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- PDB-7cwv: Crystal structure of Arabinose isomerase from hyper thermophilic ... -

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Basic information

Entry
Database: PDB / ID: 7cwv
TitleCrystal structure of Arabinose isomerase from hyper thermophilic bacterium Thermotoga maritima (TMAI) wt
ComponentsL-arabinose isomerase
KeywordsISOMERASE / hyperthermophile / 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 / 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
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.53 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
DepositionAug 31, 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

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
G: L-arabinose isomerase
H: L-arabinose isomerase
I: L-arabinose isomerase
J: L-arabinose isomerase
K: L-arabinose isomerase
L: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)681,58625
Polymers680,83512
Non-polymers75113
Water37821
1
A: L-arabinose isomerase
C: L-arabinose isomerase
D: L-arabinose isomerase
E: L-arabinose isomerase
F: L-arabinose isomerase
G: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,83913
Polymers340,4176
Non-polymers4227
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area45050 Å2
ΔGint-237 kcal/mol
Surface area88530 Å2
MethodPISA
2
H: L-arabinose isomerase
I: L-arabinose isomerase
J: L-arabinose isomerase
K: L-arabinose isomerase
hetero molecules

B: L-arabinose isomerase
L: L-arabinose isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)340,74712
Polymers340,4176
Non-polymers3306
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area45160 Å2
ΔGint-245 kcal/mol
Surface area88780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.971, 109.429, 153.854
Angle α, β, γ (deg.)98.140, 98.180, 89.970
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
L-arabinose isomerase


Mass: 56736.219 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Gene: araA, TM_0276 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9WYB3, L-arabinose isomerase
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.08 Å3/Da / Density % sol: 40.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2%(v/v) Tacsimate pH 8.0, 16% w/v Polyethylene glycol 3350, 100mM Tris pH 8.5, 16% Glycerol

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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: 3.53→50 Å / Num. obs: 62046 / % possible obs: 91.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.186 / Rpim(I) all: 0.115 / Rrim(I) all: 0.22 / Χ2: 0.632 / Net I/σ(I): 2.8 / Num. measured all: 216134
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.53-3.593.20.78630440.9680.5070.9380.49488.9
3.59-3.663.10.66129870.9870.440.7970.56287.9
3.66-3.733.20.62927480.5780.4070.7520.46782.2
3.73-3.83.20.69930520.5470.450.8340.54191.7
3.8-3.893.30.52932020.9540.3420.6320.84293.6
3.89-3.983.40.4831470.7590.2970.5660.44993.9
3.98-4.073.40.42131800.8120.2610.4970.4593.9
4.07-4.183.50.40231510.8260.2480.4730.46993.6
4.18-4.313.50.32631450.8750.20.3830.50493.5
4.31-4.453.50.26831720.9210.1650.3160.52793.7
4.45-4.613.50.23531040.9390.1440.2760.55992.8
4.61-4.793.50.21730980.9410.1340.2550.58390.1
4.79-5.013.50.19529260.9520.120.230.57986.9
5.01-5.273.70.20331810.9550.1220.2370.56395.8
5.27-5.63.70.22432270.9450.1350.2620.55895.5
5.6-6.033.70.19332270.9550.1160.2250.56694.8
6.03-6.643.60.1731480.9630.1030.1990.5993.5
6.64-7.63.50.11429480.9820.070.1340.76887.7
7.6-9.563.80.07732520.9920.0460.091.0396.1
9.56-503.70.06531070.9930.0390.0761.38392

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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: 3.53→49.74 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.802 / SU B: 77.136 / SU ML: 1.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3321 3146 5.1 %RANDOM
Rwork0.2217 ---
obs0.2273 58899 91.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 360.19 Å2 / Biso mean: 110.908 Å2 / Biso min: 5.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.41 Å2-0.38 Å2
2--0.29 Å2-0.61 Å2
3---0.16 Å2
Refinement stepCycle: final / Resolution: 3.53→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms47675 0 18 21 47714
Biso mean--101.29 27.6 -
Num. residues----5927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01348816
X-RAY DIFFRACTIONr_bond_other_d0.0020.01746360
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.63966046
X-RAY DIFFRACTIONr_angle_other_deg1.1211.577107557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76455913
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.65922.352540
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.788158862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.81415312
X-RAY DIFFRACTIONr_chiral_restr0.0510.26144
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0253814
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0210194
LS refinement shellResolution: 3.53→3.618 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.422 223 -
Rwork0.376 4043 -
obs--84.95 %

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