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- PDB-5nh7: Crystal structure of xylose isomerase from Piromyces E2 in comple... -

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Basic information

Entry
Database: PDB / ID: 5nh7
TitleCrystal structure of xylose isomerase from Piromyces E2 in complex with two Mg2+ ions and 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
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: 1.9 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: Atomic model / Data collection ...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 / 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 / _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

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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)201,40437
Polymers197,8354
Non-polymers3,56933
Water31,9771775
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37890 Å2
ΔGint-295 kcal/mol
Surface area53720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.600, 79.280, 91.969
Angle α, β, γ (deg.)115.40, 89.91, 117.13
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:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 436
2010B3 - 436
1020A2 - 437
2020C2 - 437
1030A2 - 437
2030D2 - 437
1040B3 - 436
2040C3 - 436
1050B3 - 436
2050D3 - 436
1060C2 - 437
2060D2 - 437

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 / 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

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Sugars , 3 types, 18 molecules

#3: Sugar
ChemComp-XLS / D-xylose / 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 / Xylose


Type: D-saccharide, beta linking / Mass: 150.130 Da / Num. of mol.: 6
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 / Xylose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 8
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, 1790 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#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.: 1775 / 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 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: Nov 3, 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: 1.9→39.5 Å / Num. obs: 125669 / % possible obs: 92 % / Redundancy: 2 % / Biso Wilson estimate: 1.6 Å2 / CC1/2: 0.985 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.089 / Net I/σ(I): 6.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 2 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2 / Num. unique obs: 5765 / CC1/2: 0.746 / Rpim(I) all: 0.338 / % possible all: 84.7

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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: 1.9→39.5 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.946 / SU B: 6.114 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17572 6287 5 %RANDOM
Rwork0.15266 ---
obs0.15381 119324 91.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å2-0.02 Å2
2--0.03 Å20.01 Å2
3---0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.9→39.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13871 0 223 1775 15869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914487
X-RAY DIFFRACTIONr_bond_other_d0.0050.0213401
X-RAY DIFFRACTIONr_angle_refined_deg1.3221.95719539
X-RAY DIFFRACTIONr_angle_other_deg0.988330993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72451763
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.74325.196716
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.258152544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5861552
X-RAY DIFFRACTIONr_chiral_restr0.0790.22054
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216453
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023327
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_it0.5980.8097016
X-RAY DIFFRACTIONr_mcbond_other0.5970.8097015
X-RAY DIFFRACTIONr_mcangle_it1.0211.218779
X-RAY DIFFRACTIONr_mcangle_other1.0211.218780
X-RAY DIFFRACTIONr_scbond_it1.0680.9787471
X-RAY DIFFRACTIONr_scbond_other1.0080.9647443
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.631.39610715
X-RAY DIFFRACTIONr_long_range_B_refined5.0497.87218947
X-RAY DIFFRACTIONr_long_range_B_other4.5777.09617881
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)
11A268700.04
12B268700.04
21A269080.06
22C269080.06
31A269330.05
32D269330.05
41B266930.05
42C266930.05
51B268330.05
52D268330.05
61C268580.06
62D268580.06
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.255 455 -
Rwork0.247 8163 -
obs--84.97 %
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)
10.3467-0.0380.00870.36610.00990.36670.0102-0.08490.01960.09690.02130.0784-0.0319-0.0637-0.03150.04530.01340.03180.04750.0040.0252-9.669-2.6260.634
20.3442-0.03370.05740.27050.04120.4157-0.0006-0.0625-0.01240.07250.0292-0.05860.02820.0835-0.02860.02650.0172-0.01790.046-0.00920.015228.996-12.79757.033
30.4344-0.0944-0.07210.30320.01860.37660.02510.07920.1029-0.01820.012-0.0142-0.07710.0261-0.0370.03060.00390.0150.0330.02230.028214.1429.3732.371
40.4112-0.0960.05920.32460.01560.37130.0290.0513-0.1009-0.0215-0.00660.05420.0713-0.0145-0.02240.02950.0006-0.01150.0174-0.01040.0284-0.239-27.9136.301
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 437
2X-RAY DIFFRACTION2B3 - 437
3X-RAY DIFFRACTION3C2 - 437
4X-RAY DIFFRACTION4D2 - 437

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