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

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Basic information

Entry
Database: PDB / ID: 5nhc
TitleCrystal structure of xylose isomerase from Piromyces E2 in complex with two Co2+ ions and xylulose
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
: / 4-HYDROXYPROLINE / D-XYLULOSE / Xylose isomerase
Similarity search - Component
Biological speciesPiromyces sp. E2 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.93 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 1.4Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 1.5May 1, 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 / pdbx_struct_conn_angle / 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 / _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 / _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)199,43120
Polymers197,8354
Non-polymers1,59716
Water39,3632185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32100 Å2
ΔGint-210 kcal/mol
Surface area54410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.249, 79.332, 91.359
Angle α, β, γ (deg.)115.72, 89.39, 116.87
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. 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
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Co
#3: Sugar
ChemComp-XUL / D-XYLULOSE


Type: D-saccharide / Mass: 150.130 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
#4: Chemical
ChemComp-HYP / 4-HYDROXYPROLINE / HYDROXYPROLINE


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H9NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2185 / 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 / Details: 13-15 % PEG3350, 10 mM CoCl2, 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: Mar 12, 2015
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: 1.93→47 Å / Num. obs: 122918 / % possible obs: 94.3 % / Redundancy: 2.8 % / CC1/2: 0.991 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.071 / Net I/σ(I): 10.9
Reflection shellResolution: 1.93→1.97 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.293 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 5065 / CC1/2: 0.75 / Rpim(I) all: 0.275 / % possible all: 79.3

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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: 1.93→47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 6.042 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.176 / ESU R Free: 0.14 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18784 6115 5 %RANDOM
Rwork0.15668 ---
obs0.15823 116776 94.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.459 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20.01 Å20.03 Å2
2--0.03 Å20.01 Å2
3----0.04 Å2
Refinement stepCycle: 1 / Resolution: 1.93→47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13866 0 84 2185 16135
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01914385
X-RAY DIFFRACTIONr_bond_other_d0.0050.0213351
X-RAY DIFFRACTIONr_angle_refined_deg1.381.94719397
X-RAY DIFFRACTIONr_angle_other_deg1.011330860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75251770
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.30625.216719
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02152548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8861552
X-RAY DIFFRACTIONr_chiral_restr0.0860.21999
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0216534
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023330
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_it0.5460.677044
X-RAY DIFFRACTIONr_mcbond_other0.5460.677044
X-RAY DIFFRACTIONr_mcangle_it0.9290.9988814
X-RAY DIFFRACTIONr_mcangle_other0.9290.9998815
X-RAY DIFFRACTIONr_scbond_it0.9530.7697341
X-RAY DIFFRACTIONr_scbond_other0.9530.777342
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.5561.1110580
X-RAY DIFFRACTIONr_long_range_B_refined4.736.76819393
X-RAY DIFFRACTIONr_long_range_B_other4.2635.90818019
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)
11A268170.05
12B268170.05
21A268720.05
22C268720.05
31A269820.05
32D269820.05
41B270080.04
42C270080.04
51B267720.05
52D267720.05
61C267660.05
62D267660.05
LS refinement shellResolution: 1.933→1.983 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 404 -
Rwork0.215 7684 -
obs--83.48 %
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)
10.2060.0304-0.0450.2251-0.06180.32460.0197-0.04190.03660.06170.00750.0548-0.0273-0.0415-0.02720.030.00680.01870.0252-0.00780.0231-9.073-2.49660.278
20.27720.00230.04750.21720.0210.2650.00020.0513-0.06-0.02210.01640.01910.0566-0.019-0.01660.027-0.0067-0.00740.0172-0.01410.02430.523-27.47835.694
30.20580.01830.01460.1629-0.00360.30750.0125-0.0367-0.01110.04140.0009-0.04540.02070.06-0.01340.01980.0063-0.01890.0277-0.00580.018829.544-12.81756.928
40.2574-0.0153-0.04340.1672-0.0440.32150.01620.05790.0684-0.00220.0112-0.0075-0.04810.0017-0.02740.01930.0010.00280.01660.01160.025815.0879.75832.393
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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