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- PDB-8po5: Lactobacillus plantarum LpdD -

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Basic information

Entry
Database: PDB / ID: 8po5
TitleLactobacillus plantarum LpdD
ComponentsProtein LpdD
KeywordsFLAVOPROTEIN / UbiD / UbiX / LpdD
Function / homology: / Prenylated flavin chaperone LpdD-like domain / : / Protein LpdD
Function and homology information
Biological speciesLactobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGahloth, D. / Leys, D.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: J.Biol.Chem. / Year: 2024
Title: The prFMNH 2 -binding chaperone LpdD assists UbiD decarboxylase activation.
Authors: Gahloth, D. / Fisher, K. / Marshall, S. / Leys, D.
History
DepositionJul 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 17, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein LpdD
B: Protein LpdD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8604
Polymers31,7502
Non-polymers1102
Water2,594144
1
A: Protein LpdD
hetero molecules

A: Protein LpdD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8604
Polymers31,7502
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area1970 Å2
ΔGint-28 kcal/mol
Surface area12390 Å2
MethodPISA
2
B: Protein LpdD
hetero molecules

B: Protein LpdD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8604
Polymers31,7502
Non-polymers1102
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area1910 Å2
ΔGint-28 kcal/mol
Surface area12590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.500, 92.980, 126.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-365-

HOH

21B-374-

HOH

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Components

#1: Protein Protein LpdD / Gallate decarboxylase subunit D


Mass: 15874.866 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus (bacteria) / Gene: lpdD, lp_0272
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpB1_S (others)
References: UniProt: F9UT68
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.46 Å3/Da / Density % sol: 50.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Tris-Cl pH8.5, 0.2M Magnesium chloride, 30% PEG4K

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Jan 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 2.1→75.0334 Å / Num. obs: 18833 / % possible obs: 99.67 % / Redundancy: 2 % / Biso Wilson estimate: 33.5 Å2 / CC1/2: 1 / Net I/σ(I): 9.83
Reflection shellResolution: 2.1→2.175 Å / Num. unique obs: 1841 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→75.0334 Å / SU ML: 0.2329 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.6817 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2518 877 4.66 %
Rwork0.1945 17950 -
obs0.197 18827 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 42.79 Å2
Refinement stepCycle: LAST / Resolution: 2.1→75.0334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1917 0 2 144 2063
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721957
X-RAY DIFFRACTIONf_angle_d0.86592663
X-RAY DIFFRACTIONf_chiral_restr0.0572315
X-RAY DIFFRACTIONf_plane_restr0.0056341
X-RAY DIFFRACTIONf_dihedral_angle_d2.83111163
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.230.32051510.28322937X-RAY DIFFRACTION99.77
2.23-2.40.30021400.25122952X-RAY DIFFRACTION99.9
2.4-2.650.24441190.22143001X-RAY DIFFRACTION99.94
2.65-3.030.271530.21242963X-RAY DIFFRACTION99.84
3.03-3.820.27431700.17712973X-RAY DIFFRACTION99.27
3.82-74.990.19911440.16543124X-RAY DIFFRACTION99.03
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)
15.968513887744.76723652415-4.272008641033.7969752234-3.558382395055.04931197775-0.3443298390260.418544414033-0.318516509048-0.3398083426310.4144656634390.1883162183590.309045558095-0.3178247316610.04296350213120.2593541196990.0199648628636-0.02257900525880.259047625318-0.01363659521070.350354473786-18.2417882889-27.9624304791-12.9511508085
23.0683903819-2.08341555329-3.923081569083.47464635432.366989219945.171594876540.1036806309470.3150176712-0.130427987357-0.0638066583543-0.112783342916-0.116435535536-0.0363021835516-0.1501579602660.05212803255080.216275454044-0.0165563532559-0.020397948440.2059483765430.04044034836050.213009974633-25.0396894185-23.2853209755-7.09673430523
34.5991462893-1.122179977593.670887051594.1638375424-2.567125655256.648663985930.2259444579320.5749092122890.0597794396204-0.00977074959308-0.2913155380680.0483651065611-0.548604437152-0.04144344890990.116357262490.27216477020.01939981812570.04689540344810.293790628776-0.04612909595730.191356239796-23.1495035996-12.0624077181-5.14691008153
44.12856675323-4.146111525021.572622470944.28338219798-1.005535214114.201464692-0.5586827201080.5920322941710.2956043766-0.5774788239720.299786599823-1.608490635590.8200135220141.028671211220.3553949369810.570099012594-0.2410198336460.09901759373610.6496934057550.005182690244750.505815203151-10.808839833-8.490226095721.06673777957
56.884065956740.213384782733-1.970716612521.837669410610.3812627331584.549809668570.4618640087910.0681599374884-0.168200139209-0.0552415734642-0.2175302059880.0475765202012-0.3601696542910.167119377564-0.1508056948240.3567823992320.02065226749530.003691088237410.1844508973820.009227506190930.276813440803-20.8850434347-15.6411861886-10.9817501368
63.783523304224.150926296242.472601982785.088337919910.8730768543815.056662582950.1929338245430.845636499023-0.422063876009-0.01205456584950.0646834415116-0.2390700789520.0973064513534-0.152047661137-0.2902694060580.2231784476040.06015095359880.01310513085830.2050437348080.01845529892360.217199088779-22.3307544683-22.3621249373-16.7185823532
74.296930202215.81119572216-3.937875529989.4284106356-3.653815821346.683981334710.221927717935-0.1566819423220.2228094500490.190704889817-0.350386668738-0.165674306353-0.07811380445330.1172417266710.02388681587540.2282614875690.0233838379641-0.02285416406610.223153294362-0.01987810383510.252149963969-35.1365794775-13.1338635127-45.1120005416
83.67665655674.148555579641.876157605364.557588132231.654491890313.26190598828-0.1408385019690.331146438587-0.0963035902376-0.03193982818640.1737988233950.1416298205270.0481922152411-0.0478720775839-0.07362397781240.224906378025-0.0047992504406-0.00656938234970.2128622226370.04409430494490.193569127864-28.3966196247-7.1325441597-40.5157951686
97.46838901175-5.610507953571.06581782454.84034567672-1.958853783861.774997478820.00162116377165-0.263222132043-0.1519235876660.2327739636180.1335759709440.264407245179-0.151580755043-0.0208121196113-0.1454535010250.219556529937-0.03344923188080.02613982320550.174597238299-0.02075785465140.196322184161-30.2821337004-5.15611571876-29.2946381278
108.86190534478-7.02610027792-6.632416345758.31421179226.194925897685.52855635494-0.1536699531230.653647412412-0.2187698513720.823002642038-0.1314328726981.727751197810.289576235299-1.183821609740.1161909981880.4295877828660.03861681125430.181295928520.409284353744-0.005789990283680.531668889827-42.63319597970.731931776897-25.5348127633
118.03218112899-0.266234672472.271609836323.849642506040.03625174693723.027275926990.179434459837-0.0558095531631-0.1519330544310.06407946392-0.08850746602950.3546895533040.37719109641-0.300210029393-0.08325761703310.278234698298-0.0149528833340.01182237931410.259691097244-0.002118948683170.176772344054-32.5408585893-11.026439926-32.7686080919
124.01198861575-2.88419841861-3.685879506614.652575641750.9096496954574.07473481339-0.1175236633690.246412362016-0.4860837280250.06524260001740.0962847578269-0.04836292013160.1451276737-0.2082076663680.0300835967930.22686793843-0.0360877826309-0.02460480832260.213262199808-0.007558592958970.155104649035-31.1000626287-16.8463099982-39.4460043023
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 31 )
3X-RAY DIFFRACTION3chain 'A' and (resid 32 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 62 )
5X-RAY DIFFRACTION5chain 'A' and (resid 63 through 94 )
6X-RAY DIFFRACTION6chain 'A' and (resid 95 through 121 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 10 )
8X-RAY DIFFRACTION8chain 'B' and (resid 11 through 31 )
9X-RAY DIFFRACTION9chain 'B' and (resid 32 through 52 )
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 62 )
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 94 )
12X-RAY DIFFRACTION12chain 'B' and (resid 95 through 121 )

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