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- PDB-6m6p: Structure of Marine bacterial laminarinase mutant E135A in comple... -

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Basic information

Entry
Database: PDB / ID: 6m6p
TitleStructure of Marine bacterial laminarinase mutant E135A in complex with 1,3-beta-cellotriosyl-glucose
Componentslaminarinase
KeywordsHYDROLASE
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Beta/Gamma crystallin / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Glycosyl hydrolases family 16 / Carbohydrate binding module (family 6) ...Secretion system C-terminal sorting domain / Secretion system C-terminal sorting domain / Cellulose binding, type IV / Cellulose Binding Domain Type IV / Beta/Gamma crystallin / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Glycosyl hydrolases family 16 / Carbohydrate binding module (family 6) / Gamma-crystallin-like / Glycoside hydrolase family 16 / Glycosyl hydrolases family 16 (GH16) domain profile. / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesAquimarina sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsYang, J. / Xu, Y. / Tanokura, M. / Long, L. / Miyakawa, T.
CitationJournal: Appl.Environ.Microbiol. / Year: 2020
Title: Molecular Basis for Substrate Recognition and Catalysis by a Marine Bacterial Laminarinase.
Authors: Yang, J. / Xu, Y. / Miyakawa, T. / Long, L. / Tanokura, M.
History
DepositionMar 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _citation_author.name
Revision 1.2Oct 7, 2020Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Nov 25, 2020Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.4Nov 29, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: laminarinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,4833
Polymers27,7771
Non-polymers7072
Water2,180121
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-0 kcal/mol
Surface area9520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.998, 95.644, 72.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-436-

HOH

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Components

#1: Protein laminarinase


Mass: 27776.602 Da / Num. of mol.: 1 / Mutation: E135A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquimarina sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A6F9D674*PLUS
#2: Polysaccharide beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-4)-beta-D-glucopyranose-(1-3)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 666.578 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpb1-4DGlcpb1-4DGlcpb1-3DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1a_1-5][a2122h-1b_1-5]/1-2-2-2/a3-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{[(4+1)][b-D-Glcp]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsThis protein is E135A mutant.

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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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES (pH7.0), 15% (v/v) ethanol, 28% (m/v) PEG20000

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Nov 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.21→47.82 Å / Num. obs: 11550 / % possible obs: 95.9 % / Redundancy: 6.4 % / CC1/2: 0.997 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.046 / Rrim(I) all: 0.117 / Net I/σ(I): 10.4 / Num. measured all: 74218 / Scaling rejects: 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.21-2.285.80.7047230.890.3080.77270.7
9.11-47.825.20.0741950.9940.0360.08396.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4CRQ

4crq


Resolution: 2.27→43.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.927 / SU B: 6.981 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.38 / ESU R Free: 0.234 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2284 507 4.7 %RANDOM
Rwork0.1739 ---
obs0.1764 10387 97.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.99 Å2 / Biso mean: 33.324 Å2 / Biso min: 21.43 Å2
Baniso -1Baniso -2Baniso -3
1--4.85 Å2-0 Å20 Å2
2--0.72 Å2-0 Å2
3---4.13 Å2
Refinement stepCycle: final / Resolution: 2.27→43.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 46 121 2021
Biso mean--60.2 38.12 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131964
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181632
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.6632684
X-RAY DIFFRACTIONr_angle_other_deg1.4381.5993797
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4655232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2323.303109
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84615282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.705158
X-RAY DIFFRACTIONr_chiral_restr0.0770.2261
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022207
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02449
LS refinement shellResolution: 2.271→2.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 25 -
Rwork0.236 656 -
all-681 -
obs--83.66 %

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