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- PDB-8pzh: LpdD (H61A) mutant -

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Basic information

Entry
Database: PDB / ID: 8pzh
TitleLpdD (H61A) mutant
ComponentsProtein LpdD
KeywordsFLAVOPROTEIN / small subunit / LpdD
Function / homology: / Bacterial proteasome assembling chaperone-like protein / : / PHOSPHATE ION / Protein LpdD
Function and homology information
Biological speciesLactiplantibacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 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)30,6215
Polymers30,3762
Non-polymers2453
Water1,11762
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-9 kcal/mol
Surface area12170 Å2
Unit cell
Length a, b, c (Å)52.700, 91.580, 124.690
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
11B-324-

HOH

21B-326-

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
Details: AAMATFTTEQAGYQMQAILQVIGYDLLIVVTGGTNPHIGDVTTLTASTVPETVKFPSHDGRFHKDNFISERMAKRIQR YLAGSCTITAGIHVNQITKAQIAAAAPMTDDLSRQIISWLQAHPVQAEKPEYYGQDEQPR
Source: (gene. exp.) Lactiplantibacillus plantarum (bacteria)
Gene: lpdD, lp_0272 / Production host: Escherichia coli (E. coli) / References: UniProt: F9UT68
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.48 Å3/Da / Density % sol: 50.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris-Cl pH 8.0, 20%PEG6K

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→45.68 Å / Num. obs: 20209 / % possible obs: 97.45 % / Redundancy: 2 % / Biso Wilson estimate: 42.92 Å2 / CC1/2: 1 / Net I/σ(I): 5.64
Reflection shellResolution: 2→2.092 Å / Num. unique obs: 1995 / CC1/2: 0.5

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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: 2.02→45 Å / SU ML: 0.3176 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.1121 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.246 1012 5.13 %
Rwork0.2184 18708 -
obs0.2198 19720 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.5 Å2
Refinement stepCycle: LAST / Resolution: 2.02→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1726 0 11 62 1799
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00671762
X-RAY DIFFRACTIONf_angle_d0.77262407
X-RAY DIFFRACTIONf_chiral_restr0.0516299
X-RAY DIFFRACTIONf_plane_restr0.005304
X-RAY DIFFRACTIONf_dihedral_angle_d2.93261046
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.130.35541080.37552275X-RAY DIFFRACTION83.53
2.13-2.260.36431520.33252659X-RAY DIFFRACTION99.26
2.26-2.430.3311500.28962693X-RAY DIFFRACTION99.86
2.43-2.680.31741590.25662708X-RAY DIFFRACTION99.9
2.68-3.070.27911370.24092739X-RAY DIFFRACTION99.83
3.07-3.860.2271300.19142782X-RAY DIFFRACTION99.97
3.86-450.20081760.18082852X-RAY DIFFRACTION99.74
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)
16.07887122657-4.49923407178-6.765016864133.864600536662.952832712388.19878097519-0.440220840368-0.407298288632-0.628942988580.1024745837430.1656264323590.1773742783720.3862711624660.3263407341780.3264015029260.3977662073440.0416284567452-0.05157415953340.4092557751310.04148803133420.349453819329-20.76807711-25.7152902234-10.0457913583
26.64744888926-0.7629076973460.6981530098635.44764881279-1.635893919617.558838128220.242177315128-0.01617909698430.171376303803-0.067085930829-0.1532397584590.013044595825-0.279182996522-0.0179220181063-0.09139875498260.35345508608-0.01055712339640.06716061723980.3773124843020.0282629797270.239379950143-24.4738614691-14.3553939966-5.42986019886
35.61269358035.243225971971.272059768995.146385802640.8280680384761.05689711950.361462043113-0.09823983891441.645003244641.11451289956-0.4620665186840.489796999448-1.21640597408-0.35756338664-0.01102055222180.626691640402-0.153478794158-0.07863853743250.5432604685450.06396799576770.591158405203-14.0470964314-9.491577282540.887818298343
48.08225381242.57163624542-3.327058594977.16145584952-0.4587303695639.107647422470.5884773358060.7753748761340.5729912160320.0862662920779-0.384939792318-0.0797176279242-1.16412200731-0.4627612904470.06052535893580.5361697357340.1360815613640.03215212396970.4538924101290.06364417939460.378245978563-23.7006574558-12.58306289-14.1229734972
56.28231236481.02931531113-2.718699500523.54719605450.366145479876.125861348760.0609364325291-0.304870579313-0.0656943337628-0.0737520179884-0.0202842176931-0.147673381698-0.276722188915-0.0721222954126-0.002688526452740.3311260826230.0328767799832-0.02317611421960.2812208397830.01957722674890.243047937612-20.1311329165-19.752142154-13.164749723
66.118674591358.837395826955.69646986467.445093634985.91019226345.84870039647-0.2065317168090.4584151720760.169201162609-0.3044417806330.2275259650530.2131318242750.3028364348570.2969774306870.06133830903120.4023606113330.0133648473056-0.02304172461960.3886962828610.1073425657740.367742853744-31.8530726528-10.7051924876-43.4203552284
75.55370968089-3.152535681271.768473793534.67825454321-0.4570099669725.84871139787-0.0587802482170.09658079176380.4210156729990.153281192372-0.0740302454906-0.0880655235485-0.0350489476180.0722669606740.04847862772120.272286634518-0.09735499308510.01206142652880.301902509675-0.006697126771110.273738724189-27.762331037-5.68879624944-33.5277288277
87.78663573708-3.471721115970.5168605349986.82428070843-0.2080368303953.70716474077-0.280775138011-1.540116622950.2663266251790.348425723060.2569892159290.1385261584990.374666262572-1.34591887318-0.3063388454830.5277818137990.07247221047240.09549071563440.568846236983-0.01154764900550.381842341673-34.0392415234-3.26034813287-25.588191111
95.814571826122.70778160252-0.4120007471834.062475337290.6661255221033.891167939730.03741716273440.0774948253311-0.06217175666780.302070290248-0.08393675107850.1769712950090.384841432756-0.224089975453-0.02570791236540.380728782585-0.01852783997610.01067457434570.3152378399690.04058255107440.267511817048-30.9574319169-13.6465821958-35.706709345
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 20 )
2X-RAY DIFFRACTION2chain 'A' and (resid 21 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 62 )
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 77 )
5X-RAY DIFFRACTION5chain 'A' and (resid 78 through 121 )
6X-RAY DIFFRACTION6chain 'B' and (resid -1 through 20 )
7X-RAY DIFFRACTION7chain 'B' and (resid 21 through 48 )
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 65 )
9X-RAY DIFFRACTION9chain 'B' and (resid 66 through 121 )

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