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

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Basic information

Entry
Database: PDB / ID: 5nhb
TitleCrystal structure of xylose isomerase from Piromyces E2 in complex with two Fe2+ ions
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
: / Xylose isomerase
Similarity search - Component
Biological speciesPiromyces sp. E2 (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.4May 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 / 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)198,57015
Polymers197,8354
Non-polymers73511
Water8,593477
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31460 Å2
ΔGint-271 kcal/mol
Surface area56330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.539, 79.510, 92.230
Angle α, β, γ (deg.)115.57, 89.96, 116.69
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
11ALAALAGLNGLNAA2 - 4372 - 437
21ALAALAGLNGLNBB2 - 4372 - 437
12LYSLYSTYRTYRAA3 - 4363 - 436
22LYSLYSTYRTYRCC3 - 4363 - 436
13LYSLYSTYRTYRAA3 - 4363 - 436
23LYSLYSTYRTYRDD3 - 4363 - 436
14LYSLYSTYRTYRBB3 - 4363 - 436
24LYSLYSTYRTYRCC3 - 4363 - 436
15LYSLYSTYRTYRBB3 - 4363 - 436
25LYSLYSTYRTYRDD3 - 4363 - 436
16LYSLYSGLNGLNCC3 - 4373 - 437
26LYSLYSGLNGLNDD3 - 4373 - 437

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-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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, 0.1 M FeSO4, 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 7, 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: 2.4→45.3 Å / Num. obs: 59313 / % possible obs: 85.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 4.2 Å2 / CC1/2: 0.963 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.127 / Net I/σ(I): 5.9
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4141 / CC1/2: 0.67 / Rpim(I) all: 0.386 / % possible all: 81.1

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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: 2.4→45.3 Å / Cor.coef. Fo:Fc: 0.888 / Cor.coef. Fo:Fc free: 0.856 / SU B: 25.295 / SU ML: 0.297 / Cross valid method: THROUGHOUT / ESU R Free: 0.366 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28185 2908 4.9 %RANDOM
Rwork0.24466 ---
obs0.24648 56358 85.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.773 Å2
Baniso -1Baniso -2Baniso -3
1--1.48 Å2-0.56 Å20.66 Å2
2--0.13 Å20.46 Å2
3---0.4 Å2
Refinement stepCycle: 1 / Resolution: 2.4→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13866 0 23 477 14366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01914190
X-RAY DIFFRACTIONr_bond_other_d0.0050.0213202
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.94119108
X-RAY DIFFRACTIONr_angle_other_deg1.061330482
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18951738
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51225.141708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.701152520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6931552
X-RAY DIFFRACTIONr_chiral_restr0.0780.21969
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216242
X-RAY DIFFRACTIONr_gen_planes_other0.0040.023306
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_it0.0270.2016964
X-RAY DIFFRACTIONr_mcbond_other0.0260.2016963
X-RAY DIFFRACTIONr_mcangle_it0.050.3018698
X-RAY DIFFRACTIONr_mcangle_other0.050.3018699
X-RAY DIFFRACTIONr_scbond_it0.1790.2067226
X-RAY DIFFRACTIONr_scbond_other0.0110.2017214
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.0250.30210392
X-RAY DIFFRACTIONr_long_range_B_refined2.5351.75216489
X-RAY DIFFRACTIONr_long_range_B_other2.4761.716420
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)
11A261430.05
12B261430.05
21A259210.06
22C259210.06
31A258510.06
32D258510.06
41B260020.05
42C260020.05
51B257730.07
52D257730.07
61C260970.05
62D260970.05
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.348 212 -
Rwork0.33 3934 -
obs--81.09 %
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)
10.5956-0.1585-0.08131.09510.04720.6534-0.0589-0.12730.00190.35780.09760.1954-0.0233-0.0952-0.03870.55530.3004-0.04170.2064-0.04520.0659-9.414-2.59560.771
20.5905-0.2850.02930.94720.08740.39840.01730.1307-0.2022-0.04110.01270.15790.0871-0.0484-0.030.43810.2194-0.16740.1785-0.12040.13160.022-27.86936.171
30.6994-0.1097-0.00830.8533-0.01920.4965-0.0404-0.14370.02710.30560.0749-0.22110.03490.191-0.03450.50670.2738-0.23340.2411-0.12260.118229.514-13.01657.25
40.8751-0.3747-0.15110.7483-0.11790.69670.06890.14410.1585-0.0783-0.0393-0.1122-0.12870.0615-0.02960.4310.223-0.10910.1776-0.05450.074614.8839.54232.593
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 437
2X-RAY DIFFRACTION2B2 - 437
3X-RAY DIFFRACTION3C3 - 437
4X-RAY DIFFRACTION4D3 - 437

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