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- PDB-5nha: Crystal structure of xylose isomerase from Piromyces sp. E2 in co... -

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Basic information

Entry
Database: PDB / ID: 5nha
TitleCrystal structure of xylose isomerase from Piromyces sp. E2 in complex with two Mn2+ ions and sorbitol
ComponentsXylose isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


D-xylose catabolic process to ethanol / xylose isomerase / xylose isomerase activity / metal ion binding
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
: / sorbitol / Xylose isomerase
Similarity search - Component
Biological speciesPiromyces sp. E2 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsRozeboom, H.J. / Janssen, D.B.
CitationJournal: Biochemistry / Year: 2017
Title: Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography.
Authors: Lee, M. / Rozeboom, H.J. / de Waal, P.P. / de Jong, R.M. / Dudek, H.M. / Janssen, D.B.
History
DepositionMar 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.name
Revision 1.2Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Aug 29, 2018Group: Data collection / Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Jul 29, 2020Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._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 1.5May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)199,38720
Polymers197,8354
Non-polymers1,55216
Water35,7061982
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33090 Å2
ΔGint-206 kcal/mol
Surface area54670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.961, 79.407, 91.284
Angle α, β, γ (deg.)115.67, 89.44, 116.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 2 - 437 / Label seq-ID: 2 - 437

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#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. E2 (fungus) / Gene: xylA / Plasmid: pBAD
Details (production host): pBR322 Ori and ampicillin resistance gene
Production host: Escherichia coli K-12 (bacteria) / Variant (production host): TOP10 or Neb10-beta / References: UniProt: Q9P8C9, xylose isomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#3: Sugar
ChemComp-SOR / sorbitol / D-sorbitol / D-glucitol


Type: D-saccharide / Mass: 182.172 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H14O6
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1982 / 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: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 13-15 % PEG3350, 10 mM MnCl2, 0.1 M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 9, 2015
RadiationMonochromator: Helios MX Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→46.9 Å / Num. obs: 151276 / % possible obs: 93.6 % / Redundancy: 3.9 % / CC1/2: 0.995 / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.068 / Net I/σ(I): 11.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 6329 / CC1/2: 0.583 / Rpim(I) all: 0.378 / % possible all: 79.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1200004044

Resolution: 1.8→46.9 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.253 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.113 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18141 7557 5 %RANDOM
Rwork0.15544 ---
obs0.15674 143710 93.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.707 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.03 Å20.06 Å2
2--0.03 Å20.03 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→46.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13876 0 76 1984 15936
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914334
X-RAY DIFFRACTIONr_bond_other_d0.0020.0212959
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.94519311
X-RAY DIFFRACTIONr_angle_other_deg0.954330209
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74351762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8225.141708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.917152551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1511552
X-RAY DIFFRACTIONr_chiral_restr0.0950.22000
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022942
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5270.8287015
X-RAY DIFFRACTIONr_mcbond_other0.5260.8287014
X-RAY DIFFRACTIONr_mcangle_it0.9251.2388776
X-RAY DIFFRACTIONr_mcangle_other0.9251.2398777
X-RAY DIFFRACTIONr_scbond_it0.810.9267319
X-RAY DIFFRACTIONr_scbond_other0.7830.9147303
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2791.33110508
X-RAY DIFFRACTIONr_long_range_B_refined4.03110.90717615
X-RAY DIFFRACTIONr_long_range_B_other3.75710.17317054
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A300120.04
12B300120.04
21A298920.04
22C298920.04
31A300560.03
32D300560.03
41B300300.04
42C300300.04
51B299620.04
52D299620.04
61C300100.04
62D300100.04
LS refinement shellResolution: 1.796→1.843 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 476 -
Rwork0.278 9407 -
obs--82.86 %
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)
10.2257-0.0359-0.01760.2494-0.02760.3719-0.0286-0.0710.02260.1380.04410.0549-0.0277-0.0669-0.01550.09750.04270.0240.0481-0.00160.0179-9.368-2.50260.228
20.3602-0.11160.06730.33550.0120.31640.01080.0473-0.09350.02060.01790.05140.0736-0.0043-0.02870.03570.01-0.01280.0171-0.01480.03150.315-27.67435.75
30.2298-0.08010.03810.2625-0.00340.3942-0.0261-0.04720.010.11620.0352-0.08290.02020.0737-0.00910.06790.0343-0.04790.0456-0.02090.034229.232-12.93856.984
40.3287-0.1206-0.01490.2938-0.07130.30340.00620.05280.08790.0230.0086-0.0449-0.06130.0121-0.01480.02290.0075-0.00340.020.00550.034414.7399.60632.288
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 437
2X-RAY DIFFRACTION2B2 - 437
3X-RAY DIFFRACTION3C2 - 437
4X-RAY DIFFRACTION4D2 - 437

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