl hydrolase 36 superfamily, catalytic domain / Glycoside hydrolase family 65, N-terminal domain superfamily / N-6 Adenine-specific DNA methylases signature. / DNA methylase, N-6 adenine-specific, conserved site / Galactose mutarotase-like domain superfamily / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily
Similarity search - Domain/homology
ACETATE ION / N,N'-diacetylchitobiose phosphorylase
Similarity search - Component
Biological speciesBlautia producta ATCC 27340 = DSM 2950 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsLevy, C.W.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/PR32876/PFN/20/1471/2020 India
CitationJournal: To Be Published
Title: Blautia producta is a competent degrader among human gut Firmicutes for utilizing dietary beta mixed linkage glucan
Authors: Singh, R.P. / Thankur, R. / Wagstaff, B. / Kumar, G. / Kurata, R. / Patel, D. / Miyazaki, T. / Levy, C.W. / Field, R.A.
History
DepositionNov 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: N,N'-diacetylchitobiose phosphorylase
B: N,N'-diacetylchitobiose phosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,75714
Polymers187,7172
Non-polymers1,04012
Water12,701705
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, PISA analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8500 Å2
ΔGint-64 kcal/mol
Surface area53330 Å2
Unit cell
Length a, b, c (Å)98.460, 135.290, 166.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein N,N'-diacetylchitobiose phosphorylase /


Mass: 93858.453 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Blautia producta ATCC 27340 = DSM 2950 (bacteria)
Gene: E5259_00910 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7G5MNS2

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Non-polymers , 7 types, 717 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.1 M carboxylic acids, 0.1 M Imidazole MES buffer pH 6.5, 60% precipitant mix 3 (40% v/v Glycerol, 20% w/v PEG 4000) [Morpheus G3, Molecular Dimensions]
Temp details: Cold room

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.32→52.56 Å / Num. obs: 97018 / % possible obs: 99.95 % / Redundancy: 11.7 % / Biso Wilson estimate: 55.83 Å2 / CC1/2: 0.998 / CC star: 0.999 / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.046 / Net I/σ(I): 10.92
Reflection shellResolution: 2.32→2.403 Å / Redundancy: 12.7 % / Rmerge(I) obs: 1.699 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 9562 / CC1/2: 0.602 / CC star: 0.867 / Rpim(I) all: 0.4926 / % possible all: 99.92

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
DIALSdata reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CQT

2cqt


Resolution: 2.32→52.56 Å / SU ML: 0.3329 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0047
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2224 4886 5.04 %
Rwork0.1776 92104 -
obs0.1798 96990 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.41 Å2
Refinement stepCycle: LAST / Resolution: 2.32→52.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12952 0 62 705 13719
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002413429
X-RAY DIFFRACTIONf_angle_d0.547618196
X-RAY DIFFRACTIONf_chiral_restr0.04291844
X-RAY DIFFRACTIONf_plane_restr0.00412395
X-RAY DIFFRACTIONf_dihedral_angle_d5.10081819
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.350.37411540.32153030X-RAY DIFFRACTION99.87
2.35-2.370.34821700.30683006X-RAY DIFFRACTION99.91
2.37-2.40.33081640.29883031X-RAY DIFFRACTION99.97
2.4-2.430.33041640.28213023X-RAY DIFFRACTION100
2.43-2.470.32421700.28823070X-RAY DIFFRACTION100
2.47-2.50.30941580.27293003X-RAY DIFFRACTION100
2.5-2.530.31361540.27453086X-RAY DIFFRACTION100
2.53-2.570.35891600.28423012X-RAY DIFFRACTION99.97
2.57-2.610.34231670.2773032X-RAY DIFFRACTION99.97
2.61-2.660.31411710.25333067X-RAY DIFFRACTION100
2.66-2.70.31041710.2433003X-RAY DIFFRACTION100
2.7-2.750.2821630.22493075X-RAY DIFFRACTION100
2.75-2.80.27081680.21293018X-RAY DIFFRACTION100
2.8-2.860.25711500.20543045X-RAY DIFFRACTION100
2.86-2.920.25891500.20753069X-RAY DIFFRACTION100
2.92-2.990.27721570.2023082X-RAY DIFFRACTION100
2.99-3.070.25721750.20663042X-RAY DIFFRACTION100
3.07-3.150.26851570.21223059X-RAY DIFFRACTION99.97
3.15-3.240.24621610.20363047X-RAY DIFFRACTION100
3.24-3.350.24621590.18673075X-RAY DIFFRACTION99.94
3.35-3.470.22631730.18013067X-RAY DIFFRACTION99.97
3.47-3.60.24521820.1713027X-RAY DIFFRACTION100
3.6-3.770.24281570.17533103X-RAY DIFFRACTION100
3.77-3.970.2061560.16083093X-RAY DIFFRACTION100
3.97-4.220.1991640.13823100X-RAY DIFFRACTION100
4.22-4.540.14981750.12453075X-RAY DIFFRACTION100
4.54-50.15151560.12413134X-RAY DIFFRACTION99.97
5-5.720.1861590.14253147X-RAY DIFFRACTION100
5.72-7.20.19931640.16453173X-RAY DIFFRACTION100
7.2-52.560.16921570.15953310X-RAY DIFFRACTION99.54
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)
10.952171640460.2301466108780.05598362994051.283728098150.189771645140.602947209138-0.08846417666710.03291602761650.0587955692549-0.03900211930720.0856700327032-0.0210354777855-0.1608686354760.06544750419366.42812950265E-50.632268956976-0.0159250152216-0.03509540126470.573976840334-0.003338659830810.55012719086196.873082127189.6881869617110.43392482
21.12055073144-0.0248892454799-0.1430402977521.43182844561-0.3212586267120.78548254588-0.06994628575430.08011768925640.2463816778480.02690011014080.110495482620.461830355568-0.266455868545-0.2477196601467.0068157119E-50.7201294736540.164574585572-0.03304573107320.716653418480.03033589018430.8706374225259.9381051851101.202815578113.730787656
30.448498905055-0.1492819565520.09738815538031.405677620730.09980192374930.975842839059-0.0375722525651-0.0820343193139-0.04369619234680.2229595241030.05150087762360.0755213118639-0.0452683061519-0.0623126657464-3.56376985361E-50.5629039378470.02294469862230.005219056483540.5744860998790.007287808328370.53290442437183.522959695958.2056251983123.48162895
40.769412081450.06360836503040.0279330969350.9945480427720.1943872328410.664541395915-0.06054686724530.151471156525-0.0686955966466-0.1757652781210.0403690725961-0.0105681427371-0.03512025116820.02659114742423.33059439288E-60.540609361789-0.02830972352440.0182155356110.605844655964-0.07353410412620.51987411999287.536850235346.427753950786.6201210356
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 18 through 340 )AA18 - 3401 - 323
22chain 'A' and (resid 341 through 824 )AA341 - 824324 - 807
33chain 'B' and (resid 20 through 340 )BF20 - 3401 - 321
44chain 'B' and (resid 341 through 824 )BF341 - 824322 - 805

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