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- PDB-7rsk: The crystal structure from microfluidic crystals of glycosyl hydr... -

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Basic information

Entry
Database: PDB / ID: 7rsk
TitleThe crystal structure from microfluidic crystals of glycosyl hydrolase family 2 (GH2) member from Bacteroides cellulosilyticus
ComponentsGlycosyl hydrolase family 2, sugar binding domain protein
KeywordsHYDROLASE / mycrofluidic / droplet crystals / Structural Genomics / Midwest Center for Structural Genomics / PSI-Biology / MCSG
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain ...Glycoside hydrolase family 2, domain 5 / Glycoside hydrolase family 2 C-terminal domain 5 / Domain of unknown function DUF4982 / Domain of unknown function (DUF4982) / : / Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2 / Glycosyl hydrolases family 2, sugar binding domain / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2 / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Glycosyl hydrolase family 2, sugar binding domain protein
Similarity search - Component
Biological speciesBacteroides cellulosilyticus DSM 14838 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsKim, Y. / Nocek, B. / Endres, M. / Joachimiak, G. / Johnson, J. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: The crystal structure from microfluidic crystals of glycosyl hydrolase family 2 (GH2) member from Bacteroides cellulosilyticus
Authors: Kim, Y. / Nocek, B. / Endres, M. / Joachimiak, G. / Johnson, J. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionAug 11, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycosyl hydrolase family 2, sugar binding domain protein
B: Glycosyl hydrolase family 2, sugar binding domain protein


Theoretical massNumber of molelcules
Total (without water)176,0332
Polymers176,0332
Non-polymers00
Water3,675204
1
A: Glycosyl hydrolase family 2, sugar binding domain protein


Theoretical massNumber of molelcules
Total (without water)88,0161
Polymers88,0161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Glycosyl hydrolase family 2, sugar binding domain protein


Theoretical massNumber of molelcules
Total (without water)88,0161
Polymers88,0161
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.228, 231.147, 67.558
Angle α, β, γ (deg.)90.000, 109.018, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Glycosyl hydrolase family 2, sugar binding domain protein


Mass: 88016.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides cellulosilyticus DSM 14838 (bacteria)
Gene: BACCELL_00063 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: E2N721
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
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: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 289 K / Method: microfluidic / pH: 8 / Details: 0.2 M potassium chloride and 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 57327 / % possible obs: 87.3 % / Redundancy: 3.9 % / Biso Wilson estimate: 35.76 Å2 / Rmerge(I) obs: 0.165 / Net I/σ(I): 8.9
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3 % / Rmerge(I) obs: 0.858 / Mean I/σ(I) obs: 1.75 / Num. unique obs: 2796 / CC1/2: 0.447 / % possible all: 84.5

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 6B6L

6b6l


Resolution: 2.4→39.86 Å / SU ML: 0.244 / Cross valid method: FREE R-VALUE / σ(F): 1.43 / Phase error: 22.6485
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2204 2685 4.94 %
Rwork0.1831 51664 -
obs0.1849 54349 82.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.73 Å2
Refinement stepCycle: LAST / Resolution: 2.4→39.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12302 0 0 204 12506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001612604
X-RAY DIFFRACTIONf_angle_d0.482417134
X-RAY DIFFRACTIONf_chiral_restr0.04371860
X-RAY DIFFRACTIONf_plane_restr0.0032218
X-RAY DIFFRACTIONf_dihedral_angle_d14.37874522
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.440.35221110.27571856X-RAY DIFFRACTION56.83
2.44-2.490.30911190.27512047X-RAY DIFFRACTION63.35
2.49-2.540.31681110.26612332X-RAY DIFFRACTION69.96
2.54-2.60.31951240.25982466X-RAY DIFFRACTION75.64
2.6-2.660.30321540.25292599X-RAY DIFFRACTION80.05
2.66-2.720.2961380.24932681X-RAY DIFFRACTION81.71
2.72-2.80.26481400.24782804X-RAY DIFFRACTION85.16
2.8-2.880.26441510.24282802X-RAY DIFFRACTION86.5
2.88-2.970.28991640.22952777X-RAY DIFFRACTION85.59
2.97-3.080.2771580.21672838X-RAY DIFFRACTION85.53
3.08-3.20.2351450.21932843X-RAY DIFFRACTION86.58
3.2-3.350.25771540.20322805X-RAY DIFFRACTION86.29
3.35-3.520.20871220.18452874X-RAY DIFFRACTION86.89
3.52-3.740.20581310.1622868X-RAY DIFFRACTION87.13
3.74-4.030.17971510.1552886X-RAY DIFFRACTION87.55
4.03-4.440.17041580.14312965X-RAY DIFFRACTION90.1
4.44-5.080.1741520.13223014X-RAY DIFFRACTION91.66
5.08-6.390.18181630.15573113X-RAY DIFFRACTION94.27
6.4-39.860.16541390.14513094X-RAY DIFFRACTION92.56
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)
11.184313864350.2787211073150.1748199075251.324168383940.1177503842461.599166545040.0120644574557-0.126878632971-0.3063927202750.0481762187256-0.00668814338816-0.1209233080340.445751542220.06586857733670.0162341470430.2653470050150.05601313378930.07377011729960.2375985313820.0602608118610.2250523533365.34265511358-42.577708911732.5667426376
20.3903931944860.0814672938879-0.1144552124150.471620388834-0.1460456141931.02383281953-0.0441761766770.00113015348791-0.0105077191936-0.0127721786740.006364171168160.08443098476530.0433203669104-0.0605336840210.03647109456210.153435270459-0.01963444567010.002339978203290.229767682982-0.003386181000130.186486077079-3.78384128429-20.73583084719.3772374209
30.5989547218640.0746939021429-0.3329144634081.064460102560.03588946058231.231764603620.004259634893310.01186390011430.19615226805-0.2297377403290.01652715173890.114286981856-0.3385642458980.0141671601668-0.01957633582530.335758839434-0.0201498483419-0.09060458839060.2062982999320.03524147467090.35824110739.6264853041944.552239978815.0222775355
40.568057653028-0.02067746005190.02694386576471.296083727420.08997604595420.712782180653-0.0804310056695-0.0541084420810.03388652187370.08193831589690.0711070817199-0.0865728580742-0.1038453566620.1399923164740.001860722477660.1895855116-0.0321439938985-0.04067576263470.2011332218390.009842387398390.26993122330920.84532827828.379187331323.637852591
50.5578432112620.317855236518-0.08584753330381.474806988060.3918321384680.857040593747-0.1023141661540.1159263178020.0801676137291-0.2476344446920.0933768051151-0.0283756405257-0.1154375081360.07415682779080.01773738900290.250623826658-0.0461099360106-0.04078931310240.2345215137480.04737057362080.27351934630716.823024369911.04617390730.537799644845
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 25 through 274 )AA25 - 2741 - 250
22chain 'A' and (resid 275 through 799 )AA275 - 799251 - 775
33chain 'B' and (resid 25 through 274 )BB25 - 2741 - 250
44chain 'B' and (resid 275 through 514 )BB275 - 514251 - 490
55chain 'B' and (resid 515 through 799 )BB515 - 799491 - 775

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