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- PDB-6n99: Xylose isomerase 2F1 variant from Streptomyces sp. F-1 -

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Basic information

Entry
Database: PDB / ID: 6n99
TitleXylose isomerase 2F1 variant from Streptomyces sp. F-1
ComponentsXylose isomerase
KeywordsISOMERASE / Wild type
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Divalent-metal-dependent TIM barrel enzymes / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Biological speciesStreptomyces sp. F-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMiyamoto, R.Y. / Vieira, P.S. / Murakami, M.T. / Zanphorlin, L.M.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)2018/02865-2 Brazil
Sao Paulo Research Foundation (FAPESP)2016/06509-0 Brazil
CitationJournal: Biochim Biophys Acta Gen Subj / Year: 2020
Title: Crystal structure of a novel xylose isomerase from Streptomyces sp. F-1 revealed the presence of unique features that differ from conventional classes.
Authors: Miyamoto, R.Y. / de Sousa, A.S. / Vieira, P.S. / de Melo, R.R. / Scarpassa, J.A. / Ramos, C.H.I. / Murakami, M.T. / Ruller, R. / Zanphorlin, L.M.
History
DepositionDec 1, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 3, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 11, 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

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase
B: Xylose isomerase
C: Xylose isomerase
D: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,30812
Polymers171,8774
Non-polymers4328
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31370 Å2
ΔGint-195 kcal/mol
Surface area47830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.776, 82.293, 140.313
Angle α, β, γ (deg.)90.00, 109.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Xylose isomerase


Mass: 42969.125 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. F-1 (bacteria) / Gene: xylA_1, xylA, STEPF1_01030 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1K2FKX8, xylose isomerase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 2.0 M lithium sulfate 8% 2-methyl-2,4-pentanediol 0.1 M imidazole pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.458 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 37206 / % possible obs: 97.9 % / Redundancy: 3.047 % / Net I/σ(I): 5.57
Reflection shellResolution: 2.8→2.97 Å

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Processing

Software
NameVersionClassification
PHENIX(dev_3139: ???)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1S5N
Resolution: 2.8→19.757 Å / SU ML: 0.56 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 38.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3163 1864 5.02 %
Rwork0.2665 --
obs0.269 37151 98.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→19.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12008 0 23 7 12038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312307
X-RAY DIFFRACTIONf_angle_d0.51916682
X-RAY DIFFRACTIONf_dihedral_angle_d10.1737278
X-RAY DIFFRACTIONf_chiral_restr0.0361745
X-RAY DIFFRACTIONf_plane_restr0.0042256
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7998-2.87520.39891510.40022664X-RAY DIFFRACTION99
2.8752-2.95960.40691320.38522773X-RAY DIFFRACTION99
2.9596-3.05480.43561610.36682750X-RAY DIFFRACTION99
3.0548-3.16350.48031410.43612627X-RAY DIFFRACTION97
3.1635-3.28960.37871400.32722733X-RAY DIFFRACTION99
3.2896-3.43860.3831310.29782751X-RAY DIFFRACTION99
3.4386-3.61890.37231470.2982695X-RAY DIFFRACTION98
3.6189-3.8440.36011330.30592646X-RAY DIFFRACTION97
3.844-4.13830.31761440.28072633X-RAY DIFFRACTION95
4.1383-4.55020.25881510.21772748X-RAY DIFFRACTION99
4.5502-5.19810.27541650.20722724X-RAY DIFFRACTION99
5.1981-6.50990.25421350.21872750X-RAY DIFFRACTION99
6.5099-19.75780.19761330.16542793X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.2768-0.4122-0.59091.0875-0.07992.09790.080.01220.2321-0.05360.0971-0.0194-0.32580.1434-0.17130.3759-0.0496-0.07380.26410.01780.471164.041651.883119.5363
21.4667-0.1764-0.45050.8972-0.07871.988-0.05050.1372-0.0327-0.0921-0.02140.19990.1145-0.60850.04570.3248-0.0103-0.13090.4207-0.00760.451642.317731.382242.662
30.56040.0135-0.59630.6574-0.25881.7931-0.0169-0.4863-0.04350.1085-0.0724-0.1230.13250.89290.06210.35210.1381-0.14520.68930.02080.535370.064335.597452.9211
41.56110.1622-0.990.6817-0.0591.8931-0.2438-0.2459-0.233-0.03920.0305-0.0330.43140.24130.18010.43190.0795-0.0850.2762-0.00860.466468.783622.54617.4021
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:386)
2X-RAY DIFFRACTION2(chain B and resid 3:386)
3X-RAY DIFFRACTION3(chain C and resid 3:386)
4X-RAY DIFFRACTION4(chain D and resid 3:386)

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