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Basic information

Entry
Database: PDB / ID: 5nhe
TitleCrystal structure of xylose isomerase from Piromyces E2 in complex with two Cd2+ ions and xylose
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
: / D-xylose / beta-D-xylopyranose / alpha-D-xylopyranose / Xylose isomerase
Similarity search - Component
Biological speciesPiromyces sp. E2 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 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 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 2.1May 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)201,90536
Polymers197,8354
Non-polymers4,07032
Water33,0941837
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37440 Å2
ΔGint-315 kcal/mol
Surface area53680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.640, 79.370, 92.010
Angle α, β, γ (deg.)115.37, 89.97, 117.16
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

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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. E2 (fungus) / Gene: xylA
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

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Sugars , 3 types, 16 molecules

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


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
#4: Sugar
ChemComp-XYP / beta-D-xylopyranose / beta-D-xylose / D-xylose / xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 8
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


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 6
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, 1853 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cd
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1837 / 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, 0.1 mM CdCl2, 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: Oct 27, 2014
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: 1.86→45.1 Å / Num. obs: 128136 / % possible obs: 87.8 % / Redundancy: 2 % / Biso Wilson estimate: 9.4 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.059 / Net I/σ(I): 9.4
Reflection shellResolution: 1.86→1.89 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 2 / Num. unique obs: 4052 / CC1/2: 0.644 / Rpim(I) all: 0.361 / % possible all: 55.9

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Processing

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

Resolution: 1.86→45.1 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.083 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.118 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16474 6456 5 %RANDOM
Rwork0.1404 ---
obs0.14163 121647 88.25 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 17.651 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å20.06 Å2
2--0.01 Å20.04 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.86→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13876 0 208 1837 15921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01914462
X-RAY DIFFRACTIONr_bond_other_d0.0050.0213411
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.95519497
X-RAY DIFFRACTIONr_angle_other_deg1.023331007
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.78151762
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5525.141708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.683152547
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5691552
X-RAY DIFFRACTIONr_chiral_restr0.0830.22052
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216388
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023328
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_it0.7170.9727015
X-RAY DIFFRACTIONr_mcbond_other0.7160.9717014
X-RAY DIFFRACTIONr_mcangle_it1.1871.4528776
X-RAY DIFFRACTIONr_mcangle_other1.1871.4528777
X-RAY DIFFRACTIONr_scbond_it1.4621.1937447
X-RAY DIFFRACTIONr_scbond_other1.3851.1777415
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.1821.69810670
X-RAY DIFFRACTIONr_long_range_B_refined5.3549.42219041
X-RAY DIFFRACTIONr_long_range_B_other4.9778.62317949
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)
11A269370.06
12B269370.06
21A268370.06
22C268370.06
31A267720.06
32D267720.06
41B269320.06
42C269320.06
51B268180.06
52D268180.06
61C268960.05
62D268960.05
LS refinement shellResolution: 1.863→1.911 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 393 -
Rwork0.273 7245 -
obs--71.04 %
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)
10.2996-0.07660.01440.3832-0.00590.3536-0.0138-0.0804-0.00020.10340.03740.0816-0.0253-0.0675-0.02370.04710.02890.02280.04890.00690.0199-9.753-2.66760.649
20.3383-0.16320.02650.33510.02510.32570.03360.0345-0.0978-0.0268-0.01040.07320.0807-0.0222-0.02330.04260.0077-0.02550.0179-0.01310.0372-0.257-28.04636.369
30.3275-0.07340.04360.2830.02260.3646-0.0195-0.06460.00220.0820.0387-0.06490.02050.0853-0.01920.04770.0341-0.03310.0583-0.02050.024128.93-12.957.136
40.3705-0.1353-0.03250.31140.04120.37180.02420.06420.1006-0.0240.0011-0.0419-0.07530.0246-0.02530.03360.01060.00670.0260.01350.028914.0639.25132.355
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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