[English] 日本語
Yorodumi
- PDB-8pzh: LpdD (H61A) mutant -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8pzh
TitleLpdD (H61A) mutant
ComponentsProtein LpdD
KeywordsFLAVOPROTEIN / small subunit / LpdD
Function / homology: / Prenylated flavin chaperone LpdD-like domain / : / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more