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- PDB-3i4e: Crystal structure of Isocitrate Lyase from Burkholderia pseudomallei -

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Basic information

Entry
Database: PDB / ID: 3i4e
TitleCrystal structure of Isocitrate Lyase from Burkholderia pseudomallei
ComponentsIsocitrate lyase
KeywordsLYASE / isocitrate lyase / structural genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


isocitrate lyase / isocitrate lyase activity / carboxylic acid metabolic process / 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
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsStaker, B.L. / Arakaki, T. / Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Isocitrate Lyase from Burkholderia pseudomallei
Authors: Staker, B.L. / Arakaki, T.
History
DepositionJul 1, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isocitrate lyase
B: Isocitrate lyase
C: Isocitrate lyase
D: Isocitrate lyase


Theoretical massNumber of molelcules
Total (without water)192,5084
Polymers192,5084
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28810 Å2
ΔGint-162 kcal/mol
Surface area52620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.666, 137.025, 160.162
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 5 / Auth seq-ID: 1 - 412 / Label seq-ID: 5 - 416

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Isocitrate lyase /


Mass: 48127.086 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Gene: aceA, BPSL2188 / Plasmid: AVA0421 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q63SY3, isocitrate lyase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.21 Å3/Da / Density % sol: 44.43 %
Crystal growTemperature: 293 K / pH: 5.8
Details: 24% PEG 1500, 100 MM MES, PROTEIN CONCENTRATION 22MG/ML, PH 5.8, VAPOR DIFFUSIONI, SITTING DROP, TEMPERATURE 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1
DetectorDate: Jun 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.69→48.91 Å / Num. obs: 48029 / % possible obs: 99.7 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 5.8
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.66 / % possible all: 97.9

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0088refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1IGW

1igw


Resolution: 2.69→48.91 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.867 / SU B: 15.524 / SU ML: 0.314 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.401 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.277 2426 5.1 %RANDOM
Rwork0.213 ---
obs0.216 47959 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2--2.86 Å20 Å2
3----1.66 Å2
Refinement stepCycle: LAST / Resolution: 2.69→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12580 0 0 150 12730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02212853
X-RAY DIFFRACTIONr_bond_other_d0.0010.028494
X-RAY DIFFRACTIONr_angle_refined_deg1.0191.94117435
X-RAY DIFFRACTIONr_angle_other_deg0.815320693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.10851644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81224.722593
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.073152038
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7461562
X-RAY DIFFRACTIONr_chiral_restr0.0550.21904
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214680
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022650
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3081.58160
X-RAY DIFFRACTIONr_mcbond_other0.0561.53368
X-RAY DIFFRACTIONr_mcangle_it0.577212937
X-RAY DIFFRACTIONr_scbond_it0.67134693
X-RAY DIFFRACTIONr_scangle_it1.1464.54498
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2422medium positional0.160.5
2B2422medium positional0.160.5
3C2422medium positional0.160.5
4D2422medium positional0.170.5
1A2749loose positional0.285
2B2749loose positional0.315
3C2749loose positional0.315
4D2749loose positional0.285
1A2422medium thermal0.322
2B2422medium thermal0.242
3C2422medium thermal0.242
4D2422medium thermal0.222
1A2749loose thermal0.3210
2B2749loose thermal0.2810
3C2749loose thermal0.2810
4D2749loose thermal0.2610
LS refinement shellResolution: 2.69→2.76 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.463 173 -
Rwork0.344 3219 -
obs--96.5 %

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