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- PDB-6d5b: Structure of Caldicellulosiruptor danielii CBM3 module of glycosi... -

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Basic information

Entry
Database: PDB / ID: 6d5b
TitleStructure of Caldicellulosiruptor danielii CBM3 module of glycoside hydrolase WP_045175321
Componentsglycoside hydrolase WP_045175321
KeywordsSUGAR BINDING PROTEIN / CBM3 / carbohydrate binding
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / cellulose binding / carbohydrate metabolic process
Similarity search - Function
Endoglucanase-like / Carbohydrate-binding module 3 superfamily / CBM2/CBM3, carbohydrate-binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Glycoside hydrolase WP_045175321
Similarity search - Component
Biological speciesCaldicellulosiruptor sp. Wai35.B1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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
D: glycoside hydrolase WP_045175321
E: glycoside hydrolase WP_045175321
F: glycoside hydrolase WP_045175321
G: glycoside hydrolase WP_045175321
H: glycoside hydrolase WP_045175321
I: glycoside hydrolase WP_045175321
J: glycoside hydrolase WP_045175321
K: glycoside hydrolase WP_045175321
L: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,98624
Polymers227,50512
Non-polymers48112
Water41,0382278
1
A: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,9591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,9591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,9591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,9591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,9591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,9591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,9591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,9591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
9
I: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,9591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
10
J: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,9591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
11
K: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,9591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
12
L: glycoside hydrolase WP_045175321
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9992
Polymers18,9591
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.167, 86.199, 86.567
Angle α, β, γ (deg.)83.87, 83.93, 60.55
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
glycoside hydrolase WP_045175321


Mass: 18958.756 Da / Num. of mol.: 12 / Fragment: CBM3 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: A0A4V8GZQ7*PLUS, Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2278 / 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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 8% Tacsimate, pH 4-5, 14-25% PEG3350

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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: Jun 6, 2016 / Details: HELIOS MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 144145 / % possible obs: 99.1 % / Redundancy: 5.22 % / Rsym value: 0.1233 / Net I/σ(I): 7.64
Reflection shellResolution: 2→2.1 Å / Redundancy: 3.72 % / Mean I/σ(I) obs: 1.07 / Num. unique obs: 19299 / Rpim(I) all: 0.7277 / % possible all: 97.5

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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 3ZQW

3zqw


Resolution: 2→85.91 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.922 / SU B: 5.383 / SU ML: 0.142 / Cross valid method: THROUGHOUT / ESU R: 0.179 / ESU R Free: 0.174 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24275 7170 5 %RANDOM
Rwork0.17799 ---
obs0.18121 136099 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.522 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å20.1 Å20.31 Å2
2--0.84 Å20.45 Å2
3----0.62 Å2
Refinement stepCycle: 1 / Resolution: 2→85.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14419 0 12 2278 16709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0214830
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212983
X-RAY DIFFRACTIONr_angle_refined_deg1.6731.88820174
X-RAY DIFFRACTIONr_angle_other_deg1.004330197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.14651843
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06924.92685
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.833152400
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8121560
X-RAY DIFFRACTIONr_chiral_restr0.1050.22170
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023175
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_it2.2762.6757378
X-RAY DIFFRACTIONr_mcbond_other2.2762.6757377
X-RAY DIFFRACTIONr_mcangle_it3.2993.9979219
X-RAY DIFFRACTIONr_mcangle_other3.2993.9979220
X-RAY DIFFRACTIONr_scbond_it2.3642.7647452
X-RAY DIFFRACTIONr_scbond_other2.3632.7647452
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4754.06110956
X-RAY DIFFRACTIONr_long_range_B_refined5.12331.62718721
X-RAY DIFFRACTIONr_long_range_B_other4.9631.00318151
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 501 -
Rwork0.293 9879 -
obs--96.22 %

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