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- PDB-5zu6: A CBM32 derived from alginate lyase B (AlyB-OU02) -

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Basic information

Entry
Database: PDB / ID: 5zu6
TitleA CBM32 derived from alginate lyase B (AlyB-OU02)
ComponentsCBM32 domain
KeywordsLYASE / CBM32 / alginate lyase
Function / homology
Function and homology information


Alginate lyase 2 / Alginate lyase / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding-like domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesVibrio (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsLiu, W. / Lyu, Q. / Zhang, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)41706151 China
CitationJournal: Biochim. Biophys. Acta / Year: 2018
Title: Structural and biochemical characterization of a multidomain alginate lyase reveals a novel role of CBM32 in CAZymes
Authors: Lyu, Q. / Zhang, K. / Zhu, Q. / Li, Z. / Liu, Y. / Fitzek, E. / Yohe, T. / Zhao, L. / Li, W. / Liu, T. / Yin, Y. / Liu, W.
History
DepositionMay 7, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBM32 domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3702
Polymers18,3471
Non-polymers231
Water3,855214
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7600 Å2
Unit cell
Length a, b, c (Å)43.849, 60.679, 66.894
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein CBM32 domain


Mass: 18346.881 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2S7V314*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 214 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.43 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 1.6M sodium citrate tribasic dihydrate pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 1 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 35712 / % possible obs: 100 % / Redundancy: 12.5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 21.7
Reflection shellResolution: 1.4→1.45 Å / Rmerge(I) obs: 0.47 / Num. unique obs: 3517

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZU5

5zu5


Resolution: 1.4→44.94 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.95 / SU B: 0.913 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21161 1786 5 %RANDOM
Rwork0.1891 ---
obs0.19023 33822 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.996 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å2-0 Å2
2---0.01 Å20 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.4→44.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1156 0 1 214 1371
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191216
X-RAY DIFFRACTIONr_bond_other_d0.0040.021090
X-RAY DIFFRACTIONr_angle_refined_deg1.8761.9221659
X-RAY DIFFRACTIONr_angle_other_deg0.89932514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2355161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.26725.42459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.21115189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.317156
X-RAY DIFFRACTIONr_chiral_restr0.1380.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021468
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02290
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_it1.2821.237632
X-RAY DIFFRACTIONr_mcbond_other1.2841.233631
X-RAY DIFFRACTIONr_mcangle_it1.981.849797
X-RAY DIFFRACTIONr_mcangle_other1.9791.854798
X-RAY DIFFRACTIONr_scbond_it2.2931.489584
X-RAY DIFFRACTIONr_scbond_other2.2911.493585
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3922.148863
X-RAY DIFFRACTIONr_long_range_B_refined5.63212.2151570
X-RAY DIFFRACTIONr_long_range_B_other5.3911.1231444
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 139 -
Rwork0.24 2228 -
obs--90.86 %

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