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

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Basic information

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


isocitrate lyase / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / ICL/PEPM domain / Phosphoenolpyruvate-binding domains / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
ISOCITRIC ACID / : / Isocitrate lyase
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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

Downloads & links

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Assembly

Deposited unit
A: Isocitrate lyase
D: Isocitrate lyase
G: Isocitrate lyase
J: Isocitrate lyase
M: Isocitrate lyase
P: Isocitrate lyase
S: Isocitrate lyase
V: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,37136
Polymers386,2898
Non-polymers3,08228
Water12,016667
1
A: Isocitrate lyase
D: Isocitrate lyase
G: Isocitrate lyase
J: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,68518
Polymers193,1454
Non-polymers1,54114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35010 Å2
ΔGint-174 kcal/mol
Surface area48100 Å2
MethodPISA
2
M: Isocitrate lyase
P: Isocitrate lyase
S: Isocitrate lyase
V: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)194,68518
Polymers193,1454
Non-polymers1,54114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area35170 Å2
ΔGint-176 kcal/mol
Surface area48090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.314, 157.314, 197.707
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein
Isocitrate lyase


Mass: 48286.129 Da / Num. of mol.: 8
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-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 667 / 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: 3.66 Å3/Da / Density % sol: 66.36 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: 35% MPD, 0.1M sodium acetate/acetic acid pH4.5

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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: Feb 25, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 115739 / % possible obs: 95.9 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.112 / Rpim(I) all: 0.074 / Rrim(I) all: 0.135 / Χ2: 1.977 / Net I/σ(I): 8 / Num. measured all: 331936
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.9-2.952.40.30155380.8120.2210.3761.28891.7
2.95-32.40.29354880.8130.2150.3651.34191.7
3-3.062.40.29955200.8010.220.3731.43691.3
3.06-3.122.40.27455790.850.2010.3411.36192.1
3.12-3.192.50.23655590.8860.1720.2931.47192.1
3.19-3.272.50.21956060.9050.1570.2711.53793.7
3.27-3.352.50.18856540.9220.1340.2321.58192.8
3.35-3.442.60.17256490.9390.1210.2111.66394.5
3.44-3.542.60.14757840.9630.1020.181.74795.4
3.54-3.652.80.1359130.9690.0890.1581.81396.8
3.65-3.782.90.1458070.9620.0940.172.5397.4
3.78-3.942.90.11459020.9780.0760.1382.14697.5
3.94-4.1130.10259030.9820.0660.1222.19997.6
4.11-4.333.20.10459460.9780.0670.1242.61898.9
4.33-4.63.40.09560200.9810.060.1132.60699.2
4.6-4.963.40.08359820.9880.0510.0982.06399.5
4.96-5.463.30.08759680.9880.0550.1031.83599.2
5.46-6.243.30.0959760.9890.0570.1071.78399.3
6.24-7.863.30.07560400.990.0470.0891.97999.4
7.86-503.40.06259050.9920.0390.0742.85798

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Processing

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

3e5b


Resolution: 2.9→32.05 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.876 / SU B: 14.684 / SU ML: 0.271 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.361 / ESU R Free: 0.367
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2464 5601 4.8 %RANDOM
Rwork0.1756 ---
obs0.179 110130 95.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 142.7 Å2 / Biso mean: 36.915 Å2 / Biso min: 5.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----2.77 Å2
Refinement stepCycle: final / Resolution: 2.9→32.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26328 0 184 683 27195
Biso mean--53.02 30.39 -
Num. residues----3384
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01327068
X-RAY DIFFRACTIONr_bond_other_d0.0010.01724408
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.64436684
X-RAY DIFFRACTIONr_angle_other_deg1.3371.56956320
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.71153376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.43321.6751576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.064154224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.54115224
X-RAY DIFFRACTIONr_chiral_restr0.0730.23488
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0231216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026160
LS refinement shellResolution: 2.905→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 361 -
Rwork0.234 7785 -
all-8146 -
obs--91.58 %

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