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- PDB-6gfv: M tuberculosis LpqI -

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Basic information

Entry
Database: PDB / ID: 6gfv
TitleM tuberculosis LpqI
ComponentsProbable conserved lipoprotein LpqI
KeywordsSUGAR BINDING PROTEIN / Peptidoglycan Mycobacterium GH3
Function / homology
Function and homology information


peptidoglycan turnover / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / cell wall organization / carbohydrate metabolic process / plasma membrane
Similarity search - Function
Glycoside hydrolase, family 3, N-terminal domain / Glycoside hydrolase, family 3, N-terminal / Glycoside hydrolase, family 3, N-terminal domain superfamily / Glycosyl hydrolase family 3 N terminal domain / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Beta-hexosaminidase LpqI
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.96 Å
AuthorsMoynihan, P.J. / Lovering, A.L.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N011945/1 United Kingdom
CitationJournal: Nat Commun / Year: 2019
Title: The hydrolase LpqI primes mycobacterial peptidoglycan recycling.
Authors: Moynihan, P.J. / Cadby, I.T. / Veerapen, N. / Jankute, M. / Crosatti, M. / Mukamolova, G.V. / Lovering, A.L. / Besra, G.S.
History
DepositionMay 2, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.2Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Jan 17, 2024Group: 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: Probable conserved lipoprotein LpqI
B: Probable conserved lipoprotein LpqI


Theoretical massNumber of molelcules
Total (without water)70,7522
Polymers70,7522
Non-polymers00
Water11,440635
1
A: Probable conserved lipoprotein LpqI


Theoretical massNumber of molelcules
Total (without water)35,3761
Polymers35,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Probable conserved lipoprotein LpqI


Theoretical massNumber of molelcules
Total (without water)35,3761
Polymers35,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)121.821, 89.579, 87.107
Angle α, β, γ (deg.)90.000, 125.540, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Probable conserved lipoprotein LpqI


Mass: 35375.969 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: lpqI, Rv0237 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: L7N6B0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 635 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.1M Sodium Malonate 0.1M Hepes 0.5% w/v Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 1.96→70.9 Å / Num. obs: 54634 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 17.58 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.091 / Rrim(I) all: 0.176 / Net I/σ(I): 5.6
Reflection shell

Diffraction-ID: 1 / % possible all: 99.9

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.96-2.0730.7092365879390.6120.4940.8691.4
6.2-70.883.70.052660817930.9930.0320.06113.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.5.1data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4YYF

4yyf


Resolution: 1.96→70.882 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.7
RfactorNum. reflection% reflection
Rfree0.2675 2736 5.02 %
Rwork0.2166 --
obs0.2191 54485 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 93.39 Å2 / Biso mean: 21.6744 Å2 / Biso min: 6.58 Å2
Refinement stepCycle: final / Resolution: 1.96→70.882 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 0 635 5603
Biso mean---30.64 -
Num. residues----686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085076
X-RAY DIFFRACTIONf_angle_d1.1686926
X-RAY DIFFRACTIONf_chiral_restr0.043818
X-RAY DIFFRACTIONf_plane_restr0.006930
X-RAY DIFFRACTIONf_dihedral_angle_d12.41862
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.96-1.99380.38321400.34172556269699
1.9938-2.03010.4011400.33872550269099
2.0301-2.06910.3481280.32332556268499
2.0691-2.11140.371350.30532592272799
2.1114-2.15730.37531140.29382564267899
2.1573-2.20740.30521510.2682559271099
2.2074-2.26270.33731330.269825622695100
2.2627-2.32380.3081370.254325892726100
2.3238-2.39220.2971520.24725772729100
2.3922-2.46940.26291360.239325602696100
2.4694-2.55770.34141510.23126142765100
2.5577-2.66010.29621350.225125602695100
2.6601-2.78120.2791370.23225952732100
2.7812-2.92780.29451230.220426112734100
2.9278-3.11130.23821220.21326222744100
3.1113-3.35150.2441250.192726042729100
3.3515-3.68870.21621480.161725922740100
3.6887-4.22240.20021340.153326352769100
4.2224-5.31960.18371540.14625832737100
5.3196-70.9280.22031410.177926682809100
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)
10.17420.0953-0.14180.2449-0.10670.08510.1025-0.302-0.26010.40520.0363-0.11550.3189-0.21930.00960.2897-0.0118-0.04910.32340.03180.2293-73.5764-97.9655-16.656
20.3478-0.01070.23342.4948-0.42950.0564-0.0055-0.1196-0.1580.3085-0.0099-0.10610.02950.0243-0.04220.10080.0044-0.0120.18790.01710.2252-68.5069-109.1948-29.6874
30.29080.13680.11010.63970.2230.2283-0.05880.09980.0433-0.2811-0.0135-0.18540.1160.02410.00050.1718-0.03940.02840.2294-0.00810.1909-76.9896-104.2048-52.9159
40.2298-0.08250.18230.14790.0290.4343-0.0857-0.0009-0.04650.0507-0.0760.19040.2241-0.0727-0.07590.1148-0.009-0.02880.179-0.00090.2198-83.6521-107.1733-43.4727
50.98340.41920.24211.74690.08920.785-0.07730.15520.0576-0.26010.0487-0.1547-0.00620.0166-0.04930.1068-0.00730.03430.16110.00770.1741-71.8938-89.9141-47.8472
60.42990.3565-0.0641.2077-0.37210.8497-0.01280.04210.13290.1412-0.0779-0.4329-0.03920.1302-0.02080.0969-0.0156-0.02830.16150.00290.2646-63.2844-90.2205-34.2671
70.414-0.4130.04290.5318-0.35050.95710.0375-0.24650.06550.4298-0.0751-0.20880.02940.04540.00660.2041-0.0064-0.0430.2111-0.00310.2122-69.1099-92.0592-21.8828
80.339-0.1650.08830.6089-0.25950.5289-0.0113-0.140.0568-0.06920.01050.3266-0.1524-0.1992-0.00140.240.0097-0.03370.20820.00730.1903-51.1221-71.6402-64.8165
90.48090.08940.59250.9156-0.10590.7872-0.13250.0252-0.0169-0.39170.0422-0.0079-0.1872-0.0225-0.18360.3492-0.02010.02620.1492-0.00170.1468-39.0346-64.807-65.3184
100.7202-0.3543-0.08171.4601-0.29770.9885-0.12090.14520.2582-0.35960.0457-0.6049-0.20420.1793-0.19680.2403-0.07470.07710.2278-0.04070.24-22.071-69.3436-61.0895
110.6939-0.06590.71971.55240.09140.67480.08690.11020.0753-0.40850.0047-0.4412-0.04820.17490.04350.2461-0.00870.08540.1759-0.00750.155-25.3462-79.2012-65.7483
121.2881-0.15920.13110.62860.31130.4798-0.0050.1572-0.0641-0.34020.0102-0.04920.07540.1771-0.01610.3386-0.00740.00230.1677-0.00160.1201-31.4924-89.8466-72.7983
130.66780.0207-0.00511.09640.4760.75890.03910.131-0.061-0.4898-0.05480.1869-0.0881-0.0318-0.01620.3253-0.0029-0.04890.1779-0.00460.0997-44.1226-82.6816-73.1839
140.6241-0.3719-0.25090.5237-0.20680.45960.08810.04890.1976-0.0505-0.06470.45750.1353-0.1358-0.00350.1966-0.0307-0.02090.21090.010.2138-51.9413-82.7994-62.2669
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 46:67)A46 - 67
2X-RAY DIFFRACTION2(chain A and resid 68:124)A68 - 124
3X-RAY DIFFRACTION3(chain A and resid 125:157)A125 - 157
4X-RAY DIFFRACTION4(chain A and resid 158:173)A158 - 173
5X-RAY DIFFRACTION5(chain A and resid 174:282)A174 - 282
6X-RAY DIFFRACTION6(chain A and resid 283:355)A283 - 355
7X-RAY DIFFRACTION7(chain A and resid 356:388)A356 - 388
8X-RAY DIFFRACTION8(chain B and resid 50:96)B50 - 96
9X-RAY DIFFRACTION9(chain B and resid 97:131)B97 - 131
10X-RAY DIFFRACTION10(chain B and resid 132:170)B132 - 170
11X-RAY DIFFRACTION11(chain B and resid 171:228)B171 - 228
12X-RAY DIFFRACTION12(chain B and resid 229:294)B229 - 294
13X-RAY DIFFRACTION13(chain B and resid 295:358)B295 - 358
14X-RAY DIFFRACTION14(chain B and resid 359:388)B359 - 388

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