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- PDB-3p0x: Crystal structure of isocitrate lyase from Brucella melitensis, b... -

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Basic information

Entry
Database: PDB / ID: 3p0x
TitleCrystal structure of isocitrate lyase from Brucella melitensis, bound to magnesium isocitrate
ComponentsIsocitrate lyase
KeywordsLYASE / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glyoxysome / 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
ISOCITRIC ACID / Isocitrate lyase
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of isocitrate lyase from Brucella melitensis, bound to magnesium isocitrate
Authors: SSGCID / Gardberg, A. / Edwards, T. / Gander, M. / Staker, B. / Stewart, L.
History
DepositionSep 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 9, 2011Group: Non-polymer description
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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 / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)189,83018
Polymers188,5924
Non-polymers1,23814
Water12,376687
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area31210 Å2
ΔGint-174 kcal/mol
Surface area47690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.910, 135.930, 181.790
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 / Refine code: 4 / Auth seq-ID: 1 - 450 / Label seq-ID: 1 - 450

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

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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 melitensis biovar Abortus (bacteria)
Strain: 2308 / Gene: aceA, BAB1_1631, BruAb1_1601 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2YQA0, isocitrate lyase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ICT / ISOCITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Internal tracking number 217292B10. Protein (26 mg/mL) and PACT Screen condition B10: 0.2 M MgCl2, 20% PEG6000, 0.1 M MES pH 6.0, 5 mM isocitrate, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Aug 26, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.35→47.6 Å / Num. all: 80134 / Num. obs: 79958 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 28.906 Å2 / Rmerge(I) obs: 0.101 / Net I/σ(I): 12.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
2.35-2.412.90.5632170555866581799.2
2.41-2.480.5122.217068568299.6
2.48-2.550.4272.717091553299.8
2.55-2.630.3513.317121538499.9
2.63-2.710.31417142521599.8
2.71-2.810.2624.717174506099.9
2.81-2.910.2195.9171854906100
2.91-3.030.1787.417044472299.9
3.03-3.170.1548.716573451899.9
3.17-3.320.11911.115967436199.9
3.32-3.50.09513.515160412699.9
3.5-3.720.07217.614590390299.6
3.72-3.970.06320.214231368099.8
3.97-4.290.05523.4141873463100
4.29-4.70.0527.314362317699.9
4.7-5.250.04928.6147672906100
5.25-6.070.05727150552566100
6.07-7.430.05531.1158992203100
7.43-10.510.03147.2123051743100
10.510.02847.7641999697.6

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Phasing

Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å47.63 Å
Translation2.5 Å47.63 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.004data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OQ8

3oq8


Resolution: 2.35→47.6 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.901 / SU B: 15.289 / SU ML: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3991 5 %RANDOM
Rwork0.178 ---
all0.18 80134 --
obs0.18 79682 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.264 Å2
Baniso -1Baniso -2Baniso -3
1-1.12 Å20 Å20 Å2
2---0.38 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.35→47.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12879 0 80 687 13646
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213285
X-RAY DIFFRACTIONr_bond_other_d0.0010.028853
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.94917998
X-RAY DIFFRACTIONr_angle_other_deg0.879321479
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.67151703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77824.029623
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.061152081
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5851586
X-RAY DIFFRACTIONr_chiral_restr0.0710.21939
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215244
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022802
X-RAY DIFFRACTIONr_mcbond_it0.4311.58400
X-RAY DIFFRACTIONr_mcbond_other0.1131.53461
X-RAY DIFFRACTIONr_mcangle_it0.818213272
X-RAY DIFFRACTIONr_scbond_it1.41734885
X-RAY DIFFRACTIONr_scangle_it2.344.54718
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 5293 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
AMEDIUM POSITIONAL0.290.5
BMEDIUM POSITIONAL0.380.5
CMEDIUM POSITIONAL0.30.5
DMEDIUM POSITIONAL0.270.5
AMEDIUM THERMAL0.432
BMEDIUM THERMAL0.42
CMEDIUM THERMAL0.432
DMEDIUM THERMAL0.432
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 260 -
Rwork0.269 5524 -
all-5784 -
obs-5817 98.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.28970.16170.06060.6342-0.18370.96460.00570.02580.01530.0082-0.0078-0.0036-0.2034-0.00030.00210.07220.01260.00330.0074-0.00090.016357.37166.42829.144
20.18820.06930.0660.712-0.32740.87760.0192-0.04160.00150.0699-0.112-0.15170.01860.31120.09280.03120.0002-0.03040.13930.03670.063278.057148.25446.434
30.11450.0917-0.13180.4493-0.24490.9386-0.0180.02410.0017-0.00960.0340.07430.2022-0.1908-0.01610.0751-0.05940.01240.05660.00030.02143.649133.28843.737
40.13680.1509-0.18050.4087-0.31251.242-0.04880.0439-0.0454-0.155-0.0036-0.04690.36330.02950.05240.19410.02090.03430.0293-0.01620.021861.08131.4516.168
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 450
2X-RAY DIFFRACTION2B3 - 450
3X-RAY DIFFRACTION3C3 - 450
4X-RAY DIFFRACTION4D3 - 450

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