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- PDB-1l5j: CRYSTAL STRUCTURE OF E. COLI ACONITASE B. -

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Basic information

Entry
Database: PDB / ID: 1l5j
TitleCRYSTAL STRUCTURE OF E. COLI ACONITASE B.
ComponentsAconitate hydratase 2Aconitase
KeywordsLYASE / Molecular recognition / RNA binding / Citric acid cycle / HEAT-like domain
Function / homology
Function and homology information


2-methylisocitrate dehydratase / 2-methylisocitrate dehydratase activity / : / aconitate hydratase / propionate catabolic process, 2-methylcitrate cycle / aconitate hydratase activity / glyoxylate cycle / tricarboxylic acid cycle / mRNA 3'-UTR binding / regulation of translation ...2-methylisocitrate dehydratase / 2-methylisocitrate dehydratase activity / : / aconitate hydratase / propionate catabolic process, 2-methylcitrate cycle / aconitate hydratase activity / glyoxylate cycle / tricarboxylic acid cycle / mRNA 3'-UTR binding / regulation of translation / 4 iron, 4 sulfur cluster binding / mRNA binding / metal ion binding / cytosol
Similarity search - Function
Aconitate B, HEAT-like domain / Aconitase B / Aconitase B, swivel / Aconitase B, HEAT-like domain / Aconitase B, HEAT-like domain superfamily / Aconitate hydratase 2 N-terminus / Aconitate B N-terminal domain / Aconitase, domain 2 / Aconitase; Domain 2 / Aconitase, Domain 2 ...Aconitate B, HEAT-like domain / Aconitase B / Aconitase B, swivel / Aconitase B, HEAT-like domain / Aconitase B, HEAT-like domain superfamily / Aconitate hydratase 2 N-terminus / Aconitate B N-terminal domain / Aconitase, domain 2 / Aconitase; Domain 2 / Aconitase, Domain 2 / Aconitase; domain 3 / Aconitase, domain 3 / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha domain / Aconitase/3-isopropylmalate dehydratase large subunit, alpha/beta/alpha, subdomain 1/3 / Aconitase family, 4Fe-4S cluster binding site / Aconitase, iron-sulfur domain / Aconitase family (aconitate hydratase) / Aconitase family signature 1. / Aconitase family signature 2. / Aconitase; domain 4 / Aconitase, domain 4 / Aconitase/3-isopropylmalate dehydratase, swivel / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Alpha-Beta Barrel / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FE3-S4 CLUSTER / ACONITATE ION / Aconitate hydratase B
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.4 Å
AuthorsWilliams, C.H. / Stillman, T.J. / Barynin, V.V. / Sedelnikova, S.E. / Tang, Y. / Green, J. / Guest, J.R. / Artymiuk, P.J.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: E. coli aconitase B structure reveals a HEAT-like domain with implications for protein-protein recognition.
Authors: Williams, C.H. / Stillman, T.J. / Barynin, V.V. / Sedelnikova, S.E. / Tang, Y. / Green, J. / Guest, J.R. / Artymiuk, P.J.
History
DepositionMar 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Aconitate hydratase 2
B: Aconitate hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,1366
Polymers187,2022
Non-polymers9344
Water10,269570
1
A: Aconitate hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0683
Polymers93,6011
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aconitate hydratase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,0683
Polymers93,6011
Non-polymers4672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)138.970, 169.630, 113.380
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Aconitate hydratase 2 / Aconitase / Citrate hydro-lyase 2 / Aconitase 2


Mass: 93600.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pGS783 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P36683, aconitate hydratase
#2: Chemical ChemComp-TRA / ACONITATE ION / Aconitic acid


Mass: 171.084 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H3O6
#3: Chemical ChemComp-F3S / FE3-S4 CLUSTER / Iron–sulfur cluster


Mass: 295.795 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe3S4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 570 / 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: 3.57 Å3/Da / Density % sol: 65.52 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: ammonium sulphate, HEPES, cobalt chloride, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Temperature: 17 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.2 Mammonium sulfate1reservoir
20.1 MHEPES1reservoirpH7.1
310 mM1reservoirCoCl2
440-60 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.5 / Wavelength: 0.9 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 28, 1996
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 100790 / Num. obs: 100790 / % possible obs: 96.02 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.04 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.23 / % possible all: 93.6
Reflection
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.073
Reflection shell
*PLUS
% possible obs: 94 % / Rmerge(I) obs: 0.449

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Processing

Software
NameVersionClassification
MLPHAREphasing
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MIR / Resolution: 2.4→20 Å / SU B: 5.838 / SU ML: 0.135 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.19 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.20278 5019 5 %RANDOM
Rwork0.15115 ---
obs0.15375 100790 96.02 %-
all-100790 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.576 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.75 Å2
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13104 0 38 580 13722
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02213412
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.97518198
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.20331722
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.149152407
X-RAY DIFFRACTIONr_chiral_restr0.0870.22048
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210170
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2360.36078
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.51072
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.340
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2810.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it12.37428578
X-RAY DIFFRACTIONr_mcangle_it13.099313770
X-RAY DIFFRACTIONr_scbond_it19.00824834
X-RAY DIFFRACTIONr_scangle_it18.71334422
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.278 321
Rwork0.199 6770
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 100794 / Rfactor obs: 0.151 / Rfactor Rfree: 0.204 / Rfactor Rwork: 0.151
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.007
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.183
LS refinement shell
*PLUS
Rfactor Rfree: 0.278 / Rfactor Rwork: 0.199 / Rfactor obs: 0.199

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