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- PDB-7nzq: D-lyxose isomerase from the hyperthermophilic archaeon Thermofilu... -

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Basic information

Entry
Database: PDB / ID: 7nzq
TitleD-lyxose isomerase from the hyperthermophilic archaeon Thermofilum sp complexed with D-mannose
ComponentsD-lyxose/D-mannose family sugar isomerase
KeywordsISOMERASE / Complex / thermostability / biocatalysis
Function / homology
Function and homology information


D-lyxose ketol-isomerase / isomerase activity / metal ion binding
Similarity search - Function
RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
beta-D-mannopyranose / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / D-lyxose ketol-isomerase
Similarity search - Component
Biological speciesThermofilum sp. ex4484_79 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsDe Rose, S.A. / Isupov, M.N. / Littlechild, J.A. / Schoenheit, P.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research031B0271 Germany
CitationJournal: Front Bioeng Biotechnol / Year: 2021
Title: Biochemical and Structural Characterisation of a Novel D-Lyxose Isomerase From the Hyperthermophilic Archaeon Thermofilum sp.
Authors: De Rose, S.A. / Kuprat, T. / Isupov, M.N. / Reinhardt, A. / Schonheit, P. / Littlechild, J.A.
History
DepositionMar 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / diffrn_source / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: D-lyxose/D-mannose family sugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4597
Polymers23,8981
Non-polymers5606
Water4,035224
1
AAA: D-lyxose/D-mannose family sugar isomerase
hetero molecules

AAA: D-lyxose/D-mannose family sugar isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,91714
Polymers47,7962
Non-polymers1,12112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area3770 Å2
ΔGint-15 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.909, 121.013, 70.537
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
11AAA-433-

HOH

21AAA-472-

HOH

31AAA-492-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules AAA

#1: Protein D-lyxose/D-mannose family sugar isomerase


Mass: 23898.215 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermofilum sp. ex4484_79 (archaea) / Gene: B6U94_07925 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A256XLS3
#2: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H12O6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 229 molecules

#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6
Details: 100 mM SPG ph 6.0, 25% w/v PEG 1500, 40 mM D-mannose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.57→37.692 Å / Num. obs: 29074 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.997 / Net I/σ(I): 6.6
Reflection shellResolution: 1.57→1.6 Å / Num. unique obs: 1425 / CC1/2: 0.277

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
DIALSdata reduction
Aimlessdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2y0o

2y0o


Resolution: 1.57→37.692 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.575 / SU ML: 0.082 / Cross valid method: FREE R-VALUE / ESU R: 0.085 / ESU R Free: 0.09 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2176 1439 4.956 %
Rwork0.1755 27597 -
all0.178 --
obs-29036 99.852 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 25.025 Å2
Baniso -1Baniso -2Baniso -3
1-0.497 Å2-0 Å2-0 Å2
2---0.034 Å20 Å2
3----0.463 Å2
Refinement stepCycle: LAST / Resolution: 1.57→37.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1464 0 33 224 1721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121687
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.6682301
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.745214
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.46921.584101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.13615312
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3761515
X-RAY DIFFRACTIONr_chiral_restr0.1140.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021295
X-RAY DIFFRACTIONr_nbd_refined0.2060.2797
X-RAY DIFFRACTIONr_nbtor_refined0.3190.21082
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1430.2185
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2620.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.219
X-RAY DIFFRACTIONr_mcbond_it1.8822.122758
X-RAY DIFFRACTIONr_mcangle_it2.6483.17957
X-RAY DIFFRACTIONr_scbond_it3.0032.469929
X-RAY DIFFRACTIONr_scangle_it4.1553.5521325
X-RAY DIFFRACTIONr_lrange_it6.58241.6147219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.57-1.6110.3331250.3381970X-RAY DIFFRACTION99.5722
1.611-1.6550.336940.3231976X-RAY DIFFRACTION99.711
1.655-1.7030.345910.31919X-RAY DIFFRACTION99.851
1.703-1.7550.305910.2751850X-RAY DIFFRACTION99.9485
1.755-1.8130.29850.251822X-RAY DIFFRACTION99.8952
1.813-1.8760.2691160.2221705X-RAY DIFFRACTION100
1.876-1.9470.284760.211703X-RAY DIFFRACTION99.8316
1.947-2.0260.224880.1891626X-RAY DIFFRACTION99.7091
2.026-2.1160.199900.1771541X-RAY DIFFRACTION99.9387
2.116-2.220.217830.1661480X-RAY DIFFRACTION99.7447
2.22-2.3390.19640.1641450X-RAY DIFFRACTION100
2.339-2.4810.194670.1511344X-RAY DIFFRACTION99.8585
2.481-2.6520.217620.1591286X-RAY DIFFRACTION99.9259
2.652-2.8640.191610.1571193X-RAY DIFFRACTION100
2.864-3.1370.216560.1481102X-RAY DIFFRACTION100
3.137-3.5060.178370.1451015X-RAY DIFFRACTION100
3.506-4.0460.163530.134891X-RAY DIFFRACTION99.8942
4.046-4.950.207350.117770X-RAY DIFFRACTION100
4.95-6.9770.157420.167594X-RAY DIFFRACTION100
6.977-37.6920.283230.219360X-RAY DIFFRACTION99.2228

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