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- PDB-5i7g: Metal free Glucose Isomerase collected at room temperature using ... -

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Basic information

Entry
Database: PDB / ID: 5i7g
TitleMetal free Glucose Isomerase collected at room temperature using the HC1b humidity controller
ComponentsXylose isomerase
KeywordsISOMERASE / Room temperature Metal-free
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. / 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 speciesStreptomyces rubiginosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsSandy, J.
CitationJournal: To Be Published
Title: Metal free Glucose Isomerase collected at room temperature using the HC1b humidity controller
Authors: Sandy, J.
History
DepositionFeb 17, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 24, 2016Provider: repository / Type: Initial release
Revision 2.0May 8, 2024Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Xylose isomerase


Theoretical massNumber of molelcules
Total (without water)43,2831
Polymers43,2831
Non-polymers00
Water5,314295
1
A: Xylose isomerase

A: Xylose isomerase

A: Xylose isomerase

A: Xylose isomerase


Theoretical massNumber of molelcules
Total (without water)173,1334
Polymers173,1334
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_557-x,y,-z+21
crystal symmetry operation4_557x,-y,-z+21
Buried area30120 Å2
ΔGint-110 kcal/mol
Surface area45600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.815, 99.698, 102.755
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-426-

HOH

21A-652-

HOH

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 2.78 Å3/Da / Density % sol: 55.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 10 mM Hepes pH 7.5, 1.6 M Ammonium Sulphate

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Data collection

DiffractionMean temperature: 295 K
Ambient temp details: Collected using HC1b humidity controller
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 17, 2014
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.21→69.28 Å / Num. obs: 145645 / % possible obs: 99.8 % / Redundancy: 6.5 % / CC1/2: 0.992 / Rmerge(I) obs: 0.121 / Net I/σ(I): 6
Reflection shellResolution: 1.21→1.24 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.68 / Mean I/σ(I) obs: 1 / % possible all: 99.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
DIALSdata reduction
DIALSdata scaling
PHphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→51.378 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.66
RfactorNum. reflection% reflection
Rfree0.1617 7173 4.94 %
Rwork0.1371 --
obs0.1383 145344 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.34 Å2
Refinement stepCycle: LAST / Resolution: 1.21→51.378 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2998 0 0 295 3293
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0163184
X-RAY DIFFRACTIONf_angle_d1.6064340
X-RAY DIFFRACTIONf_dihedral_angle_d17.1451187
X-RAY DIFFRACTIONf_chiral_restr0.178459
X-RAY DIFFRACTIONf_plane_restr0.01589
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.22380.3842190.34434573X-RAY DIFFRACTION98
1.2238-1.23820.34822620.33584422X-RAY DIFFRACTION98
1.2382-1.25330.35022570.33174518X-RAY DIFFRACTION99
1.2533-1.26910.35452300.32384487X-RAY DIFFRACTION98
1.2691-1.28580.34382320.32074550X-RAY DIFFRACTION99
1.2858-1.30340.38022650.31374525X-RAY DIFFRACTION99
1.3034-1.32210.32612300.30324544X-RAY DIFFRACTION99
1.3221-1.34180.33192480.28614573X-RAY DIFFRACTION99
1.3418-1.36280.30692040.27084626X-RAY DIFFRACTION99
1.3628-1.38510.26852410.26384532X-RAY DIFFRACTION99
1.3851-1.4090.28752550.24984547X-RAY DIFFRACTION100
1.409-1.43460.27762470.23594577X-RAY DIFFRACTION100
1.4346-1.46220.27342430.21384592X-RAY DIFFRACTION100
1.4622-1.49210.21952540.20144605X-RAY DIFFRACTION100
1.4921-1.52450.21912310.18394585X-RAY DIFFRACTION100
1.5245-1.560.20672170.17064629X-RAY DIFFRACTION100
1.56-1.5990.19562320.14944599X-RAY DIFFRACTION100
1.599-1.64220.1822510.13654628X-RAY DIFFRACTION100
1.6422-1.69050.15332330.11954583X-RAY DIFFRACTION100
1.6905-1.74510.15252320.10924647X-RAY DIFFRACTION100
1.7451-1.80750.14652470.10294603X-RAY DIFFRACTION100
1.8075-1.87990.12711940.09854670X-RAY DIFFRACTION100
1.8799-1.96540.11912050.09074656X-RAY DIFFRACTION100
1.9654-2.0690.12242170.09164660X-RAY DIFFRACTION100
2.069-2.19870.11362830.09164627X-RAY DIFFRACTION100
2.1987-2.36840.11522550.09134626X-RAY DIFFRACTION100
2.3684-2.60680.11872380.09874690X-RAY DIFFRACTION100
2.6068-2.98390.1392590.11234668X-RAY DIFFRACTION100
2.9839-3.75930.12212850.11164700X-RAY DIFFRACTION100
3.7593-51.42390.12542070.1194929X-RAY DIFFRACTION100

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