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- PDB-5nh4: Crystal structure of xylose isomerase from Piromyces E2 in comple... -

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Basic information

Entry
Database: PDB / ID: 5nh4
TitleCrystal structure of xylose isomerase from Piromyces E2 in complex with one Mg2+ ions and glycerol
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
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 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _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)199,23322
Polymers197,8354
Non-polymers1,39818
Water29,5091638
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33450 Å2
ΔGint-204 kcal/mol
Surface area54420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.606, 79.365, 92.096
Angle α, β, γ (deg.)115.50, 90.15, 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
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1638 / 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: 13-16 % PEG 3350, 0.01 M MgCl2, 0,1 M Hepes 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: Sep 4, 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: 1.8→46.6 Å / Num. obs: 149911 / % possible obs: 93.4 % / Redundancy: 4 % / Biso Wilson estimate: 6.5 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.089 / Rpim(I) all: 0.064 / Net I/σ(I): 8.4
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 6403 / CC1/2: 0.688 / Rpim(I) all: 0.26 / % possible all: 80.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata scaling
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NH5

5nh5


Resolution: 1.8→46.46 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.987 / SU ML: 0.114 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.142 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22944 7495 5 %RANDOM
Rwork0.19412 ---
obs0.19588 142387 93.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 18.034 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å2-0.05 Å2-0.02 Å2
2--0.03 Å20.01 Å2
3---0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.8→46.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13876 0 85 1638 15599
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01914279
X-RAY DIFFRACTIONr_bond_other_d0.0070.0213310
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.94419213
X-RAY DIFFRACTIONr_angle_other_deg1.123330738
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.06751748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64225.141708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.695152532
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1851552
X-RAY DIFFRACTIONr_chiral_restr0.0940.21986
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216284
X-RAY DIFFRACTIONr_gen_planes_other0.0060.023312
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_it0.7080.9616980
X-RAY DIFFRACTIONr_mcbond_other0.7070.9616979
X-RAY DIFFRACTIONr_mcangle_it1.1341.4388720
X-RAY DIFFRACTIONr_mcangle_other1.1351.4388721
X-RAY DIFFRACTIONr_scbond_it1.1281.0887299
X-RAY DIFFRACTIONr_scbond_other1.1281.0897299
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7541.57710490
X-RAY DIFFRACTIONr_long_range_B_refined4.5848.92418422
X-RAY DIFFRACTIONr_long_range_B_other4.5848.92418422
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)
11A269030.05
12B269030.05
21A268510.06
22C268510.06
31A268520.06
32D268520.06
41B268820.06
42C268820.06
51B269060.06
52D269060.06
61C269830.05
62D269830.05
LS refinement shellResolution: 1.802→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 499 -
Rwork0.299 9407 -
obs--83.62 %
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)
10.45520.04220.01650.4429-0.06380.31220.0036-0.10410.05250.13430.02940.1388-0.0211-0.0552-0.0330.06180.02470.04080.0440.00150.0478-10.215-2.43760.856
20.5123-0.05430.00150.42080.03010.27880.0030.0818-0.1476-0.03950.00930.05730.0738-0.0295-0.01220.04-0.007-0.01250.0179-0.02050.0496-0.806-27.81436.549
30.46650.01160.0150.38340.01540.3396-0.0091-0.1185-0.03760.10150.0117-0.11550.02290.0772-0.00260.04090.0229-0.03260.06150.00290.039628.472-12.76657.252
40.5113-0.0771-0.07450.3540.00850.29820.00750.08420.1585-0.03790.0139-0.0367-0.04690.0144-0.02140.03820.00340.00490.0220.02580.049713.6119.50532.582
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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