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- PDB-7njg: Xylose isomerase grown inside HARE serial crystallography chip -

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Basic information

Entry
Database: PDB / ID: 7njg
TitleXylose isomerase grown inside HARE serial crystallography chip
ComponentsXylose isomerase
KeywordsISOMERASE / serial crystallography / xylose isomerase / vapour diffusion / silicon chip
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. / 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: 1.9 Å
AuthorsNorton-Baker, B. / Mehrabi, P. / Boger, J. / Schonherr, R. / von Stetten, D. / Schikora, H. / Martin, R.W. / Miller, R.J.D. / Redecke, L. / Schulz, E.C.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: A simple vapor-diffusion method enables protein crystallization inside the HARE serial crystallography chip.
Authors: Norton-Baker, B. / Mehrabi, P. / Boger, J. / Schonherr, R. / von Stetten, D. / Schikora, H. / Kwok, A.O. / Martin, R.W. / Miller, R.J.D. / Redecke, L. / Schulz, E.C.
History
DepositionFeb 16, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3422
Polymers43,2831
Non-polymers591
Water4,774265
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)173,3698
Polymers173,1334
Non-polymers2364
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area30990 Å2
ΔGint-153 kcal/mol
Surface area47120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.450, 99.750, 103.150
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-509-

HOH

21A-654-

HOH

31A-693-

HOH

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Components

#1: Protein Xylose isomerase


Mass: 43283.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rubiginosus (bacteria) / Gene: xylA / Production host: Streptomyces rubiginosus (bacteria) / References: UniProt: P24300, xylose isomerase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / 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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 35% (w/v) PEG3350, 200 mM lithium sulfate and 10 mM Hepes/NaOH, pH 7.5

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.7→71.04 Å / Num. obs: 38718 / % possible obs: 100 % / Redundancy: 111 % / Biso Wilson estimate: 20.81 Å2 / CC1/2: 0.7891 / Net I/σ(I): 2.3
Reflection shellResolution: 1.9→49.88 Å / Num. unique obs: 3834 / CC1/2: 0.4149
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHENIX1.18.2_3874refinement
CrystFELdata reduction
CrystFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6QNI

6qni


Resolution: 1.9→51.57 Å / SU ML: 0.2229 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6984
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.244 1953 5.04 %
Rwork0.2016 36765 -
obs0.2036 38718 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.74 Å2
Refinement stepCycle: LAST / Resolution: 1.9→51.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 1 265 3312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00333151
X-RAY DIFFRACTIONf_angle_d0.59754269
X-RAY DIFFRACTIONf_chiral_restr0.0396438
X-RAY DIFFRACTIONf_plane_restr0.0043584
X-RAY DIFFRACTIONf_dihedral_angle_d16.88831165
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.311680.28022584X-RAY DIFFRACTION100
1.95-20.32261770.27232540X-RAY DIFFRACTION100
2-2.060.29121560.26422585X-RAY DIFFRACTION100
2.06-2.130.29571600.23652545X-RAY DIFFRACTION99.96
2.13-2.20.28471340.22962645X-RAY DIFFRACTION100
2.2-2.290.30131210.2222596X-RAY DIFFRACTION100
2.29-2.390.25411160.21492632X-RAY DIFFRACTION100
2.39-2.520.23871440.21182603X-RAY DIFFRACTION99.96
2.52-2.680.28141240.22132623X-RAY DIFFRACTION100
2.68-2.880.26421650.20532590X-RAY DIFFRACTION100
2.88-3.170.20981190.19522673X-RAY DIFFRACTION100
3.17-3.630.19331030.17682664X-RAY DIFFRACTION100
3.63-4.580.20251190.15842703X-RAY DIFFRACTION100
4.58-51.570.20591470.18172782X-RAY DIFFRACTION100

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