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- PDB-6hhn: Crystal structure of L-rhamnose mutarotase FA22100 from Formosa a... -

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Basic information

Entry
Database: PDB / ID: 6hhn
TitleCrystal structure of L-rhamnose mutarotase FA22100 from Formosa agariphila
ComponentsL-rhamnose mutarotase
KeywordsISOMERASE / monosaccharide mutarotase rhamnose Formosa agariphila
Function / homology
Function and homology information


rhamnose metabolic process / L-rhamnose mutarotase / L-rhamnose mutarotase activity / cytoplasm
Similarity search - Function
L-rhamnose mutarotase / Rhamnose/fucose mutarotase / L-rhamnose mutarotase / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-rhamnose mutarotase
Similarity search - Component
Biological speciesFormosa agariphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 Å
AuthorsRoret, T. / Prechoux, A. / Michel, G. / Czjzek, M.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyNo. ANR-14-CE19- 0020-01 France
French National Research AgencyNo. ANR-10-BTBR-04 France
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: A marine bacterial enzymatic cascade degrades the algal polysaccharide ulvan.
Authors: Reisky, L. / Prechoux, A. / Zuhlke, M.K. / Baumgen, M. / Robb, C.S. / Gerlach, N. / Roret, T. / Stanetty, C. / Larocque, R. / Michel, G. / Song, T. / Markert, S. / Unfried, F. / Mihovilovic, ...Authors: Reisky, L. / Prechoux, A. / Zuhlke, M.K. / Baumgen, M. / Robb, C.S. / Gerlach, N. / Roret, T. / Stanetty, C. / Larocque, R. / Michel, G. / Song, T. / Markert, S. / Unfried, F. / Mihovilovic, M.D. / Trautwein-Schult, A. / Becher, D. / Schweder, T. / Bornscheuer, U.T. / Hehemann, J.H.
History
DepositionAug 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jan 17, 2024Group: 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: L-rhamnose mutarotase


Theoretical massNumber of molelcules
Total (without water)13,4171
Polymers13,4171
Non-polymers00
Water2,216123
1
A: L-rhamnose mutarotase

A: L-rhamnose mutarotase


Theoretical massNumber of molelcules
Total (without water)26,8342
Polymers26,8342
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area3190 Å2
ΔGint-23 kcal/mol
Surface area10720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.913, 70.913, 54.407
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein L-rhamnose mutarotase


Mass: 13417.033 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Formosa agariphila (bacteria) / Gene: BN863_22100 / Production host: Escherichia coli (E. coli) / References: UniProt: T2KM13, L-rhamnose mutarotase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.55 Å3/Da / Density % sol: 51.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100 mM Sodium acetate pH4.6 4.3 M Sodium formate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97914 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 1.47→43.17 Å / Num. obs: 24225 / % possible obs: 99.5 % / Redundancy: 9.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.032 / Rpim(I) all: 0.012 / Rrim(I) all: 0.034 / Net I/σ(I): 32.3
Reflection shellResolution: 1.47→1.55 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 6.6 / Num. unique obs: 3383 / CC1/2: 0.983 / Rpim(I) all: 0.107 / Rrim(I) all: 0.315 / % possible all: 97.2

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Processing

Software
NameClassification
XDSdata reduction
Aimlessdata scaling
Cootmodel building
MOLREPphasing
PHENIXrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QLX

2qlx


Resolution: 1.47→43.166 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.25
RfactorNum. reflection% reflection
Rfree0.1721 1183 4.89 %
Rwork0.148 --
obs0.1491 24172 99.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.47→43.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms824 0 0 123 947
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008874
X-RAY DIFFRACTIONf_angle_d0.8891180
X-RAY DIFFRACTIONf_dihedral_angle_d22.347334
X-RAY DIFFRACTIONf_chiral_restr0.083121
X-RAY DIFFRACTIONf_plane_restr0.005154
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4666-1.53330.21691440.14752726X-RAY DIFFRACTION97
1.5333-1.61420.18631390.11712827X-RAY DIFFRACTION99
1.6142-1.71530.18821510.11772817X-RAY DIFFRACTION100
1.7153-1.84780.14491430.12472858X-RAY DIFFRACTION100
1.8478-2.03370.16061520.12562875X-RAY DIFFRACTION100
2.0337-2.3280.17031500.132887X-RAY DIFFRACTION100
2.328-2.93290.15831480.15932930X-RAY DIFFRACTION100
2.9329-43.18460.18181560.16263069X-RAY DIFFRACTION99

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