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- PDB-1f61: CRYSTAL STRUCTURE OF ISOCITRATE LYASE FROM MYCOBACTERIUM TUBERCULOSIS -

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Basic information

Entry
Database: PDB / ID: 1f61
TitleCRYSTAL STRUCTURE OF ISOCITRATE LYASE FROM MYCOBACTERIUM TUBERCULOSIS
ComponentsISOCITRATE LYASE
KeywordsLYASE / ALPHA-BETA BARREL / SWAPPED HELICES / APO-ENZYME / OPEN CONFORMATION / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


methylisocitrate lyase / methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / zymogen binding / glyoxylate cycle / tricarboxylic acid cycle / cellular response to hypoxia ...methylisocitrate lyase / methylisocitrate lyase activity / isocitrate lyase / isocitrate lyase activity / isocitrate metabolic process / response to host immune response / zymogen binding / glyoxylate cycle / tricarboxylic acid cycle / cellular response to hypoxia / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Isocitrate lyase / Isocitrate lyase family / Isocitrate lyase/phosphorylmutase, conserved site / Isocitrate lyase signature. / 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 1 / Isocitrate lyase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSharma, V. / Sharma, S. / Hoener zu Bentrup, K.H. / McKinney, J.D. / Russell, D.G. / Jacobs Jr., W.R. / Sacchettini, J.C. / TB Structural Genomics Consortium (TBSGC)
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Structure of isocitrate lyase, a persistence factor of Mycobacterium tuberculosis.
Authors: Sharma, V. / Sharma, S. / Hoener zu Bentrup, K. / McKinney, J.D. / Russell, D.G. / Jacobs Jr., W.R. / Sacchettini, J.C.
History
DepositionJun 19, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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.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_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_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_conn.ptnr2_label_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,4604
Polymers94,4112
Non-polymers492
Water12,466692
1
A: ISOCITRATE LYASE
B: ISOCITRATE LYASE
hetero molecules

A: ISOCITRATE LYASE
B: ISOCITRATE LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,9198
Polymers188,8224
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area29140 Å2
ΔGint-190 kcal/mol
Surface area53440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)130.245, 130.245, 288.405
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-977-

HOH

21A-978-

HOH

31A-1049-

HOH

41B-976-

HOH

51B-979-

HOH

61B-1013-

HOH

71B-1077-

HOH

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Components

#1: Protein ISOCITRATE LYASE /


Mass: 47205.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Species: Mycobacterium tuberculosis / Strain: H37RV / Plasmid: PET30B / Production host: Escherichia coli (E. coli)
References: UniProt: P0A5H3, UniProt: P9WKK7*PLUS, isocitrate lyase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 692 / 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: 3.74 Å3/Da / Density % sol: 67.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium citrate, HEPES, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
10.1 MTris-HCl1reservoir
20.2 Msodium acetate1reservoir
320-30 %(w/v)PEG40001reservoir
41
51

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONAPS 19-ID10.9791
SYNCHROTRONAPS 14-BM-D20.9798
Detector
TypeIDDetectorDate
ADSC QUANTUM 11CCDApr 13, 1999
ADSC2CCDJun 13, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97981
ReflectionResolution: 2→20 Å / Num. all: 97699 / Num. obs: 97699 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 11.08 % / Biso Wilson estimate: 21.2 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.5
Reflection shellResolution: 2→2.07 Å / Redundancy: 10 % / Rmerge(I) obs: 0.37 / Num. unique all: 9617 / % possible all: 100
Reflection
*PLUS
Num. measured all: 1082279
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.37

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 2→20 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 665225.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.191 8587 10 %RANDOM
Rwork0.165 ---
all0.175 86163 --
obs0.165 77576 88 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.25 Å2 / ksol: 0.387 e/Å3
Displacement parametersBiso mean: 30.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.26 Å21.66 Å20 Å2
2--3.26 Å20 Å2
3----6.51 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6484 0 2 692 7178
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d22.7
X-RAY DIFFRACTIONc_improper_angle_d1.04
X-RAY DIFFRACTIONc_mcbond_it0.751.5
X-RAY DIFFRACTIONc_mcangle_it1.212
X-RAY DIFFRACTIONc_scbond_it1.222
X-RAY DIFFRACTIONc_scangle_it1.872.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.244 1389 10.1 %
Rwork0.211 12410 -
obs--86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.9 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.04
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.244 / % reflection Rfree: 10.1 % / Rfactor Rwork: 0.211

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