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- PDB-7bjz: GLUCOSE ISOMERASE S171W in H32 -

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Basic information

Entry
Database: PDB / ID: 7bjz
TitleGLUCOSE ISOMERASE S171W in H32
ComponentsXylose isomerase
KeywordsISOMERASE
Function / homology
Function and homology information


xylose isomerase / xylose isomerase activity / D-xylose metabolic process / magnesium ion binding / identical protein binding / cytoplasm
Similarity search - Function
Xylose isomerase, actinobacteria / Xylose isomerase / Xylose isomerase family profile. / Xylose isomerase-like, TIM barrel domain / Xylose isomerase-like TIM barrel / Xylose isomerase-like superfamily
Similarity search - Domain/homology
: / Xylose isomerase
Similarity search - Component
Biological speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 Å
AuthorsSleutel, M.
Funding support Belgium, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO)G0H5316N Belgium
Research Foundation - Flanders (FWO)1516215N Belgium
Citation
Journal: Nat Commun / Year: 2021
Title: Nucleation of protein mesocrystals via oriented attachment.
Authors: Van Driessche, A.E.S. / Van Gerven, N. / Joosten, R.R.M. / Ling, W.L. / Bacia, M. / Sommerdijk, N. / Sleutel, M.
#1: Journal: Biorxiv / Year: 2020
Title: Nonclassical nucleation of protein mesocrystals via oriented attachment
Authors: Van Driessche, A.E.S. / Van Gerven, N. / Joosten, R.R.M. / Sommerdijk, A.J.M. / Sleutel, M.
History
DepositionJan 14, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _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
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,9266
Polymers86,7072
Non-polymers2204
Water21612
1
A: Xylose isomerase
B: Xylose isomerase
hetero molecules

A: Xylose isomerase
B: Xylose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,85312
Polymers173,4134
Non-polymers4408
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area31980 Å2
ΔGint-162 kcal/mol
Surface area45850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.850, 132.850, 234.850
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 387
2010B1 - 387

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Components

#1: Protein Xylose isomerase


Mass: 43353.363 Da / Num. of mol.: 2
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: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: Mn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 294 K / Method: batch mode
Details: 30 mg.mL-1 50mM Hepes 7.0 100mM MgCl2 8% (w/v) PEG1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.13→55.87 Å / Num. obs: 44769 / % possible obs: 99.9 % / Redundancy: 13.5 % / CC1/2: 0.998 / Net I/σ(I): 11.2
Reflection shellResolution: 2.13→2.19 Å / Num. unique obs: 3281 / CC1/2: 0.562

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
xia2data reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9XIA

9xia


Resolution: 2.13→55.87 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.08 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.256 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2233 5 %RANDOM
Rwork0.20297 ---
obs0.2045 42530 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.006 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20.23 Å2-0 Å2
2--0.45 Å2-0 Å2
3----1.47 Å2
Refinement stepCycle: 1 / Resolution: 2.13→55.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6094 0 4 12 6110
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0136258
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175666
X-RAY DIFFRACTIONr_angle_refined_deg1.491.6458474
X-RAY DIFFRACTIONr_angle_other_deg1.2991.58313052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0345772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.66320.931408
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.7415984
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5981568
X-RAY DIFFRACTIONr_chiral_restr0.0680.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.027272
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021500
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_it3.5884.9113092
X-RAY DIFFRACTIONr_mcbond_other3.5824.913091
X-RAY DIFFRACTIONr_mcangle_it4.7687.3643864
X-RAY DIFFRACTIONr_mcangle_other4.7687.3653865
X-RAY DIFFRACTIONr_scbond_it4.085.3633164
X-RAY DIFFRACTIONr_scbond_other4.085.3653165
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.9267.8964611
X-RAY DIFFRACTIONr_long_range_B_refined7.38856.8326801
X-RAY DIFFRACTIONr_long_range_B_other7.38856.8346802
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 12687 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.03 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.13→2.185 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 164 -
Rwork0.303 3113 -
obs--99.97 %

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