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- PDB-4r1q: Crystal Structure of Thermophilic Geobacillus kaustophilus L-Arab... -

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Basic information

Entry
Database: PDB / ID: 4r1q
TitleCrystal Structure of Thermophilic Geobacillus kaustophilus L-Arabinose isomerase in complex with L-arabitol
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 D-xylulose 5-phosphate / manganese ion binding / cytosol
Similarity search - Function
Rossmann fold - #10940 / : / : / 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 ...Rossmann fold - #10940 / : / : / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / L-arabinitol / L-arabinose isomerase
Similarity search - Component
Biological speciesGeobacillus kaustophilus HTA426 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.248 Å
AuthorsChoi, J.M. / Lee, Y.J. / Lee, D.W. / Lee, S.H.
CitationJournal: to be published
Title: Crystal Structure of Thermophilic L-Arabinose Isomerase with L-Arabitol 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 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)339,07218
Polymers337,8296
Non-polymers1,24312
Water29,6351645
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area40090 Å2
ΔGint-231 kcal/mol
Surface area89850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.514, 146.263, 215.677
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: Chemical
ChemComp-SST / L-arabinitol / (2S,4S)-pentane-1,2,3,4,5-pentol


Mass: 152.146 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C5H12O5
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 1645 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 1.8M Na-K phosphate, 4% acetone, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1.000001 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2013
RadiationMonochromator: DCM Si(111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000001 Å / Relative weight: 1
ReflectionResolution: 2.248→50 Å / Num. all: 175982 / Num. obs: 174510 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 29.94 Å2 / Rmerge(I) obs: 0.112 / Rsym value: 0.112 / Net I/σ(I): 20.576
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 5.286 / Num. unique all: 8686 / Rsym value: 0.459 / % possible all: 99.4

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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: 4R1P

4r1p


Resolution: 2.248→49.079 Å / FOM work R set: 0.866 / SU ML: 0.23 / σ(F): 1.36 / Phase error: 20.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2012 8050 5.01 %Random
Rwork0.1538 ---
obs0.1562 160597 90.26 %-
all-160597 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 94.44 Å2 / Biso min: 8.15 Å2
Refinement stepCycle: LAST / Resolution: 2.248→49.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23677 0 66 1645 25388
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00824334
X-RAY DIFFRACTIONf_angle_d1.07432943
X-RAY DIFFRACTIONf_chiral_restr0.0753489
X-RAY DIFFRACTIONf_plane_restr0.0054309
X-RAY DIFFRACTIONf_dihedral_angle_d14.5778871
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 (%)
2.2483-2.27390.24281650.15863431359661
2.2739-2.30060.22741960.15333783397968
2.3006-2.32870.25752290.16083912414170
2.3287-2.35820.23442330.1624037427073
2.3582-2.38920.22612210.1674256447776
2.3892-2.42190.24632330.16994344457778
2.4219-2.45650.24792370.17124486472380
2.4565-2.49320.25542340.17774658489283
2.4932-2.53210.22952490.17874793504285
2.5321-2.57370.25832600.16584875513588
2.5737-2.6180.25372540.17075036529090
2.618-2.66560.23272740.17385094536892
2.6656-2.71690.2422580.17185237549593
2.7169-2.77240.23972980.17345317561595
2.7724-2.83260.22222850.16955362564796
2.8326-2.89850.22012910.17555423571497
2.8985-2.9710.2323080.17525481578998
2.971-3.05130.23873240.17545494581898
3.0513-3.14110.23683080.17395571587999
3.1411-3.24240.2252840.16375605588999
3.2424-3.35830.2052650.157156425907100
3.3583-3.49270.18313050.14725622592799
3.4927-3.65160.192760.14275586586299
3.6516-3.84410.1683240.13315599592399
3.8441-4.08480.16842790.12895559583898
4.0848-4.40.16013050.12885534583998
4.4-4.84250.16152930.12335506579997
4.8425-5.54240.15712780.13615685596399
5.5424-6.97960.19722770.16025782605999
6.9796-49.09030.18973070.16555837614498

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