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- PDB-6n98: Xylose isomerase 1F1 variant from Streptomyces sp. F-1 -

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Basic information

Entry
Database: PDB / ID: 6n98
TitleXylose isomerase 1F1 variant from Streptomyces sp. F-1
ComponentsXylose isomerase
KeywordsISOMERASE / Wild type / bacteria
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: 1.55 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.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,7229
Polymers43,0971
Non-polymers6258
Water7,260403
1
A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,88936
Polymers172,3894
Non-polymers2,50032
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
Buried area36900 Å2
ΔGint-428 kcal/mol
Surface area46550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.100, 92.900, 99.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Xylose isomerase


Mass: 43097.195 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. F-1 (bacteria) / Gene: xylA_2, xylA, STEPF1_06097 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1K2FZ20, xylose isomerase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris propane pH 7.0 2.5 M ammonium sulfate

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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: Sep 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.458 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 52732 / % possible obs: 89.8 % / Redundancy: 12.48 % / Net I/σ(I): 18.08
Reflection shellResolution: 1.55→1.64 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

1s5n


Resolution: 1.55→31.77 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2144 2641 5.03 %
Rwork0.1925 --
obs0.1936 52504 89.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→31.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3020 0 32 403 3455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063120
X-RAY DIFFRACTIONf_angle_d0.8174231
X-RAY DIFFRACTIONf_dihedral_angle_d15.6731829
X-RAY DIFFRACTIONf_chiral_restr0.048435
X-RAY DIFFRACTIONf_plane_restr0.006564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.57740.27561320.22132349X-RAY DIFFRACTION81
1.5774-1.60780.26051300.19962460X-RAY DIFFRACTION85
1.6078-1.64060.23791340.19852587X-RAY DIFFRACTION89
1.6406-1.67630.24281340.21012674X-RAY DIFFRACTION91
1.6763-1.71530.26931370.24342639X-RAY DIFFRACTION91
1.7153-1.75810.29031510.2162627X-RAY DIFFRACTION92
1.7581-1.80570.2411500.19452661X-RAY DIFFRACTION92
1.8057-1.85880.261640.20382679X-RAY DIFFRACTION92
1.8588-1.91880.46591030.42442035X-RAY DIFFRACTION69
1.9188-1.98740.36641030.31982202X-RAY DIFFRACTION75
1.9874-2.06690.27941180.24162671X-RAY DIFFRACTION90
2.0669-2.1610.2771130.21882639X-RAY DIFFRACTION90
2.161-2.27490.3119990.27742430X-RAY DIFFRACTION82
2.2749-2.41740.23111500.17772747X-RAY DIFFRACTION94
2.4174-2.60390.20051760.18162804X-RAY DIFFRACTION96
2.6039-2.86580.20471780.18262779X-RAY DIFFRACTION96
2.8658-3.28010.20721340.17272917X-RAY DIFFRACTION97
3.2801-4.13120.16331500.15062917X-RAY DIFFRACTION97
4.1312-31.77690.14221850.14313046X-RAY DIFFRACTION99
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.2726-1.84840.02644.2324-1.04050.309-0.2817-0.86910.39450.60310.1096-0.1812-0.3224-0.4280.16510.27210.0460.02960.2904-0.04750.205526.723113.179472.7267
27.277-5.4345-4.91085.38566.17128.1660.38250.5265-0.0196-0.5087-0.48910.1997-0.2633-0.65750.15370.20590.00870.03620.2969-0.00470.24916.51941.248859.023
31.68510.15950.18181.7496-0.1192.5163-0.0214-0.05150.08410.07090.00580.4214-0.1447-0.59210.01360.17590.07240.03330.3169-0.0530.282913.415416.03466.5144
40.51250.2505-0.02110.2602-0.00651.8430.0045-0.0010.07550.0697-0.03890.1536-0.1935-0.33650.02710.18530.07830.00110.2034-0.02080.216523.539621.210646.9835
52.6335-1.6535-0.62644.92881.24980.989-0.0139-0.16260.16070.07780.04960.1757-0.2867-0.1866-0.02410.23690.05530.00870.1559-0.01270.153129.367320.697351.6935
60.72860.1718-0.0371.374-0.96972.18310.01240.01190.02350.0624-0.04650.0737-0.1276-0.06850.03680.12070.00520.0040.1126-0.02360.138738.642114.962459.6618
73.20941.57391.6511.33180.96462.09340.0756-0.18680.03260.1437-0.09250.0867-0.1227-0.16440.02420.17620.00720.03350.1624-0.02530.148432.1126.921172.25
87.05944.0624-3.75066.7383-0.56945.42350.2507-0.57950.21040.6647-0.3337-0.1594-0.16470.50280.12960.2271-0.0635-0.0760.2298-0.00720.184160.436413.216176.5103
97.852.9436-1.17994.58890.34261.99670.1760.01630.3460.4386-0.1033-0.2762-0.64340.3977-0.01870.2535-0.1182-0.03060.1942-0.0220.232362.484226.343366.0581
102.3227-1.66064.44375.8122-3.5128.5276-0.0214-0.06420.37630.161-0.4381-1.2526-0.94390.81740.40360.4345-0.2510.06710.46020.00680.50973.213332.706856.5578
115.79613.1342-2.05073.8849-1.49412.8338-0.111-0.1575-0.18710.0834-0.0834-0.460.10920.39010.15440.1529-0.013-0.06220.2124-0.00060.175761.80917.764270.2861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 4:19)
2X-RAY DIFFRACTION2(chain A and resid 20:39)
3X-RAY DIFFRACTION3(chain A and resid 40:81)
4X-RAY DIFFRACTION4(chain A and resid 82:167)
5X-RAY DIFFRACTION5(chain A and resid 168:192)
6X-RAY DIFFRACTION6(chain A and resid 193:278)
7X-RAY DIFFRACTION7(chain A and resid 279:322)
8X-RAY DIFFRACTION8(chain A and resid 323:332)
9X-RAY DIFFRACTION9(chain A and resid 333:344)
10X-RAY DIFFRACTION10(chain A and resid 345:354)
11X-RAY DIFFRACTION11(chain A and resid 355:382)

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