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- PDB-5nh6: Crystal structure of xylose isomerase from Piromyces E2 Complexed... -

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Basic information

Entry
Database: PDB / ID: 5nh6
TitleCrystal structure of xylose isomerase from Piromyces E2 Complexed with one Mg2+ ion and xylitol
ComponentsXylose isomerase
KeywordsISOMERASE / TIM-barrel
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
Xylitol / Xylose isomerase
Similarity search - Component
Biological speciesPiromyces sp. E2 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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)198,82915
Polymers197,8354
Non-polymers99411
Water33,0761836
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31930 Å2
ΔGint-204 kcal/mol
Surface area54460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.820, 79.340, 91.800
Angle α, β, γ (deg.)115.42, 90.18, 116.72
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: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAGLNGLNAA2 - 4372 - 437
21ALAALAGLNGLNBB2 - 4372 - 437
12ALAALAGLNGLNAA2 - 4372 - 437
22ALAALAGLNGLNCC2 - 4372 - 437
13LYSLYSTYRTYRAA3 - 4363 - 436
23LYSLYSTYRTYRDD3 - 4363 - 436
14ALAALAGLNGLNBB2 - 4372 - 437
24ALAALAGLNGLNCC2 - 4372 - 437
15LYSLYSTYRTYRBB3 - 4363 - 436
25LYSLYSTYRTYRDD3 - 4363 - 436
16LYSLYSTYRTYRCC3 - 4363 - 436
26LYSLYSTYRTYRDD3 - 4363 - 436

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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Sugar
ChemComp-XYL / Xylitol / D-Xylitol


Type: D-saccharide / Mass: 152.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H12O5
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1836 / 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 % PEG 3350, 10 mM MgCl2, 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: Sep 24, 2014
RadiationMonochromator: Helios MX mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→36.1 Å / Num. obs: 163788 / % possible obs: 93.3 % / Redundancy: 4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.047 / Net I/σ(I): 14
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 4 % / Rmerge(I) obs: 0.431 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 7762 / CC1/2: 0.792 / Rpim(I) all: 0.316 / % possible all: 79.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: D_1200004044

Resolution: 1.75→36.1 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / SU B: 3.876 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.093 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16079 8165 5 %RANDOM
Rwork0.13983 ---
obs0.14087 155574 93.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 17.719 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.02 Å2-0 Å2
2--0.01 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.75→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13871 0 59 1836 15766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914261
X-RAY DIFFRACTIONr_bond_other_d0.0050.0213279
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.94419204
X-RAY DIFFRACTIONr_angle_other_deg1.046330673
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6351749
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.6825.141708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.102152535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.031552
X-RAY DIFFRACTIONr_chiral_restr0.0810.21987
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216284
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023312
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_it0.6960.9766978
X-RAY DIFFRACTIONr_mcbond_other0.6960.9766977
X-RAY DIFFRACTIONr_mcangle_it1.151.468718
X-RAY DIFFRACTIONr_mcangle_other1.151.468719
X-RAY DIFFRACTIONr_scbond_it1.3431.1317283
X-RAY DIFFRACTIONr_scbond_other1.3291.1267271
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1521.62210464
X-RAY DIFFRACTIONr_long_range_B_refined5.1779.38418698
X-RAY DIFFRACTIONr_long_range_B_other4.7678.48417579
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)
11A267580.06
12B267580.06
21A268590.05
22C268590.05
31A266420.06
32D266420.06
41B266780.07
42C266780.07
51B267410.05
52D267410.05
61C266760.06
62D266760.06
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 561 -
Rwork0.255 11066 -
obs--89.25 %
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)
10.2529-0.11550.03940.40330.0040.3412-0.0444-0.0769-0.02030.15270.05640.0925-0.0107-0.0603-0.0120.08090.04160.03990.05090.01610.023-9.781-2.42860.517
20.3654-0.20550.00020.36010.0110.32730.02330.05180.095-0.0057-0.0031-0.0857-0.0590.0292-0.02020.020.00630.00920.02060.0090.032114.1459.24732.229
30.348-0.19270.04620.4189-0.00640.29430.01420.0276-0.10370.01080.0080.10.0736-0.0125-0.02210.03290.007-0.00910.0117-0.0070.0389-0.396-27.96436.276
40.2386-0.0891-0.00110.33880.05250.3442-0.0343-0.04850.02730.12330.0541-0.09640.03720.0871-0.01980.06270.0434-0.04530.0567-0.02710.034128.856-12.90257.021
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 DIFFRACTION4D3 - 437

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