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- PDB-6d5c: Structure of Caldicellulosiruptor danielii GH10 module of glycosi... -

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Basic information

Entry
Database: PDB / ID: 6d5c
TitleStructure of Caldicellulosiruptor danielii GH10 module of glycoside hydrolase WP_045175321
Componentsglycoside hydrolase WP_045175321
KeywordsHYDROLASE / GH10 / glycoside hydrolase
Function / homology
Function and homology information


endo-1,4-beta-xylanase activity / endo-1,4-beta-xylanase / polysaccharide catabolic process
Similarity search - Function
Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel ...Glycosyl hydrolases family 10, active site / Glycosyl hydrolases family 10 (GH10) active site. / Glycosyl hydrolases family 10 (GH10) domain profile. / Glycoside hydrolase family 10 / Glycoside hydrolase family 10 domain / Glycosyl hydrolase family 10 / Glycosyl hydrolase family 10 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / Beta-xylanase
Similarity search - Component
Biological speciesCaldicellulosiruptor sp. Wai35.B1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAlahuhta, P.M. / Lunin, V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
Department of Energy (DOE, United States) United States
CitationJournal: AIChE J. / Year: 2019
Title: Novel multidomain, multifunctional glycoside hydrolases from highly lignocellulolytic Caldicellulosiruptor species
Authors: Conway, J.M. / Crosby, J.R. / Hren, A.P. / Southerland, R.T. / Lee, L.L. / Lunin, V.V. / Alahuhta, P.M. / Himmel, M.E. / Bomble, Y.J. / Adams, M.W.W. / Kelly, R.M.
History
DepositionApr 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycoside hydrolase WP_045175321
B: glycoside hydrolase WP_045175321
C: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,72135
Polymers121,9553
Non-polymers2,76632
Water23,0771281
1
A: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,64413
Polymers40,6521
Non-polymers99312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,78714
Polymers40,6521
Non-polymers1,13513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2908
Polymers40,6521
Non-polymers6387
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.307, 98.497, 78.810
Angle α, β, γ (deg.)90.00, 93.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein glycoside hydrolase WP_045175321


Mass: 40651.699 Da / Num. of mol.: 3 / Fragment: GH10 module
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caldicellulosiruptor sp. Wai35.B1 (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: A0A4V8GZQ8*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds

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Non-polymers , 5 types, 1313 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1281 / 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

CrystalDensity Matthews: 2.75 Å3/Da / Density % sol: 55.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris, pH 8-9, 1.5-2.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: May 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 104001 / % possible obs: 100 % / Redundancy: 6.03 % / Rsym value: 0.068 / Net I/σ(I): 14.32
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.54 % / Mean I/σ(I) obs: 2.11 / Num. unique obs: 14807 / Rsym value: 0.4469 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
SAINTdata reduction
PROTEUM PLUSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5AY7

5ay7


Resolution: 1.9→86.48 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.029 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.144 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23331 5058 4.9 %RANDOM
Rwork0.17882 ---
obs0.18147 98265 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.186 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å2-0.92 Å2
2---1.51 Å2-0 Å2
3---1.17 Å2
Refinement stepCycle: 1 / Resolution: 1.9→86.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8280 0 156 1281 9717
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0198983
X-RAY DIFFRACTIONr_bond_other_d0.0030.027955
X-RAY DIFFRACTIONr_angle_refined_deg1.8041.92212210
X-RAY DIFFRACTIONr_angle_other_deg1.075318564
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.85251079
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09124.46435
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.564151523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4351538
X-RAY DIFFRACTIONr_chiral_restr0.1210.21263
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02110024
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021922
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3632.4894223
X-RAY DIFFRACTIONr_mcbond_other2.3632.494224
X-RAY DIFFRACTIONr_mcangle_it3.0963.7225333
X-RAY DIFFRACTIONr_mcangle_other3.0963.7235334
X-RAY DIFFRACTIONr_scbond_it3.1172.8124760
X-RAY DIFFRACTIONr_scbond_other3.1142.8124758
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4594.16878
X-RAY DIFFRACTIONr_long_range_B_refined6.14130.70811225
X-RAY DIFFRACTIONr_long_range_B_other6.14130.7111226
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 384 -
Rwork0.269 7267 -
obs--99.61 %

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