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- PDB-3e5b: 2.4 A crystal structure of isocitrate lyase from brucella melitensis -

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Basic information

Entry
Database: PDB / ID: 3e5b
Title2.4 A crystal structure of isocitrate lyase from brucella melitensis
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 / 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 / Isocitrase
Similarity search - Component
Biological speciesBrucella abortus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.37 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: 2.4 A crystal structure of isocitrate lyase from brucella melitensis
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionAug 13, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)188,5924
Polymers188,5924
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26390 Å2
ΔGint-165 kcal/mol
Surface area50140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.255, 137.209, 182.448
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsauthors state that the biological unit is the same as asymmetric unit.

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Components

#1: Protein
isocitrate lyase / / AceA


Mass: 47148.051 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus (bacteria) / Strain: BIOVAR ABORTUS 2308 / Gene: aceA, BruAb1_1601 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q57BR0, UniProt: Q2YQA0*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.56 Å3/Da / Density % sol: 52.02 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 30% PEG 4000, 0.1M TRIS pH 8.5, 0.2M LITHIUM SULFATE, 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: ADSC QUANTUM 315 / 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: 2.37→50 Å / Num. obs: 77975 / % possible obs: 99.6 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.119 / Χ2: 0.955
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.4970.78376850.41999.4
2.49-2.5970.55977050.43899.7
2.59-2.77.10.4276920.51699.7
2.7-2.8570.31777000.57999.6
2.85-3.0270.23377280.74799.6
3.02-3.2670.18177510.93199.7
3.26-3.587.10.14577761.2699.8
3.58-4.17.10.11578621.469100
4.1-5.177.10.09879001.59399.7
5.17-507.20.08781761.599.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 39.49 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å45.61 Å
Translation3 Å45.61 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.006data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.252 / WRfactor Rwork: 0.208 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.812 / SU B: 8.614 / SU ML: 0.2 / SU R Cruickshank DPI: 0.358 / SU Rfree: 0.249 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.358 / ESU R Free: 0.249 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.251 3913 5 %RANDOM
Rwork0.207 ---
obs0.209 77771 98.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 87.94 Å2 / Biso mean: 57.361 Å2 / Biso min: 35.06 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--1.39 Å20 Å2
3----1.27 Å2
Refinement stepCycle: LAST / Resolution: 2.37→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12256 0 0 102 12358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02212521
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.94716948
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74551583
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.01623.97597
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.417152014
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4421584
X-RAY DIFFRACTIONr_chiral_restr0.0870.21815
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.029712
X-RAY DIFFRACTIONr_nbd_refined0.1990.25780
X-RAY DIFFRACTIONr_nbtor_refined0.2990.28588
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1210.2381
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0810.210
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.24
X-RAY DIFFRACTIONr_mcbond_it0.5561.58075
X-RAY DIFFRACTIONr_mcangle_it0.973212459
X-RAY DIFFRACTIONr_scbond_it1.3735090
X-RAY DIFFRACTIONr_scangle_it2.2894.54488
LS refinement shellResolution: 2.371→2.432 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 222 -
Rwork0.293 4266 -
all-4488 -
obs--78.38 %

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