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- PDB-4r1o: Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arab... -

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Basic information

Entry
Database: PDB / ID: 4r1o
TitleCrystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase
ComponentsL-arabinose isomerase
KeywordsISOMERASE / Hexamer / Thermophile / thermostable / AI fold
Function / homology
Function and homology information


L-arabinose isomerase / L-arabinose isomerase activity / L-arabinose catabolic process to xylulose 5-phosphate / manganese ion binding / cytosol
Similarity search - Function
Rossmann fold - #10940 / L-arabinose isomerase / L-arabinose isomerase, C-terminal / L-arabinose isomerase, N-terminal domain superfamily / L-arabinose isomerase / L-arabinose isomerase C-terminal domain / L-fucose/L-arabinose isomerase, C-terminal / L-fucose isomerase, N-terminal/central domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-arabinose isomerase
Similarity search - Component
Biological speciesGeobacillus kaustophilus HTA426 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 Å
AuthorsChoi, J.M. / Lee, Y.J. / Lee, D.W. / Lee, S.H.
CitationJournal: to be published
Title: Crystal Structure of Thermophilic apo L-Arabinose Isomerase from Geobacillus kaustophilus
Authors: Choi, J.M. / Lee, Y.J. / Lee, D.W. / Lee, S.H.
History
DepositionAug 7, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Structure summary
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: 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


Theoretical massNumber of molelcules
Total (without water)337,8296
Polymers337,8296
Non-polymers00
Water21,2941182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area39340 Å2
ΔGint-212 kcal/mol
Surface area89030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.725, 140.746, 215.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
L-arabinose isomerase


Mass: 56304.891 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus HTA426 (bacteria)
Gene: araA, GK1904 / Plasmid: pET28a(+)-GKAI / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q5KYP7, L-arabinose isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1182 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS RESIDUE IS BASED ON YP_147757 OF GENBANK.

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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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.8M Na-K phosphate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1.0015 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Nov 16, 2013
RadiationMonochromator: DCM Si(111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0015 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 133329 / Num. obs: 133329 / % possible obs: 96.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 25.61 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 14.091
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 3.746 / Num. unique all: 6024 / Rsym value: 0.458 / % possible all: 94.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GKAI with MN

Resolution: 2.401→45.323 Å / FOM work R set: 0.8468 / SU ML: 0.27 / σ(F): 1.36 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2158 6606 5.01 %Random
Rwork0.1643 ---
obs0.1669 131875 94.85 %-
all-131875 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.6 Å2 / Biso mean: 17.04 Å2 / Biso min: 1.02 Å2
Refinement stepCycle: LAST / Resolution: 2.401→45.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23661 0 0 1182 24843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00724255
X-RAY DIFFRACTIONf_angle_d1.09132843
X-RAY DIFFRACTIONf_chiral_restr0.0753473
X-RAY DIFFRACTIONf_plane_restr0.0054305
X-RAY DIFFRACTIONf_dihedral_angle_d15.4218857
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4006-2.42790.30141780.18563410358878
2.4279-2.45650.2822030.18753796399987
2.4565-2.48640.29092130.18723842405589
2.4864-2.51790.26472120.18363937414990
2.5179-2.5510.25322250.18214001422692
2.551-2.5860.26432330.18124013424693
2.586-2.62290.25892110.18194043425493
2.6229-2.66210.26582070.18684102430994
2.6621-2.70360.272150.19274091430694
2.7036-2.7480.25742090.20464122433195
2.748-2.79530.27022310.19814154438595
2.7953-2.84620.26991990.19994212441196
2.8462-2.90090.25262210.19744157437896
2.9009-2.96010.27592170.20454186440396
2.9601-3.02450.24612030.20394219442296
3.0245-3.09480.26362270.19994205443296
3.0948-3.17220.26752200.18924270449097
3.1722-3.25790.25422110.18234291450297
3.2579-3.35380.2182160.15914232444897
3.3538-3.4620.1952210.14714267448897
3.462-3.58570.19322480.14394285453398
3.5857-3.72920.17182040.13674324452898
3.7292-3.89880.17392280.12544309453798
3.8988-4.10420.16462250.12044299452498
4.1042-4.36120.15712520.12694305455798
4.3612-4.69760.15712560.11994351460798
4.6976-5.16970.16941990.13014425462499
5.1697-5.91640.20152440.15164443468799
5.9164-7.44860.21412520.17754453470599
7.4486-45.33120.20832260.20754525475196

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