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- PDB-6vbk: Crystal structure of N-terminal domain of Mycobacterium tuberculo... -

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Basic information

Entry
Database: PDB / ID: 6vbk
TitleCrystal structure of N-terminal domain of Mycobacterium tuberculosis complex Lon protease
ComponentsLon211
KeywordsHYDROLASE / Lon protease
Function / homologyMethane Monooxygenase Hydroxylase; Chain G, domain 1 - #1480 / LON domain-like / Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Roll / Up-down Bundle / Mainly Beta / Mainly Alpha
Function and homology information
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBi, F.K. / Chen, C. / Chen, X.Y. / Guo, C.Y. / Lin, D.H.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China) China
Citation
Journal: Protein Sci. / Year: 2019
Title: Crystal structure of the N domain of Lon protease from Mycobacterium avium complex.
Authors: Chen, X. / Zhang, S. / Bi, F. / Guo, C. / Feng, L. / Wang, H. / Yao, H. / Lin, D.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionDec 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lon211
B: Lon211
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0853
Polymers44,9932
Non-polymers921
Water4,143230
1
A: Lon211
hetero molecules

B: Lon211


Theoretical massNumber of molelcules
Total (without water)45,0853
Polymers44,9932
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-x-1,y-1/2,-z1
Buried area1450 Å2
ΔGint-9 kcal/mol
Surface area22360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.344, 77.454, 53.252
Angle α, β, γ (deg.)90.000, 93.257, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Lon211


Mass: 22496.547 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Production host: Escherichia coli K-12 (bacteria)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.3 Å3/Da / Density % sol: 46.61 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: PEG 6000, Citric acid / PH range: 4.6-4.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97891 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97891 Å / Relative weight: 1
ReflectionResolution: 1.997→50 Å / Num. obs: 27491 / % possible obs: 98.97 % / Redundancy: 6.8 % / Biso Wilson estimate: 50.79 Å2 / CC1/2: 0.998 / Net I/σ(I): 1344
Reflection shellResolution: 1.997→2.069 Å / Num. unique obs: 2622 / CC1/2: 0.82

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
PHENIXmodel building
HKL-3000data scaling
REFMACphasing
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IHG

6ihg


Resolution: 2→43.83 Å / SU ML: 0.2836 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Phase error: 32.3195
RfactorNum. reflection% reflection
Rfree0.2395 1390 5.06 %
Rwork0.2022 --
obs0.2042 27489 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.78 Å2
Refinement stepCycle: LAST / Resolution: 2→43.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 6 230 3353
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643169
X-RAY DIFFRACTIONf_angle_d0.79684319
X-RAY DIFFRACTIONf_chiral_restr0.055514
X-RAY DIFFRACTIONf_plane_restr0.004569
X-RAY DIFFRACTIONf_dihedral_angle_d20.27561186
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.34921070.3022495X-RAY DIFFRACTION95.17
2.07-2.150.31951220.27322668X-RAY DIFFRACTION99.89
2.15-2.250.29311250.26462627X-RAY DIFFRACTION99.85
2.25-2.370.3151450.26652621X-RAY DIFFRACTION99.89
2.37-2.520.30681380.26222583X-RAY DIFFRACTION97.91
2.52-2.710.32071520.24522611X-RAY DIFFRACTION99.93
2.71-2.980.28161510.24322634X-RAY DIFFRACTION99.89
2.98-3.410.25891570.21112575X-RAY DIFFRACTION98.52
3.41-4.30.20221390.18042645X-RAY DIFFRACTION99.82
4.3-5.430.20871540.172640X-RAY DIFFRACTION98.17
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)
13.65728343427-1.304701709410.736947649990.687577817283-0.9543613058211.82406397947-0.1675854280270.5313656502050.439539737067-0.3104185313030.0727472714-0.59159316161-0.5696187093650.3748639594610.5351210599230.537005981309-0.1068404271620.06988282597470.583621198314-0.1778208262880.779378292221-0.79141819016116.7765740465-24.8161864956
25.63177904772-1.11535972355-3.789807030765.0097078906-1.018552145113.27257385155-0.320704642114-0.458840066339-0.3263945375910.217095715106-0.192643283522-0.972767230890.6369142602550.364131213390.2774676765250.5447957605010.01362563481840.01139215842780.485390513902-0.08226488204090.683550560733-3.92037334924.50318898648-21.9239211768
32.44204364781-1.40773128592-0.02370472822592.565896425320.1023768994322.449674357760.06813912467260.353810918822-0.0218494230409-0.2037161348510.0186740806925-0.241172816207-0.3188797256890.0255558488099-0.1223000200290.399217546155-0.0192590301892-0.003828273336650.375680830037-0.09488512384120.371512481274-17.980476660517.312224475-26.0541484757
41.244754624310.0660974311939-0.0361762601187-0.03445280852850.2452128128394.15646534779-0.3653669482970.09622183003960.1392347495230.106309558326-0.110757703536-0.06238354723640.3816884681450.2038745753480.4981171884950.4961725086470.05834286018440.01565151770580.37094976276-0.0003442086300680.573227505845-36.944401875329.36172635197.67790723244
54.39204859777-1.074106141-0.1725822993413.648645463321.6952524064.19752694944-0.703881257967-0.110562832032-0.0831486100008-0.11269535114-0.1641451284361.437549070440.533748792701-1.629004374160.6204878517490.442431710012-0.0385523053388-0.03098025697120.617387756783-0.2003182438530.568069120511-49.440958578124.1121054891-7.21513705612
60.161108370297-0.2138664885890.1401848353668.7441051162-2.758889721460.9971719333640.4170031455650.253001564581.071187798820.09246204999840.4176856286310.0578544840994-2.04872154253-0.849435742444-0.8683713943131.308504773940.1587181774950.2690928063830.8698186850250.128255017450.784363625342-45.241977201542.7252553738-9.8743031882
76.3625735855-2.354685492762.423093284839.40024564944-6.625570521474.77431265488-0.34354093689-1.51134133422-1.280498260170.959045505434-0.3936197963550.08508429590620.219505061235-0.4720261057280.9002288969790.92336459106-0.03413907799760.2307852396570.8989097394550.0358678297820.57335897814-44.225688363919.37191598855.14910747311
85.25384294517-1.60738133428-0.8252057036973.806751667121.316326728342.97691279893-0.478968372223-0.8230291517160.1707992936360.4068321608760.122764916010.375550353512-0.1563631407190.04708566737640.3008267712010.4727168102720.05699951907850.00842487412570.603296623942-0.03265304702470.39038875517-40.580362761426.5046494892-1.12928782573
95.16651302441-2.931233045250.4123252124636.177948947430.5859532656584.61153947864-0.688396840238-0.958716811944-0.4640270887490.9476119585350.899859969212-0.5449459301030.1844160476220.679596627051-0.09914953450220.4821103283620.1617918649820.01207748722740.5435955570610.01806851149840.498864280237-20.597293056813.3384847729-5.50720615384
102.86356450928-2.24030673408-0.6639264765773.19239899908-0.5392618286410.964126057455-1.07577117248-1.59190138662-0.6151870141891.670659603921.024864055690.1521787415990.108535648263-0.09499692824160.1218345541221.138892542090.3999422406230.3635057690481.058491610240.4576856625990.73662475741-32.284414427412.4761129144.40230719309
114.36788792694-2.83655358265-0.5103004094564.839200006061.014356949993.29513206874-0.749898314477-1.86227188773-1.021220607882.074675890790.703020253134-0.1129129508770.278048232002-0.06850675979920.001771974401061.086742295240.4211685547930.09338014507181.057014786990.4275295253330.787683611432-23.21698194349.675671623215.01351086412
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 70 )
3X-RAY DIFFRACTION3chain 'A' and (resid 71 through 212 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 28 )
5X-RAY DIFFRACTION5chain 'B' and (resid 29 through 51 )
6X-RAY DIFFRACTION6chain 'B' and (resid 52 through 64 )
7X-RAY DIFFRACTION7chain 'B' and (resid 65 through 78 )
8X-RAY DIFFRACTION8chain 'B' and (resid 79 through 132 )
9X-RAY DIFFRACTION9chain 'B' and (resid 133 through 177 )
10X-RAY DIFFRACTION10chain 'B' and (resid 178 through 194 )
11X-RAY DIFFRACTION11chain 'B' and (resid 195 through 210 )

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