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- PDB-6lrp: Crystal structure of isocitrate lyase (Caur_3889) from Chloroflex... -

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Basic information

Entry
Database: PDB / ID: 6lrp
TitleCrystal structure of isocitrate lyase (Caur_3889) from Chloroflexus aurantiacus in complex with manganese ion
ComponentsIsocitrate lyase
KeywordsLYASE / isocitrate lyase / manganese ion / TIM-barrel
Function / homology
Function and homology information


isocitrate lyase / isocitrate lyase activity / carboxylic acid metabolic process / metal ion binding
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / ICL/PEPM domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
3,6,9,12,15-PENTAOXAHEPTADECANE / Isocitrate lyase
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsLee, S.H. / Kim, K.J.
CitationJournal: To Be Published
Title: Structural studies reveal the molecular mechanism of isocitrate lyase from Chloroflexus aurantiacus
Authors: Lee, S.H. / Kim, K.J.
History
DepositionJan 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6293
Polymers48,2861
Non-polymers3422
Water4,486249
1
A: Isocitrate lyase
hetero molecules

A: Isocitrate lyase
hetero molecules

A: Isocitrate lyase
hetero molecules

A: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,51412
Polymers193,1454
Non-polymers1,3708
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_455y-1/2,x+1/2,-z+1/21
crystal symmetry operation10_455-x-1,-y,z1
crystal symmetry operation16_445-y-1/2,-x-1/2,-z+1/21
Buried area31080 Å2
ΔGint-153 kcal/mol
Surface area47230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.772, 92.772, 216.114
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122

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Components

#1: Protein Isocitrate lyase


Mass: 48286.129 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl) (bacteria)
Gene: Caur_3889 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9WDE7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-P3G / 3,6,9,12,15-PENTAOXAHEPTADECANE


Mass: 250.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 48.91 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 8% PEG 8000, 0.2M Tris-HCl pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 15, 2017
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 28958 / % possible obs: 96.4 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.036 / Rrim(I) all: 0.107 / Χ2: 2.132 / Net I/σ(I): 10.9 / Num. measured all: 197726
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.093.80.30913550.5250.1610.3521.4392.9
2.09-2.124.20.28914230.6010.1470.3261.47995.4
2.12-2.164.30.27513950.6690.1360.311.33395.1
2.16-2.214.60.26614180.7320.1270.2971.42795.3
2.21-2.264.60.25614010.8230.1210.2851.38294.3
2.26-2.314.80.24213840.8250.1090.2671.62894.8
2.31-2.375.10.23614100.9140.1060.2611.5395.2
2.37-2.435.30.21214260.9090.0920.2331.49895.3
2.43-2.55.50.20114070.9380.0840.2191.51896.2
2.5-2.585.80.18214220.9490.0740.1981.59194.9
2.58-2.686.20.16714350.9630.0660.1811.66395.9
2.68-2.786.50.14914100.9750.0570.1611.7196.1
2.78-2.916.90.13714560.9830.0510.1471.83996.9
2.91-3.067.60.12114650.9880.0430.1291.90597.7
3.06-3.258.20.10714700.9930.0360.1141.96597.7
3.25-3.519.30.09414960.9940.030.0992.26498.7
3.51-3.8610.70.08915120.9970.0270.0943.13499.1
3.86-4.4210.50.07315100.9960.0220.0773.398.7
4.42-5.5610.50.06215330.9990.0180.0642.53298.7
5.56-5010.40.06316300.9980.0190.0662.68698.1

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E5B

3e5b


Resolution: 2.05→31.59 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 5.134 / SU ML: 0.129 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.163
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2231 1401 4.8 %RANDOM
Rwork0.1747 ---
obs0.177 27556 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 116.78 Å2 / Biso mean: 22.274 Å2 / Biso min: 8.25 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å2-0 Å2-0 Å2
2--0.68 Å2-0 Å2
3----1.35 Å2
Refinement stepCycle: final / Resolution: 2.05→31.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 23 254 3307
Biso mean--37.86 29.77 -
Num. residues----390
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133119
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172837
X-RAY DIFFRACTIONr_angle_refined_deg1.4961.6424221
X-RAY DIFFRACTIONr_angle_other_deg1.3761.5696540
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.885389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26921.547181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.95815483
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4411526
X-RAY DIFFRACTIONr_chiral_restr0.0690.2395
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023586
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02712
LS refinement shellResolution: 2.051→2.104 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 94 -
Rwork0.313 1932 -
all-2026 -
obs--92.94 %

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