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- PDB-8g8k: Crystal structure of Rv1916 (residues 233-398) -

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Basic information

Entry
Database: PDB / ID: 8g8k
TitleCrystal structure of Rv1916 (residues 233-398)
ComponentsPutative isocitrate lyase subunit B
KeywordsBIOSYNTHETIC PROTEIN / Isocitrate lyase / tuberculosis
Function / homologyisocitrate lyase / isocitrate lyase activity / Isocitrate lyase / Isocitrate lyase family / carboxylic acid metabolic process / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / DI(HYDROXYETHYL)ETHER / Putative isocitrate lyase subunit B
Function and homology information
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsKwai, B.X.C. / Bashiri, G. / Leung, I.K.H.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Chembiochem / Year: 2023
Title: Mycobacterium tuberculosis Rv1916 is an Acetyl-CoA-Binding Protein.
Authors: Huang, E.Y. / Kwai, B.X.C. / Bhusal, R.P. / Bashiri, G. / Leung, I.K.H.
History
DepositionFeb 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jul 26, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative isocitrate lyase subunit B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2677
Polymers18,8511
Non-polymers4166
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)86.046, 86.046, 73.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Putative isocitrate lyase subunit B / ICL / Isocitrase / Isocitratase


Mass: 18850.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: aceAb, Rv1916, RVBD_1916, LH57_10435, P425_01981 / Production host: Escherichia coli (E. coli) / References: UniProt: O07717, isocitrate lyase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.61 Å3/Da / Density % sol: 65.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% (w/v) PEG3350, 0.2 M potassium thiocyanate, 0.1 M Bis-Tris propane pH 7.5

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Data collection

DiffractionMean temperature: 85 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953724 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953724 Å / Relative weight: 1
ReflectionResolution: 1.54→46.89 Å / Num. obs: 41501 / % possible obs: 100 % / Redundancy: 26.6 % / CC1/2: 0.999 / Net I/σ(I): 12
Reflection shellResolution: 1.54→1.57 Å / Num. unique obs: 2033 / CC1/2: 0.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→46.89 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.193 / SU ML: 0.041 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.057
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.19 2110 5.092 %RANDOM
Rwork0.1702 39325 --
all0.171 ---
obs-41435 99.993 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.503 Å2
Baniso -1Baniso -2Baniso -3
1--0.534 Å20 Å20 Å2
2---0.534 Å20 Å2
3---1.068 Å2
Refinement stepCycle: LAST / Resolution: 1.54→46.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1328 0 27 89 1444
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0121395
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161395
X-RAY DIFFRACTIONr_angle_refined_deg1.7761.6621878
X-RAY DIFFRACTIONr_angle_other_deg0.6031.5773198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9465167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.09514
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.63210260
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.441068
X-RAY DIFFRACTIONr_chiral_restr0.0960.2211
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021618
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02326
X-RAY DIFFRACTIONr_nbd_refined0.210.2267
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1850.21230
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2676
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.2806
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1530.254
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1090.29
X-RAY DIFFRACTIONr_nbd_other0.1430.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1950.212
X-RAY DIFFRACTIONr_mcbond_it2.272.536653
X-RAY DIFFRACTIONr_mcbond_other2.272.535653
X-RAY DIFFRACTIONr_mcangle_it3.2994.54816
X-RAY DIFFRACTIONr_mcangle_other3.3014.54817
X-RAY DIFFRACTIONr_scbond_it4.5313.081742
X-RAY DIFFRACTIONr_scbond_other4.5283.087743
X-RAY DIFFRACTIONr_scangle_it6.7185.3621059
X-RAY DIFFRACTIONr_scangle_other6.7155.3671060
X-RAY DIFFRACTIONr_lrange_it7.63725.61543
X-RAY DIFFRACTIONr_lrange_other7.62525.4441538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.580.2811400.2782870X-RAY DIFFRACTION100
1.58-1.6230.2441340.2652797X-RAY DIFFRACTION99.9659
1.623-1.670.2521560.2352716X-RAY DIFFRACTION100
1.67-1.7220.2381520.2162618X-RAY DIFFRACTION100
1.722-1.7780.2171440.192542X-RAY DIFFRACTION100
1.778-1.840.1921280.172491X-RAY DIFFRACTION100
1.84-1.910.191140.162419X-RAY DIFFRACTION100
1.91-1.9870.1741220.1542311X-RAY DIFFRACTION100
1.987-2.0760.1651240.1512197X-RAY DIFFRACTION100
2.076-2.1770.1941200.1452129X-RAY DIFFRACTION100
2.177-2.2940.1881100.1392027X-RAY DIFFRACTION100
2.294-2.4330.186940.151931X-RAY DIFFRACTION100
2.433-2.60.1751000.1521812X-RAY DIFFRACTION100
2.6-2.8080.206970.1611683X-RAY DIFFRACTION100
2.808-3.0750.194880.1691584X-RAY DIFFRACTION100
3.075-3.4360.198850.1831420X-RAY DIFFRACTION100
3.436-3.9640.209720.1861266X-RAY DIFFRACTION100
3.964-4.8460.135550.141100X-RAY DIFFRACTION100
4.846-6.8180.182430.201879X-RAY DIFFRACTION100
6.818-46.890.199320.182533X-RAY DIFFRACTION100

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