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- PDB-6jhj: Structure of Marine bacterial laminarinase mutant-E135A -

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Basic information

Entry
Database: PDB / ID: 6jhj
TitleStructure of Marine bacterial laminarinase mutant-E135A
ComponentsLamCAT
KeywordsHYDROLASE
Function / homologyJelly Rolls - #200 / Jelly Rolls / Sandwich / Mainly Beta
Function and homology information
Biological speciesAquimarina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsYang, J. / Xu, Y. / Miyakawa, T. / Tanokura, M. / Long, L.
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
DepositionFeb 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 30, 2020Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.country ..._audit_author.name / _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 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: LamCAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8172
Polymers27,7771
Non-polymers401
Water4,468248
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-12 kcal/mol
Surface area9670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.808, 94.606, 72.442
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-410-

HOH

21A-588-

HOH

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Components

#1: Protein LamCAT


Mass: 27776.602 Da / Num. of mol.: 1 / Mutation: E135A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquimarina (bacteria) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O
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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 5% (v/v) ethonal, 28% PEG20000 100 mM MES pH7.0

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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 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: 1.69→47.3 Å / Num. obs: 22574 / % possible obs: 96.5 % / Redundancy: 6 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 24.2
Reflection shellResolution: 1.69→1.79 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.593 / Num. unique obs: 945 / % possible all: 73.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4crq

4crq


Resolution: 1.69→39.607 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 2.382 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18483 1209 5.1 %RANDOM
Rwork0.15023 ---
obs0.15191 22574 91.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.799 Å2
Baniso -1Baniso -2Baniso -3
1--1.65 Å2-0 Å2-0 Å2
2--3.04 Å2-0 Å2
3----1.39 Å2
Refinement stepCycle: 1 / Resolution: 1.69→39.607 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1854 0 1 248 2103
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191916
X-RAY DIFFRACTIONr_bond_other_d0.0030.021679
X-RAY DIFFRACTIONr_angle_refined_deg1.7251.8742611
X-RAY DIFFRACTIONr_angle_other_deg1.02833837
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7015232
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06424.356101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.07915282
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.379158
X-RAY DIFFRACTIONr_chiral_restr0.1240.2264
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022253
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02517
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_it2.1042.237925
X-RAY DIFFRACTIONr_mcbond_other2.0722.236924
X-RAY DIFFRACTIONr_mcangle_it2.8863.3451155
X-RAY DIFFRACTIONr_mcangle_other2.8853.3461156
X-RAY DIFFRACTIONr_scbond_it3.122.503991
X-RAY DIFFRACTIONr_scbond_other3.1182.506992
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5453.6581456
X-RAY DIFFRACTIONr_long_range_B_refined5.98822.448852
X-RAY DIFFRACTIONr_long_range_B_other5.72922.0638644
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.693→1.737 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 45 -
Rwork0.301 846 -
obs--47.17 %

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