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- PDB-8pzo: LpdD -

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Basic information

Entry
Database: PDB / ID: 8pzo
TitleLpdD
ComponentsProtein LpdD
KeywordsFLAVOPROTEIN / small subunit / LpdD
Function / homology: / Bacterial proteasome assembling chaperone-like protein / Protein LpdD
Function and homology information
Biological speciesLactobacillus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 27, 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)30,4686
Polymers30,3762
Non-polymers924
Water4,846269
1
A: Protein LpdD
hetero molecules

A: Protein LpdD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4686
Polymers30,3762
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area2150 Å2
ΔGint-44 kcal/mol
Surface area11460 Å2
MethodPISA
2
B: Protein LpdD
hetero molecules

B: Protein LpdD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4686
Polymers30,3762
Non-polymers924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-11
Buried area2240 Å2
ΔGint-44 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.143, 92.849, 125.009
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-428-

HOH

21B-419-

HOH

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Components

#1: Protein Protein LpdD / Gallate decarboxylase subunit D


Mass: 15188.139 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 (E. coli) / References: UniProt: F9UT68
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.54 Å3/Da / Density % sol: 51.54 %
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: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→46.42 Å / Num. obs: 21329 / % possible obs: 97.34 % / Redundancy: 2 % / Biso Wilson estimate: 21.27 Å2 / CC1/2: 1 / Net I/σ(I): 16.94
Reflection shellResolution: 2→2.072 Å / Num. unique obs: 2092 / 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→46.42 Å / SU ML: 0.1792 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.8717 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2308 1058 5.09 %
Rwork0.1853 19709 -
obs0.1877 20767 97.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.27 Å2
Refinement stepCycle: LAST / Resolution: 2→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1855 0 4 269 2128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671901
X-RAY DIFFRACTIONf_angle_d0.76942593
X-RAY DIFFRACTIONf_chiral_restr0.051312
X-RAY DIFFRACTIONf_plane_restr0.0048333
X-RAY DIFFRACTIONf_dihedral_angle_d2.66931331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.2481300.20032441X-RAY DIFFRACTION98.54
2.09-2.20.25251330.20332473X-RAY DIFFRACTION99.28
2.2-2.340.42311020.32562089X-RAY DIFFRACTION83.5
2.34-2.520.24881330.19062499X-RAY DIFFRACTION99.32
2.52-2.770.23491430.18512496X-RAY DIFFRACTION99.74
2.77-3.170.23751450.18282519X-RAY DIFFRACTION99.81
3.17-40.21871430.16252511X-RAY DIFFRACTION98.66
4-46.420.16811290.15682681X-RAY DIFFRACTION99.82
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)
12.38707991524-1.606238117541.94018636113.58239867896-1.124026744382.35698803267-0.0877540335376-0.254109743713-0.1272048192640.1086030907520.0228358616373-0.06882127016850.06852573836570.06311393598610.06509363306860.1389303880680.02034627015030.004146375387320.0856269350935-0.01660270519570.0908365361009-21.8387914809-7.64142744403-21.7040182278
25.840388762555.212135891761.224835900654.688978682831.120395691472.90968044643-0.3605157525070.483869409786-0.369704170189-0.6060406940980.147815122269-0.2134777658580.007651696077330.02189570918650.1702837577360.2149263449790.02789669452920.0154965622830.149173204347-0.01940391741390.142292208381-27.3646738259-6.71385629951-37.0041183521
30.77044080436-0.607348225395-0.05966566239465.182904412781.318936261346.266007785120.1590606625450.739951338831-0.09922159403720.284467913399-0.252264486394-2.047198716720.488116889891.799660075150.1151358432440.3836082044060.04616798141160.05965781108810.7488951854640.05542496910930.662317266685-10.2056152389-3.33225150353-34.9176638456
44.899840475680.7069671768031.357575827572.923344603030.2648308632832.289813670080.09526428103090.216880181998-0.305702036057-0.122397904569-0.135266841672-0.1363277591010.2687739069190.08185250475260.03820230126690.2042186367380.02670886916930.009894270824470.128624621998-0.002575329762210.114197087415-25.3915171064-11.4845433862-30.5767538844
58.200414554682.1131827814-3.18427228423.7434465046-0.5282388159923.68146468736-0.482537240870.182093917605-0.062723460438-0.1407078197520.266004249375-0.249858767940.4945722859730.1281790476180.1612195565820.2129229919630.072958643466-0.02514483849080.1145273132950.0491025594520.154394095961-19.2084757036-15.3763311919-24.3694224493
62.980223828580.685517681697-1.647384735832.15304797708-1.341415738753.468462021480.1483911326190.00161809786725-0.05164807414630.112368612791-0.04661557366260.00806439458004-0.1256738563960.217012697847-0.09997887480530.133160242586-0.02286906098880.005849005771990.131779049588-0.03721551267210.0992572654066-29.9644203772-20.215192718-55.0692259321
75.076162889050.5581900420070.7082436923112.375083789362.000728273016.94654982689-0.2202088434610.05567484908280.5482469638210.0517611453576-0.3676870872750.686599975818-0.315745162958-1.422483523380.5222135030130.4418303161070.130654111795-0.01987136345520.609689777263-0.0447848978850.505959371617-42.9998865242-11.0327541213-59.2986503517
86.011289689661.23990028795-2.237472874462.689929198372.455883932045.47598488410.0999711876595-0.5186852115690.05060459336080.07356048431880.0873752794490.094563129433-0.5010465250630.485360835974-0.00319905488010.221269516548-0.03620587361290.02997379744790.181317082991-0.00693866462990.14363375064-27.1096668505-14.2331256534-47.2989282212
97.85561880710.301980268991-1.96208488932.55819780836-0.09516514525183.551075124640.151311113422-0.0127613390558-0.2626258375840.0450640620028-0.02493020705240.212573435746-0.0294753176548-0.48439020875-0.06286814397360.227063747473-0.01466287843860.01981114530880.2738527403510.02080840075770.113681595956-35.8779530898-17.9437375896-55.3152613182
108.35422327589-5.498815066961.877276048535.56421499776-0.3845237197284.723326989460.0342822802949-0.232827071585-0.09840914511720.243959907244-0.02068328816750.0006451760341590.03605184521440.0434001664325-0.02431951471050.188259437166-0.07873705587750.003456363062150.12475651390.01204586662890.0889284326748-30.5403429802-22.4449975646-45.864257648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 65 )
4X-RAY DIFFRACTION4chain 'A' and (resid 66 through 89 )
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 121 )
6X-RAY DIFFRACTION6chain 'B' and (resid -1 through 52 )
7X-RAY DIFFRACTION7chain 'B' and (resid 53 through 65 )
8X-RAY DIFFRACTION8chain 'B' and (resid 66 through 77 )
9X-RAY DIFFRACTION9chain 'B' and (resid 78 through 94 )
10X-RAY DIFFRACTION10chain 'B' and (resid 95 through 121 )

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