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- PDB-5nhm: Crystal structure of apo xylose isomerase from Piromyces E2 -

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Basic information

Entry
Database: PDB / ID: 5nhm
TitleCrystal structure of apo xylose isomerase from Piromyces E2
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
ACETIC ACID / Xylose isomerase
Similarity search - Component
Biological speciesPiromyces sp.
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.67 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 1.3May 1, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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)198,98417
Polymers197,8354
Non-polymers1,14913
Water41,7412317
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32370 Å2
ΔGint-185 kcal/mol
Surface area54180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.931, 79.286, 91.106
Angle α, β, γ (deg.)115.77, 89.50, 116.73
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
11LYSLYSTYRTYRAA3 - 4363 - 436
21LYSLYSTYRTYRBB3 - 4363 - 436
12LYSLYSTYRTYRAA3 - 4363 - 436
22LYSLYSTYRTYRCC3 - 4363 - 436
13ALAALAGLNGLNAA2 - 4372 - 437
23ALAALAGLNGLNDD2 - 4372 - 437
14LYSLYSGLNGLNBB3 - 4373 - 437
24LYSLYSGLNGLNCC3 - 4373 - 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. (strain 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2317 / 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 / pH: 7 / Details: 13-15 % PEG3350, Hepes buffer pH 7

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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: Aug 25, 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: 1.67→59 Å / Num. obs: 187268 / % possible obs: 93.3 % / Redundancy: 4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.054 / Net I/σ(I): 9.1
Reflection shellResolution: 1.67→1.7 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.286 / Mean I/σ(I) obs: 3.7 / Num. unique obs: 8864 / CC1/2: 0.84 / Rpim(I) all: 0.206 / % possible all: 88.9

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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: 1.67→59 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.104 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21005 9338 5 %RANDOM
Rwork0.18372 ---
obs0.18504 177867 93.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 14.024 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å2-0 Å2
2---0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 1.67→59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13866 0 70 2317 16253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01914309
X-RAY DIFFRACTIONr_bond_other_d0.0040.0213306
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.94419269
X-RAY DIFFRACTIONr_angle_other_deg0.937330738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.69551758
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49625.169712
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.569152538
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9311552
X-RAY DIFFRACTIONr_chiral_restr0.0790.21987
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216378
X-RAY DIFFRACTIONr_gen_planes_other0.0030.023322
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_it0.4630.7427004
X-RAY DIFFRACTIONr_mcbond_other0.4610.7417001
X-RAY DIFFRACTIONr_mcangle_it0.7891.118758
X-RAY DIFFRACTIONr_mcangle_other0.7891.118759
X-RAY DIFFRACTIONr_scbond_it0.7680.8317305
X-RAY DIFFRACTIONr_scbond_other0.7680.8327306
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.2031.20810508
X-RAY DIFFRACTIONr_long_range_B_refined4.8127.7719699
X-RAY DIFFRACTIONr_long_range_B_other4.8117.77119700
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)
11A270000.05
12B270000.05
21A270020.04
22C270020.04
31A269810.06
32D269810.06
41B270470.05
42C270470.05
51B268230.06
52D268230.06
61C267990.06
62D267990.06
LS refinement shellResolution: 1.67→1.713 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 617 -
Rwork0.231 12614 -
obs--88.94 %
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)
10.26510.0674-0.05440.2249-0.04260.26640.0259-0.03930.04720.0626-0.00530.0796-0.0279-0.0495-0.02060.0217-0.00370.02580.0395-0.00340.0352-9.209-2.48560.029
20.29790.03530.00750.20870.03240.254-0.00810.0576-0.0743-0.00880.00480.02720.0569-0.02730.00330.0172-0.0156-0.00090.0352-0.01490.03140.397-27.53735.545
30.28670.04490.01640.16160.0030.30580.022-0.0433-0.01670.0302-0.0137-0.06340.0110.0717-0.00830.0108-0.0107-0.0120.04260.00250.027429.336-12.95456.648
40.32010.0156-0.08870.2029-0.01540.28720.01430.07050.1019-0.01040.0143-0.008-0.05450.0103-0.02860.0138-0.00740.00680.03360.02490.037614.9469.65532.155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 437
2X-RAY DIFFRACTION2B3 - 437
3X-RAY DIFFRACTION3C3 - 437
4X-RAY DIFFRACTION4D2 - 437

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