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- PDB-2ajt: Crystal structure of L-Arabinose Isomerase from E.coli -

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Basic information

Entry
Database: PDB / ID: 2ajt
TitleCrystal structure of L-Arabinose Isomerase from E.coli
ComponentsL-arabinose isomerase
KeywordsISOMERASE / Arabinose catabolism / Carbohydrate metabolism / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


L-arabinose isomerase / L-arabinose isomerase activity / L-arabinose catabolic process to xylulose 5-phosphate / arabinose catabolic process / 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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsManjasetty, B.A. / Fedorov, E.V. / Almo, S.C. / Chance, M.R. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Escherichia coli L-Arabinose Isomerase (ECAI), The Putative Target of Biological Tagatose Production
Authors: Manjasetty, B.A. / Chance, M.R.
History
DepositionAug 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE According to aminoacid sequence database reference, the database conflicts with the ...SEQUENCE According to aminoacid sequence database reference, the database conflicts with the previous citations with regard to PRO 72 which is an ARG in the database. Author sequence is consistent with the previous citations, Lee et al., (1986) Gene; Yura et al., (1992) Nucleic Acids Res., which suggest a proline at position 72

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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


Theoretical massNumber of molelcules
Total (without water)168,3293
Polymers168,3293
Non-polymers00
Water1,58588
1
A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase

A: L-arabinose isomerase
B: L-arabinose isomerase
C: L-arabinose isomerase


Theoretical massNumber of molelcules
Total (without water)336,6586
Polymers336,6586
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area37080 Å2
ΔGint-181 kcal/mol
Surface area96410 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)116.539, 116.539, 214.330
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein L-arabinose isomerase /


Mass: 56109.695 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: araA / Plasmid: PET T7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P08202, L-arabinose isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / 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: 2.5 Å3/Da / Density % sol: 50.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, Trisodium citrate dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTAM Q315 / Detector: CCD / Date: Apr 11, 2005 / Details: Mirrors
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→19.84 Å / Num. all: 44290 / Num. obs: 44290 / Redundancy: 4.1 % / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 16.3
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2 / Rsym value: 0.6 / % possible all: 98.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.6→19.84 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.89 / SU B: 31.479 / SU ML: 0.312 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.407 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27796 2246 5.1 %RANDOM
Rwork0.21726 ---
obs0.2203 42044 84.5 %-
all-42044 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.114 Å2
Baniso -1Baniso -2Baniso -3
1-2.55 Å21.27 Å20 Å2
2--2.55 Å20 Å2
3----3.82 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11392 0 0 88 11480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02111674
X-RAY DIFFRACTIONr_bond_other_d0.0020.0210325
X-RAY DIFFRACTIONr_angle_refined_deg1.2871.93115912
X-RAY DIFFRACTIONr_angle_other_deg0.806323860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04651491
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.33524.547530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.36151772
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8381550
X-RAY DIFFRACTIONr_chiral_restr0.0710.21783
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213301
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022364
X-RAY DIFFRACTIONr_nbd_refined0.2270.22669
X-RAY DIFFRACTIONr_nbd_other0.1870.211001
X-RAY DIFFRACTIONr_nbtor_refined0.180.25652
X-RAY DIFFRACTIONr_nbtor_other0.0870.26674
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2304
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0070.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.230
X-RAY DIFFRACTIONr_symmetry_vdw_other0.280.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3651.57578
X-RAY DIFFRACTIONr_mcbond_other0.061.53051
X-RAY DIFFRACTIONr_mcangle_it0.572211819
X-RAY DIFFRACTIONr_scbond_it0.84234667
X-RAY DIFFRACTIONr_scangle_it1.3434.54093
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 132 -
Rwork0.252 2221 -
obs--62.53 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4560.00970.13850.6929-0.04131.856-0.04220.24340.119-0.13840.00390.0512-0.3353-0.17470.0383-0.3624-0.141-0.02140.0604-0.0258-0.2587-34.827951.412138.6758
20.5390.20670.15940.78950.30942.02010.09220.067-0.15190.0350.0399-0.2539-0.0840.5371-0.1321-0.3949-0.1357-0.00980.011-0.0144-0.04920.581845.591170.4332
30.99480.68020.09290.91260.58442.1872-0.15020.21170.4871-0.3551-0.05850.226-1.2705-0.40770.20870.5582-0.0682-0.1208-0.04160.0146-0.0483-22.799686.484869.5287
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 4981 - 498
2X-RAY DIFFRACTION2BB1 - 4981 - 498
3X-RAY DIFFRACTION3CC1 - 4981 - 498

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