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- PDB-7nzo: D-lyxose isomerasefrom the hyperthermophilic archaeon Thermofilum sp -

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Basic information

Entry
Database: PDB / ID: 7nzo
TitleD-lyxose isomerasefrom the hyperthermophilic archaeon Thermofilum sp
ComponentsD-lyxose/D-mannose family sugar isomerase
KeywordsISOMERASE / Complex / thermostability / biocatalysis.
Function / homologyD-lyxose ketol-isomerase / RmlC-like cupin domain superfamily / isomerase activity / RmlC-like jelly roll fold / metal ion binding / : / D-lyxose ketol-isomerase
Function and homology information
Biological speciesThermofilum sp. ex4484_79 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 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 / struct_ncs_dom_lim
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Oct 23, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,58915
Polymers47,7962
Non-polymers79313
Water4,450247
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.770, 86.910, 54.030
Angle α, β, γ (deg.)90.000, 112.930, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: 0 - 174 / Label seq-ID: 24 - 198

Dom-IDAuth asym-IDLabel asym-ID
1AAAA
2BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

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


Mass: 23898.215 Da / Num. of mol.: 2
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: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 7 / Details: 150 mM Potassium bromide, 30% w/v PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.67→39.26 Å / Num. obs: 43436 / % possible obs: 92.2 % / Redundancy: 6.2 % / CC1/2: 0.999 / Net I/σ(I): 19.4
Reflection shellResolution: 1.67→1.7 Å / Num. unique obs: 1266 / CC1/2: 0.326

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Y0O

2y0o


Resolution: 1.67→39.252 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.034 / SU ML: 0.091 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.103 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2107 2053 4.73 %
Rwork0.1792 41355 -
all0.181 --
obs-43408 92.132 %
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: 41.016 Å2
Baniso -1Baniso -2Baniso -3
1-2.535 Å20 Å20.653 Å2
2---2.531 Å20 Å2
3----0.409 Å2
Refinement stepCycle: LAST / Resolution: 1.67→39.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2907 0 46 247 3200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0123112
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.6654198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3965376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.86221.348178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.97215561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6651527
X-RAY DIFFRACTIONr_chiral_restr0.1140.2397
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022359
X-RAY DIFFRACTIONr_nbd_refined0.2080.21398
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.2237
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.245
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1580.29
X-RAY DIFFRACTIONr_mcbond_it3.343.7211438
X-RAY DIFFRACTIONr_mcangle_it4.2415.5461800
X-RAY DIFFRACTIONr_scbond_it4.84.2121674
X-RAY DIFFRACTIONr_scangle_it6.5536.0822386
X-RAY DIFFRACTIONr_lrange_it8.33471.76913108
X-RAY DIFFRACTIONr_ncsr_local_group_10.0710.055925
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.070520.0501
12BBBX-RAY DIFFRACTIONLocal ncs0.070520.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.67-1.7130.421000.43617850.43534640.1850.24854.41690.433
1.713-1.760.421190.41621630.41633930.4510.45167.25610.411
1.76-1.8110.371340.33924730.34132660.5830.59879.82240.322
1.811-1.8670.2921300.30227770.30132040.770.73190.73030.276
1.867-1.9280.2821300.25129260.25331050.7940.81898.42190.222
1.928-1.9950.241130.21128670.21229810.8850.90299.96650.179
1.995-2.070.2361560.19627580.19829140.9190.9251000.168
2.07-2.1550.2081270.18126390.18227670.9280.9499.96390.157
2.155-2.250.2211320.17925470.18126790.9310.9441000.158
2.25-2.360.244920.18724650.18925570.9240.9371000.169
2.36-2.4870.2231020.17223090.17424110.9310.9511000.158
2.487-2.6370.2091060.16822060.1723120.9440.951000.156
2.637-2.8180.242950.17820710.18121660.9410.9451000.17
2.818-3.0430.2331110.1818950.18320070.9330.94299.95020.175
3.043-3.3310.194920.17717760.17818680.9460.9511000.18
3.331-3.7210.214880.17416000.17616890.9510.96399.94080.182
3.721-4.290.153780.14814170.14814950.9750.9771000.162
4.29-5.2390.126620.11812060.11812680.9820.9841000.141
5.239-7.3430.234590.1799270.1829880.9520.96599.79760.203
7.343-39.2520.24270.2055480.2075760.9430.96699.82640.257

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