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- PDB-7cxo: Crystal structure of Arabinose isomerase from hybrid AI10 -

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Basic information

Entry
Database: PDB / ID: 7cxo
TitleCrystal structure of Arabinose isomerase from hybrid AI10
ComponentsL-arabinose isomerase
KeywordsISOMERASE / hybrid / Arabinose isomerase
Function / homology
Function and homology information


L-arabinose isomerase / L-arabinose isomerase activity / L-arabinose catabolic process to D-xylulose 5-phosphate / manganese ion binding / cytosol / cytoplasm
Similarity search - Function
: / : / L-arabinose isomerase central domain / L-arabinose isomerase / L-arabinose isomerase, C-terminal / L-arabinose isomerase, N-terminal domain superfamily / L-arabinose isomerase N-terminal domain / L-arabinose isomerase C-terminal domain / L-fucose/L-arabinose isomerase, C-terminal / L-fucose isomerase, N-terminal/central domain superfamily
Similarity search - Domain/homology
: / L-arabinose isomerase / L-arabinose isomerase / L-arabinose isomerase
Similarity search - Component
Biological speciesAlicyclobacillus sp. TP-7 (bacteria)
Geobacillus kaustophilus (bacteria)
Escherichia coli O157:H7 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsHoang, N.K.Q. / Dhanasingh, I. / Cao, T.P. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H.
CitationJournal: To Be Published
Title: Crystal structure of Arabinose isomerase from hyper thermophilic hybrid AI10
Authors: Hoang, N.K.Q. / Dhanasingh, I. / Cao, T.P. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H.
History
DepositionSep 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase
D: L-arabinose isomerase
E: L-arabinose isomerase
F: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)336,30117
Polymers335,5116
Non-polymers79011
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area42120 Å2
ΔGint-231 kcal/mol
Surface area87400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)148.476, 258.575, 165.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
L-arabinose isomerase


Mass: 55918.539 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Chimeric protein
Source: (gene. exp.) Alicyclobacillus sp. TP-7 (bacteria), (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria), (gene. exp.) Escherichia coli O157:H7 (bacteria)
Gene: araA, araA, GK1904, araA, Z0070, ECs0066 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: K0IGW6, UniProt: Q5KYP7, UniProt: P58538, L-arabinose isomerase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.37 Å3/Da / Density % sol: 48.11 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 30% (v/v) Polyethylene glycol 400, 100mM Sodium cacodylate/ Hydrochloric acid pH 6.5, 200mM Lithium sulfate

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.97942 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 54358 / % possible obs: 99.8 % / Redundancy: 9.5 % / Rmerge(I) obs: 0.187 / Rpim(I) all: 0.062 / Rrim(I) all: 0.197 / Χ2: 0.643 / Net I/σ(I): 3.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.2-3.269.20.97526900.6650.3281.0310.42199.9
3.26-3.319.20.87226700.7050.2940.9220.433100
3.31-3.389.10.76226920.7680.2580.8060.456100
3.38-3.458.90.61326950.8550.2110.650.51499.8
3.45-3.528.20.53226970.8760.1920.5670.5100
3.52-3.69.60.47626810.9190.1580.5030.504100
3.6-3.699.90.42627110.9320.1380.4490.567100
3.69-3.799.90.3527020.9610.1130.3680.597100
3.79-3.919.80.31726860.9580.1040.3340.67999.9
3.91-4.039.90.25427130.9760.0820.2680.63100
4.03-4.189.90.23127160.9790.0740.2420.678100
4.18-4.349.80.20526870.9840.0660.2160.70499.9
4.34-4.549.10.16727200.9880.0560.1760.8100
4.54-4.789.30.14427150.9910.0480.1520.79299.9
4.78-5.0810.30.14227400.9910.0450.1490.751100
5.08-5.4710.20.13527360.9930.0430.1420.695100
5.47-6.029.90.13727340.9920.0440.1440.643100
6.02-6.898.90.11527580.9930.040.1220.64799.8
6.89-8.6710.10.07827700.9980.0250.0820.75199.9
8.67-509.30.06328450.9990.0210.0671.00698

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AJT

2ajt


Resolution: 3.2→48.89 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.882 / SU B: 29.624 / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.587 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2606 4.8 %RANDOM
Rwork0.1756 ---
obs0.1802 51716 98.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 204.28 Å2 / Biso mean: 75.389 Å2 / Biso min: 17.43 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 3.2→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23387 0 36 114 23537
Biso mean--85.59 52.67 -
Num. residues----2961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01323962
X-RAY DIFFRACTIONr_bond_other_d0.0010.01722080
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.6332426
X-RAY DIFFRACTIONr_angle_other_deg1.21.57650991
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.52952954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.44621.9911361
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.857154011
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0515178
X-RAY DIFFRACTIONr_chiral_restr0.0490.22939
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0227193
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025345
LS refinement shellResolution: 3.2→3.283 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 194 -
Rwork0.267 3681 -
obs--99.97 %

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