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- PDB-3eol: 2.0A crystal structure of isocitrate lyase from Brucella melitens... -

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Basic information

Entry
Database: PDB / ID: 3eol
Title2.0A crystal structure of isocitrate lyase from Brucella melitensis (P43212)
Componentsisocitrate lyase
KeywordsLYASE / BRUCELLA / MELITENSIS / ISOCITRATE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID
Function / homology
Function and homology information


isocitrate lyase / isocitrate lyase activity / carboxylic acid metabolic process / 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
DI(HYDROXYETHYL)ETHER / Isocitrate lyase / Isocitrate lyase
Similarity search - Component
Biological speciesBrucella melitensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structures of isocitrate lyase from Brucella melitensis
Authors: SSGCID
History
DepositionSep 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: isocitrate lyase
B: isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7175
Polymers94,4122
Non-polymers3043
Water4,035224
1
A: isocitrate lyase
B: isocitrate lyase
hetero molecules

A: isocitrate lyase
B: isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,43310
Polymers188,8244
Non-polymers6096
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area20410 Å2
ΔGint-118 kcal/mol
Surface area53750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.702, 79.702, 281.595
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein isocitrate lyase / E.C.4.1.3.1


Mass: 47206.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: BIOVAR ABORTUS 2308 / Gene: BMEI0409 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q8YIN4, UniProt: Q2YQA0*PLUS, isocitrate lyase
#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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.37 Å3/Da / Density % sol: 48.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion
Details: 20% PEG 8000, 0.05M KH2PO4, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 9, 2008 / Details: ADJUSTABLE FOCUSING MIRRORS
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→39.84 Å / Num. obs: 62451 / % possible obs: 99.9 % / Redundancy: 6.64 % / Rmerge(I) obs: 0.156 / Χ2: 0.97 / Scaling rejects: 3133
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
2-2.077.780.6252.14749861051.01100
2.07-2.157.820.5472.44822261621.03100
2.15-2.257.740.4882.84761461471.04100
2.25-2.377.490.4263.24617561531.05100
2.37-2.527.20.363.84457561741.05100
2.52-2.716.730.2934.44200862131.03100
2.71-2.996.120.2155.53841562360.9499.9
2.99-3.425.440.156.73443662690.8299.9
3.42-4.314.830.10793144863250.8399.5
4.31-39.845.40.067163724866670.7599.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 49.74 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å39.9 Å
Translation3 Å39.9 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.7Ldata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.925 / WRfactor Rfree: 0.281 / WRfactor Rwork: 0.237 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.814 / SU B: 4.652 / SU ML: 0.13 / SU R Cruickshank DPI: 0.182 / SU Rfree: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.263 3161 5.1 %RANDOM
Rwork0.221 ---
all0.223 62437 --
obs0.223 62437 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 67.16 Å2 / Biso mean: 37.863 Å2 / Biso min: 23.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å20 Å2
2---0.57 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5596 0 20 224 5840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225736
X-RAY DIFFRACTIONr_bond_other_d0.0010.022
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9557735
X-RAY DIFFRACTIONr_angle_other_deg0.48933
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.125716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63823.824272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.81415941
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.791541
X-RAY DIFFRACTIONr_chiral_restr0.0870.2831
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024398
X-RAY DIFFRACTIONr_gen_planes_other0.0040.022
X-RAY DIFFRACTIONr_nbd_refined0.20.22600
X-RAY DIFFRACTIONr_nbtor_refined0.3020.23910
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.2174
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1920.226
X-RAY DIFFRACTIONr_mcbond_it0.7521.53680
X-RAY DIFFRACTIONr_mcangle_it1.19125658
X-RAY DIFFRACTIONr_scbond_it1.92332341
X-RAY DIFFRACTIONr_scangle_it3.1284.52076
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 229 -
Rwork0.291 4299 -
all-4528 -
obs--99.93 %

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