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- PDB-7cx7: Crystal structure of Arabinose isomerase from hybrid AI8 -

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Basic information

Entry
Database: PDB / ID: 7cx7
TitleCrystal structure of Arabinose isomerase from hybrid AI8
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
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 speciesGeobacillus kaustophilus (bacteria)
Alicyclobacillus sp. TP-7 (bacteria)
Alicyclobacillus acidocaldarius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 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 bacterium Thermotoga maritima (TMAI) wt
Authors: Hoang, N.K.Q. / Dhanasingh, I. / Cao, T.P. / Sung, J.Y. / Shin, S.M. / Lee, D.W. / Lee, S.H.
History
DepositionSep 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 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

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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)337,33625
Polymers335,6866
Non-polymers1,65019
Water7,206400
1
A: L-arabinose isomerase
B: L-arabinose isomerase
E: L-arabinose isomerase
hetero molecules

C: L-arabinose isomerase
D: L-arabinose isomerase
F: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)337,33625
Polymers335,6866
Non-polymers1,65019
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area45530 Å2
ΔGint-334 kcal/mol
Surface area84070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)204.591, 81.907, 192.001
Angle α, β, γ (deg.)90.000, 117.900, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
L-arabinose isomerase


Mass: 55947.586 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: Chimeric protein
Source: (gene. exp.) Geobacillus kaustophilus (strain HTA426) (bacteria), (gene. exp.) Alicyclobacillus sp. TP-7 (bacteria), (gene. exp.) Alicyclobacillus acidocaldarius (bacteria)
Gene: araA, GK1904, araA / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q5KYP7, UniProt: K0IGW6, UniProt: Q2VMT2, L-arabinose isomerase
#2: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 35% (v/v) MPD, 100mM Imidazole/ Hydrochloric acid pH 8.0, 200mM Magnesium chloride

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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: 2.49→50 Å / Num. obs: 97080 / % possible obs: 99.2 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.05 / Rrim(I) all: 0.131 / Χ2: 0.563 / Net I/σ(I): 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.546.60.85147760.7220.3560.9240.48999.5
2.54-2.596.60.76748110.7490.320.8330.49699.1
2.59-2.646.30.67648510.7740.290.7370.5198.8
2.64-2.696.30.55947810.850.240.610.4598.4
2.69-2.7570.51348140.8920.2070.5540.51299.8
2.75-2.8270.46748540.9080.1880.5040.52499.7
2.82-2.8970.39448590.9280.1590.4250.5399.5
2.89-2.966.90.33248630.9510.1350.3590.53199.8
2.96-3.056.80.28348700.9590.1160.3060.54499.7
3.05-3.156.70.22648540.9720.0930.2450.55699.1
3.15-3.266.30.18447580.9740.0790.2010.57797.9
3.26-3.396.80.14348330.9880.0590.1540.5599.4
3.39-3.5570.12249100.9910.0490.1310.60499.6
3.55-3.736.90.148660.9940.0410.1080.59699.6
3.73-3.976.90.08448620.9950.0340.0910.63799.6
3.97-4.276.50.07148170.9960.030.0780.64997.7
4.27-4.770.0648640.9970.0240.0640.61499.4
4.7-5.3870.06249350.9970.0250.0670.63399.8
5.38-6.786.60.06248690.9970.0260.0680.59198.2
6.78-506.70.04250330.9980.0180.0460.63999

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Processing

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

2ajt


Resolution: 2.49→48.59 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.895 / SU B: 13.144 / SU ML: 0.284 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.347 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 4784 4.9 %RANDOM
Rwork0.192 ---
obs0.1957 92249 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 148.6 Å2 / Biso mean: 46.375 Å2 / Biso min: 17.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å2-0 Å20.03 Å2
2---0.04 Å20 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 2.49→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23440 0 87 400 23927
Biso mean--72.34 39.08 -
Num. residues----2964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01324096
X-RAY DIFFRACTIONr_bond_other_d0.0010.01722154
X-RAY DIFFRACTIONr_angle_refined_deg1.541.63732602
X-RAY DIFFRACTIONr_angle_other_deg1.2861.57351105
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.16552955
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.15721.1551394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.243153972
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.91415210
X-RAY DIFFRACTIONr_chiral_restr0.0640.22943
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0227323
X-RAY DIFFRACTIONr_gen_planes_other0.0020.025571
LS refinement shellResolution: 2.492→2.557 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 351 -
Rwork0.286 6346 -
all-6697 -
obs--92.35 %

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