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- PDB-7cmx: Isocitrate lyase from Bacillus cereus ATCC 14579 -

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Basic information

Entry
Database: PDB / ID: 7cmx
TitleIsocitrate lyase from Bacillus cereus ATCC 14579
ComponentsIsocitrate lyase
KeywordsLYASE / Isocitrate lyase / Bacillus cereus / Glyoxylate cycle / Metal utilization enzyme
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
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsKim, K. / Ki, D. / Lee, S.H.
CitationJournal: To Be Published
Title: Isocitrate lyase from Bacillus cereus ATCC 14579
Authors: Kim, K. / Ki, D. / Lee, S.H.
History
DepositionJul 29, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 4, 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
B: Isocitrate lyase
C: Isocitrate lyase
D: Isocitrate lyase


Theoretical massNumber of molelcules
Total (without water)191,9144
Polymers191,9144
Non-polymers00
Water17,817989
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, size-exclusive chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30900 Å2
ΔGint-154 kcal/mol
Surface area50550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.920, 123.539, 170.688
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Isocitrate lyase /


Mass: 47978.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711) (bacteria)
Gene: BC_1128 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q81GQ9, isocitrate lyase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 989 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 16% PEG3350, 4% Tacsimate pH 5.0

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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: Apr 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 141236 / % possible obs: 96.1 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.045 / Rrim(I) all: 0.132 / Χ2: 2.497 / Net I/σ(I): 9.3 / Num. measured all: 962437
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.79-1.823.50.35666330.2790.1970.4121.36791.3
1.82-1.853.70.34466200.3630.1840.3931.38691.2
1.85-1.8940.32666920.4410.1680.371.38191.7
1.89-1.934.20.31367130.5380.1570.3541.4392.7
1.93-1.974.50.29567530.6310.140.331.49692.8
1.97-2.0250.27668920.7180.1240.3061.58794.8
2.02-2.075.40.25769730.820.1120.2821.66695.7
2.07-2.125.80.23870730.870.10.261.72696.6
2.12-2.186.20.22471120.8970.090.2421.79397.4
2.18-2.266.50.2170800.9240.0830.2271.86997.2
2.26-2.346.70.19370680.9450.0750.2081.90796.8
2.34-2.436.90.18171040.950.0690.1951.9797.2
2.43-2.547.10.16771260.970.0620.1792.06797
2.54-2.677.50.14971490.9780.0540.1592.23397.6
2.67-2.847.80.13671870.9830.0480.1442.39197.5
2.84-3.068.40.1272370.9880.0410.1272.57698.2
3.06-3.379.10.10772730.9920.0350.1132.92298.2
3.37-3.8610.70.09573850.9950.0290.13.75199.4
3.86-4.8611.20.08174530.9960.0250.0854.03799.4
4.86-5010.20.07777130.9960.0240.083.65298.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I4E

3i4e


Resolution: 1.79→33.17 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.373 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 7221 5.1 %RANDOM
Rwork0.1753 ---
obs0.1775 133989 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.71 Å2 / Biso mean: 13.159 Å2 / Biso min: 2.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.16 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.79→33.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13099 0 0 989 14088
Biso mean---21.61 -
Num. residues----1687
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01313371
X-RAY DIFFRACTIONr_bond_other_d0.0010.01712087
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.63918097
X-RAY DIFFRACTIONr_angle_other_deg1.4161.57628041
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6851683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.18422.896732
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.4152216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5441580
X-RAY DIFFRACTIONr_chiral_restr0.0790.21731
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215297
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022855
LS refinement shellResolution: 1.791→1.838 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 474 -
Rwork0.327 9084 -
all-9558 -
obs--88.77 %

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