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- PDB-7cmy: Isocitrate lyase from Bacillus cereus ATCC 14579 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 7cmy
TitleIsocitrate lyase from Bacillus cereus ATCC 14579 in complex with Magnessium ion, glyoxylate, and succinate
ComponentsIsocitrate lyase
KeywordsLYASE / Isocitrate lyase / Bacillus cereus / Glyoxylate cycle / Metal utilization enzyme
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
GLYOXYLIC ACID / SUCCINIC ACID / Isocitrate lyase
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKim, K. / Ki, D. / Lee, S.H.
CitationJournal: To Be Published
Title: Isocitrate lyase from Bacillus cereus ATCC 14579 in complex with Magnessium ion, glyoxylate, and succinate
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
C: Isocitrate lyase
A: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,3908
Polymers95,9572
Non-polymers4336
Water3,477193
1
C: Isocitrate lyase
A: Isocitrate lyase
hetero molecules

C: Isocitrate lyase
A: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,78016
Polymers191,9144
Non-polymers86612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area32640 Å2
ΔGint-171 kcal/mol
Surface area50740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.910, 94.910, 196.156
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Isocitrate lyase


Mass: 47978.539 Da / Num. of mol.: 2
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)
Strain: ATCC 14579 / DSM 31 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NRRL B-3711
Gene: BC_1128 / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q81GQ9, isocitrate lyase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H2O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.3 Å3/Da / Density % sol: 46.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 50% PEG 400, 100mM CHES pH 9.5, 200mM NaCl

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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: Jul 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 31543 / % possible obs: 98.3 % / Redundancy: 5.3 % / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.086 / Rrim(I) all: 0.199 / Χ2: 3.343 / Net I/σ(I): 7.7 / Num. measured all: 168058
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.545.51.20115490.6250.5561.331.89999.3
2.54-2.595.50.92415580.6720.4271.0241.94799
2.59-2.645.50.77815580.7570.360.8622.09599.1
2.64-2.695.50.715590.7720.3250.7762.19999.2
2.69-2.755.70.69115400.7970.3160.7642.20899.2
2.75-2.825.60.62115760.8460.2860.6872.33899.4
2.82-2.895.70.54915690.8660.2530.6082.62199.5
2.89-2.965.70.45815630.8880.2110.5072.82899.4
2.96-3.055.70.41115770.9110.190.4552.9499.6
3.05-3.155.70.40715850.9170.1860.453.02299.8
3.15-3.265.70.31416000.9410.1450.3483.41299.8
3.26-3.395.60.25615690.9620.1190.2843.81399.5
3.39-3.555.40.21115900.9720.10.2354.199.3
3.55-3.735.30.16215750.9780.0780.1814.47998.9
3.73-3.975.10.13515920.9840.0660.1524.75298.2
3.97-4.274.80.10815650.9870.0550.1224.81897.7
4.27-4.74.80.10215820.9880.0510.1154.93997.2
4.7-5.384.80.09615810.9910.0480.1084.77496.6
5.38-6.7850.09716340.990.0480.114.43796.9
6.78-504.20.06816210.9940.0380.0794.60590

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Processing

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

3i4e


Resolution: 2.5→36.28 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.899 / SU B: 11.185 / SU ML: 0.251 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.753 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 1563 5 %RANDOM
Rwork0.1964 ---
obs0.2007 29820 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.53 Å2 / Biso mean: 45.827 Å2 / Biso min: 24.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å2-0 Å20 Å2
2---0.25 Å20 Å2
3---0.51 Å2
Refinement stepCycle: final / Resolution: 2.5→36.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6454 0 28 193 6675
Biso mean--56.72 46.04 -
Num. residues----832
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136628
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175991
X-RAY DIFFRACTIONr_angle_refined_deg1.6721.648964
X-RAY DIFFRACTIONr_angle_other_deg1.3291.57613896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.525831
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.96922.735362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.586151094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7711540
X-RAY DIFFRACTIONr_chiral_restr0.0770.2855
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027578
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021414
LS refinement shellResolution: 2.5→2.56 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.325 104 -
Rwork0.22 2204 -
obs--99.06 %

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