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- PDB-3lg3: 1.4A Crystal Structure of Isocitrate Lyase from Yersinia pestis CO92 -

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Basic information

Entry
Database: PDB / ID: 3lg3
Title1.4A Crystal Structure of Isocitrate Lyase from Yersinia pestis CO92
ComponentsIsocitrate lyase
KeywordsLYASE / Isocitrate Lyase / Conserved / CD / Proteomics evidence (Cytoplasmid or periplasmic) / Drug target functions / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
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
Isocitrate lyase / Isocitrate lyase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsSharma, S.S. / Brunzelle, J.S. / Skarina, T. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To be Published
Title: 1.4A Crystal Structure of Isocitrate Lyase from Yersinia pestis CO92
Authors: Sharma, S.S. / Brunzelle, J.S. / Wawrzak, Z. / Skarina, T. / Gordon, E. / Savchenko, A. / Anderson, W.F.
History
DepositionJan 19, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 14, 2011Group: Structure summary
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Isocitrate lyase
B: Isocitrate lyase


Theoretical massNumber of molelcules
Total (without water)96,3732
Polymers96,3732
Non-polymers00
Water21,1321173
1
A: Isocitrate lyase
B: Isocitrate lyase

A: Isocitrate lyase
B: Isocitrate lyase


Theoretical massNumber of molelcules
Total (without water)192,7464
Polymers192,7464
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area28470 Å2
ΔGint-181 kcal/mol
Surface area54560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.163, 115.133, 174.835
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-954-

HOH

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Components

#1: Protein Isocitrate lyase


Mass: 48186.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: aceA, y0016, YPO3725, YP_3087 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Codonplus(de3) Ril
References: UniProt: Q7CLE1, UniProt: A0A2S9PCG6*PLUS, isocitrate lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1173 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.46 Å3/Da / Density % sol: 49.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M LiCitrate, PEG3350 20%, 10mm iso Citric acid, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 7, 2009 / Details: Be Lenes
RadiationMonochromator: Single Diamond 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. all: 185843 / Num. obs: 185843 / % possible obs: 99.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 28.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.519 / Mean I/σ(I) obs: 2.86 / Num. unique all: 9150 / % possible all: 99.4

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
CRANKphasing
ARP/wARPmodel building
PHENIX(phenix.refine: 1.4_115)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.4→24.558 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1653 9030 5.02 %RANDOM
Rwork0.1311 ---
obs0.1329 179982 96.39 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.003 Å2 / ksol: 0.375 e/Å3
Refinement stepCycle: LAST / Resolution: 1.4→24.558 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6452 0 0 1173 7625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056878
X-RAY DIFFRACTIONf_angle_d0.9139374
X-RAY DIFFRACTIONf_dihedral_angle_d16.3622459
X-RAY DIFFRACTIONf_chiral_restr0.066997
X-RAY DIFFRACTIONf_plane_restr0.0041253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.44690.23178200.157515575X-RAY DIFFRACTION89
1.4469-1.50480.20878700.135916228X-RAY DIFFRACTION92
1.5048-1.57330.17378840.114416699X-RAY DIFFRACTION95
1.5733-1.65620.17778930.114416976X-RAY DIFFRACTION96
1.6562-1.760.16139230.111617149X-RAY DIFFRACTION97
1.76-1.89580.15689500.116417342X-RAY DIFFRACTION98
1.8958-2.08650.1599070.121817588X-RAY DIFFRACTION99
2.0865-2.38820.14669190.12317699X-RAY DIFFRACTION100
2.3882-3.0080.16079090.135217805X-RAY DIFFRACTION100
3.008-24.56140.1559550.137817891X-RAY DIFFRACTION98

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