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- PDB-4lnc: Neutron structure of the cyclic glucose bound Xylose Isomerase E1... -

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Basic information

Entry
Database: PDB / ID: 4lnc
TitleNeutron structure of the cyclic glucose bound Xylose Isomerase E186Q mutant
ComponentsXylose isomerase
KeywordsISOMERASE / MUTANT ENZYME / METALLOENZYME / TWO METAL BINDING SITES
Function / homology
Function and homology information


xylose isomerase / D-xylose metabolic process / xylose isomerase activity / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / 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
DEUTERATED WATER / alpha-D-glucopyranose / : / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 2.19 Å
AuthorsMunshi, P. / Meilleur, F. / Myles, D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Neutron structure of the cyclic glucose-bound xylose isomerase E186Q mutant.
Authors: Munshi, P. / Snell, E.H. / van der Woerd, M.J. / Judge, R.A. / Myles, D.A. / Ren, Z. / Meilleur, F.
History
DepositionJul 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2014Group: Database references
Revision 1.2Apr 25, 2018Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.type / _diffrn_source.pdbx_synchrotron_site ..._diffrn_detector.type / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.3Jun 13, 2018Group: Data collection / Experimental preparation
Category: diffrn / diffrn_detector ...diffrn / diffrn_detector / diffrn_radiation / diffrn_radiation_wavelength / diffrn_source / exptl / exptl_crystal / exptl_crystal_grow
Revision 1.4Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5105
Polymers43,1951
Non-polymers3144
Water5,206289
1
A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules

A: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,03820
Polymers172,7814
Non-polymers1,25716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_656-x+1,y,-z+11
crystal symmetry operation4_566x,-y+1,-z+11
Buried area31430 Å2
ΔGint-237 kcal/mol
Surface area45580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.970, 99.520, 102.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-722-

DOD

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Components

#1: Protein Xylose isomerase /


Mass: 43195.277 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: Escherichia coli (E. coli) / References: UniProt: P24300, xylose isomerase
#2: Sugar ChemComp-GLC / alpha-D-glucopyranose / alpha-D-glucose / D-glucose / glucose / Glucose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-glucopyranoseCOMMON NAMEGMML 1.0
a-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-DOD / water / Heavy water


Mass: 18.015 Da / Num. of mol.: 289 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.84 %
Crystal growTemperature: 295 K / pH: 7.7
Details: Large crystals were grown in 1.5 ml Eppendorf tubes with 15% ammonium sulfate, 72 mg/ml D-xylose isomerase at ph 7.7, Batch method, temperature 295K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: ILL / Beamline: H142 / Wavelength: 3.6-5.0 / Wavelength: 3.6-5.0
DetectorType: EMBL PROTOTYPE LADI-I / Detector: IMAGE PLATE / Date: Jun 4, 2000 / Details: Ni/Ti MULTILAYER
RadiationMonochromator: Ni/Ti MULTILAYER / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
13.61
251
Reflection

Entry-ID: 4LNC

Resolution (Å)Num. obs% possible obs (%)Redundancy (%)Rmerge(I) obsRsym valueDiffraction-IDNet I/σ(I)
2.17-41.123649936.60.2760.276111.7
1.83-253531783.22.40.1730.17324.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
2.17-2.292.50.2143.50.214166.7
1.83-1.922.10.243.40.24264.6

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Processing

Software
NameVersionClassification
Quasi-LaueDiffractometerdata collection
PHENIX(phenix.refine: 1.8_1069)refinement
LAUEGENdata reduction
SCALAdata scaling
PHENIXphasing
Refinement

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Stereochemistry target values: ML / Solvent model: FLAT BULK SOLVENT MODEL

Resolution (Å)Refine-IDRfactor RfreeRfactor RworkRfactor obsNum. reflection RfreeNum. reflection obs% reflection Rfree (%)% reflection obs (%)Diffraction-IDBiso max (Å2)Biso mean (Å2)Biso min (Å2)Num. reflection Rworkσ(F)
2.19-41.1NEUTRON DIFFRACTION0.3220.2840.2882357236289.9893.11
1.84-14.54X-RAY DIFFRACTION0.2090.150.15635183515910.0183.2261.4522.68267.85316411.35
Refinement stepCycle: LAST / Resolution: 2.19→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 15 289 3331
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0227253
NEUTRON DIFFRACTIONf_angle_d2.13612339
NEUTRON DIFFRACTIONf_dihedral_angle_d19.2471871
NEUTRON DIFFRACTIONf_chiral_restr0.156440
NEUTRON DIFFRACTIONf_plane_restr0.0131387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.19-2.22960.4403530.382532NEUTRON DIFFRACTION40
2.2296-2.2780.41131240.39611054NEUTRON DIFFRACTION81
2.278-2.3310.38111380.36771189NEUTRON DIFFRACTION90
2.331-2.38930.38571340.35211256NEUTRON DIFFRACTION93
2.3893-2.45390.3771310.33971274NEUTRON DIFFRACTION96
2.4539-2.52610.38061470.34171289NEUTRON DIFFRACTION97
2.5261-2.60760.37991500.3291289NEUTRON DIFFRACTION98
2.6076-2.70080.32891320.3141318NEUTRON DIFFRACTION98
2.7008-2.80890.34161600.30541292NEUTRON DIFFRACTION98
2.8089-2.93670.32561440.30231343NEUTRON DIFFRACTION98
2.9367-3.09150.32621540.27811302NEUTRON DIFFRACTION99
3.0915-3.28510.30041420.26491340NEUTRON DIFFRACTION99
3.2851-3.53870.29461490.23781319NEUTRON DIFFRACTION99
3.5387-3.89450.27431480.21091336NEUTRON DIFFRACTION98
3.8945-4.45750.19011480.17651357NEUTRON DIFFRACTION99
4.4575-5.61370.23341440.17631359NEUTRON DIFFRACTION99
5.6137-41.11260.21931590.16881422NEUTRON DIFFRACTION98
1.8372-1.86230.2532780.1735604X-RAY DIFFRACTION41
1.8623-1.88890.26491500.18251291X-RAY DIFFRACTION87
1.8889-1.9170.24141450.17371362X-RAY DIFFRACTION90
1.917-1.94690.23991640.15941375X-RAY DIFFRACTION91
1.9469-1.97870.25211450.16191335X-RAY DIFFRACTION90
1.9787-2.01280.23921430.15951345X-RAY DIFFRACTION90
2.0128-2.04930.21811440.14931360X-RAY DIFFRACTION89
2.0493-2.08860.23131560.14421331X-RAY DIFFRACTION89
2.0886-2.13110.22381340.1421357X-RAY DIFFRACTION89
2.1311-2.17730.19261550.14791315X-RAY DIFFRACTION88
2.1773-2.22770.20981490.15641319X-RAY DIFFRACTION87
2.2277-2.28320.20661510.1561322X-RAY DIFFRACTION88
2.2832-2.34470.21361500.1581288X-RAY DIFFRACTION87
2.3447-2.41340.20981240.14881332X-RAY DIFFRACTION86
2.4134-2.49090.24781460.16051306X-RAY DIFFRACTION85
2.4909-2.57950.22791490.17511292X-RAY DIFFRACTION86
2.5795-2.68220.25281480.17221312X-RAY DIFFRACTION85
2.6822-2.80340.23481440.16441250X-RAY DIFFRACTION84
2.8034-2.95010.21341430.17221301X-RAY DIFFRACTION84
2.9501-3.13320.23951360.17241255X-RAY DIFFRACTION83
3.1332-3.37230.22661430.15391251X-RAY DIFFRACTION82
3.3723-3.70660.18561440.13551245X-RAY DIFFRACTION81
3.7066-4.23130.13061310.11391227X-RAY DIFFRACTION79
4.2313-5.28810.16151330.10761207X-RAY DIFFRACTION77
5.2881-14.54540.18841130.16561059X-RAY DIFFRACTION65

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