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- PDB-6t8e: Crystal structure of native xylose isomerase from Piromyces E2 gr... -

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Basic information

Entry
Database: PDB / ID: 6t8e
TitleCrystal structure of native xylose isomerase from Piromyces E2 grown in yeast, in complex with xylose
ComponentsXylose isomerase
KeywordsISOMERASE / TIM-barrel
Function / homology
Function and homology information


xylose catabolic process to ethanol / xylose isomerase / xylose isomerase activity / metal ion binding / cytoplasm
Similarity search - Function
Xylose isomerase, bacterial-type / 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
D-xylose / beta-D-xylopyranose / alpha-D-xylopyranose / Xylose isomerase
Similarity search - Component
Biological speciesPiromyces sp.
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.86 Å
AuthorsRozeboom, H.J. / Janssen, D.B.
CitationJournal: Biotechnol Biofuels / Year: 2020
Title: Structure-based directed evolution improves S. cerevisiae growth on xylose by influencing in vivo enzyme performance.
Authors: Lee, M. / Rozeboom, H.J. / Keuning, E. / de Waal, P. / Janssen, D.B.
History
DepositionOct 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 6, 2021Group: Data collection / Database references / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 / pdbx_contact_author / pdbx_database_proc
Item: _chem_comp.pdbx_synonyms / _citation.journal_volume ..._chem_comp.pdbx_synonyms / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)202,13141
Polymers197,8354
Non-polymers4,29637
Water34,3551907
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area38910 Å2
ΔGint-305 kcal/mol
Surface area53290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.454, 79.267, 91.878
Angle α, β, γ (deg.)115.460, 89.990, 117.070
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Xylose isomerase /


Mass: 49458.672 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Piromyces sp. (strain E2) (fungus) / Strain: E2 / Gene: xylA / Production host: Saccharomyces cerevisiae (brewer's yeast) / Strain (production host): DS75543 / References: UniProt: Q9P8C9, xylose isomerase

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Sugars , 3 types, 22 molecules

#3: Sugar
ChemComp-XLS / D-xylose / D-XYLOSE (LINEAR FORM) / Xylose


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
#4: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-xylopyranoseCOMMON NAMEGMML 1.0
b-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Sugar
ChemComp-XYS / alpha-D-xylopyranose / alpha-D-xylose / D-xylose / xylose / XYLOPYRANOSE / Xylose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DXylpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-xylopyranoseCOMMON NAMEGMML 1.0
a-D-XylpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
XylSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 1922 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1907 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 14-17 % PEG3350, HEPES, pH 7

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Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 27, 2018
RadiationMonochromator: HELIOS MX Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.86→46.6 Å / Num. obs: 135735 / % possible obs: 93.6 % / Redundancy: 2.1 % / CC1/2: 0.931 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.06 / Rrim(I) all: 0.09 / Net I/σ(I): 7.1
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.38 / Num. unique obs: 5669 / CC1/2: 0.286 / Rpim(I) all: 0.35 / Rrim(I) all: 0.518 / % possible all: 79.1

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.2data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
REFMAC5.8.0238phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5NH5
Resolution: 1.86→46.6 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.711 / SU ML: 0.088 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.12
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1763 6788 5 %RANDOM
Rwork0.1386 ---
obs0.1405 128946 93.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.52 Å2 / Biso mean: 18.438 Å2 / Biso min: 6.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20.55 Å2-0.11 Å2
2---0.28 Å2-0.36 Å2
3----0.32 Å2
Refinement stepCycle: final / Resolution: 1.86→46.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13876 0 263 1907 16046
Biso mean--39.96 27.57 -
Num. residues----1744
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01314490
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713046
X-RAY DIFFRACTIONr_angle_refined_deg1.551.66319534
X-RAY DIFFRACTIONr_angle_other_deg1.4431.60330438
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.68151756
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.6824.105760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.367152540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9471552
X-RAY DIFFRACTIONr_chiral_restr0.0790.21872
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216140
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022992
LS refinement shellResolution: 1.86→1.909 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 454 -
Rwork0.254 8434 -
all-8888 -
obs--82.83 %
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)
10.19460.0032-0.00380.1258-0.01160.20240.019-0.05820.02330.04710.01040.0536-0.0176-0.0344-0.02940.02330.00440.0240.02860.00250.0282-9.7472-2.785360.5569
20.1959-0.00010.0420.0892-0.03370.17780.0109-0.039-0.0150.02950.0058-0.0280.00990.0471-0.01670.01280.0067-0.0130.0296-0.00770.013628.831-13.129457.0472
30.1967-0.0169-0.00510.1231-0.0190.19950.02410.04650.064-0.01020.00380.0005-0.03590.0156-0.02790.01110.00240.01310.01360.01390.025514.01589.179732.3022
40.2152-0.01810.00220.11590.02120.19710.01390.024-0.0536-0.01660.00180.02870.0409-0.0129-0.01560.015-0.0015-0.01170.004-0.00390.0206-0.2338-28.140536.0954
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 454
2X-RAY DIFFRACTION2B1 - 454
3X-RAY DIFFRACTION3C1 - 454
4X-RAY DIFFRACTION4D1 - 454

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