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- PDB-6g1o: Structure of Pseudomonas aeruginosa Isocitrate Lyase, ICL -

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Basic information

Entry
Database: PDB / ID: 6g1o
TitleStructure of Pseudomonas aeruginosa Isocitrate Lyase, ICL
ComponentsIsocitrate lyase
KeywordsLYASE / Isocitrate lyase / Pseudomonas / TCA cycle
Function / homology
Function and homology information


negative regulation of single-species biofilm formation on inanimate substrate / isocitrate lyase / isocitrate lyase activity / glyoxylate cycle / tricarboxylic acid cycle / metal ion binding
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / ICL/PEPM domain / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
Similarity search - Domain/homology
GLYOXYLIC ACID / Isocitrate lyase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.882 Å
AuthorsCrousilles, A. / Welch, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council United Kingdom
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Gluconeogenic precursor availability regulates flux through the glyoxylate shunt inPseudomonas aeruginosa.
Authors: Crousilles, A. / Dolan, S.K. / Brear, P. / Chirgadze, D.Y. / Welch, M.
History
DepositionMar 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Sep 26, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1813
Polymers54,0671
Non-polymers1142
Water3,279182
1
A: Isocitrate lyase
hetero molecules

A: Isocitrate lyase
hetero molecules

A: Isocitrate lyase
hetero molecules

A: Isocitrate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,72512
Polymers216,2684
Non-polymers4568
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area26190 Å2
ΔGint-177 kcal/mol
Surface area71930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.943, 116.023, 128.533
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Isocitrate lyase / ICL / Isocitrase / Isocitratase


Mass: 54067.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) (bacteria)
Gene: PA2634 / Production host: Escherichia coli (E. coli) / Variant (production host): DH5a / References: UniProt: Q9I0K4, isocitrate lyase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-GLV / GLYOXYLIC ACID / GLYOXALATE / GLYOXYLATE


Mass: 74.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / 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: 2.79 Å3/Da / Density % sol: 55.93 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, sitting drop
Details: HEPES 0.1 M pH 5, CaCl2 0.1 M, 20% (w/v) PEG 6000, glycerol 5%, glyoxylate 1 mM and 2% thymol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 13, 2016
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.88→29.492 Å / Num. obs: 48981 / % possible obs: 99.4 % / Redundancy: 12.4 % / Biso Wilson estimate: 26.42 Å2 / Rrim(I) all: 0.0267 / Net I/σ(I): 1.08
Reflection shellResolution: 1.88→1.93 Å / Redundancy: 8.4 % / Num. unique obs: 3287 / Rrim(I) all: 0.387 / % possible all: 92.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation1.88 Å29.49 Å
Translation1.88 Å29.49 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASER2.5.7phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I4E

3i4e


Resolution: 1.882→29.491 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 19.78
RfactorNum. reflection% reflection
Rfree0.2064 2438 4.98 %
Rwork0.174 --
obs0.1756 48981 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.98 Å2 / Biso mean: 35.0135 Å2 / Biso min: 12.04 Å2
Refinement stepCycle: final / Resolution: 1.882→29.491 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 6 182 3986
Biso mean--52.86 32.55 -
Num. residues----486
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 17

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8823-1.92070.30711380.32452417255590
1.9207-1.96250.27291470.23532705285299
1.9625-2.00810.23291400.20327212861100
2.0081-2.05830.23161400.191427142854100
2.0583-2.1140.26031360.191427582894100
2.114-2.17620.20521560.183127312887100
2.1762-2.24640.24151350.173627132848100
2.2464-2.32660.18541400.16627602900100
2.3266-2.41970.20821260.163427372863100
2.4197-2.52980.19371360.163327802916100
2.5298-2.66310.21881270.173327542881100
2.6631-2.82980.21041520.17727412893100
2.8298-3.04810.22461610.176427382899100
3.0481-3.35450.24351710.18627322903100
3.3545-3.8390.21521410.168127992940100
3.839-4.83330.16261610.145227982959100
4.8333-29.49470.17231310.171529453076100

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