PDB-8pzo: LpdD - Yorodumi

ID or keywords:

Entry

Database: PDB / ID: 8pzo

Title

LpdD

Components

Protein LpdD

Keywords

FLAVOPROTEIN / small subunit / LpdD

Function / homology

: / Bacterial proteasome assembling chaperone-like protein / Protein LpdD

Function and homology information

Biological species

Lactobacillus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

Gahloth, D. / Leys, D.

Funding support

European Union, 1items

Citation

Journal: 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

Deposition	Jul 27, 2023	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jan 17, 2024	Provider: repository / Type: Initial release
Revision 1.1	Jan 29, 2025	Group: 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 viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	8pzo.cif.gz	137.5 KB	Display	PDBx/mmCIF format
PDB format	pdb8pzo.ent.gz	88.4 KB	Display	PDB format
PDBx/mmJSON format	8pzo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	8pzo_validation.pdf.gz	423 KB	Display	wwPDB validaton report
Full document	8pzo_full_validation.pdf.gz	424.2 KB	Display
Data in XML	8pzo_validation.xml.gz	14 KB	Display
Data in CIF	8pzo_validation.cif.gz	20.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/pz/8pzo ftp://data.pdbj.org/pub/pdb/validation_reports/pz/8pzo	HTTPS FTP

-
Related structure data

Related structure data	8p4wC 8po5C 8pzhC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Protein LpdD

B: Protein LpdD

hetero molecules

30.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Protein LpdD

hetero molecules

A: Protein LpdD

hetero molecules

defined by author&software
30.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Protein LpdD

hetero molecules

B: Protein LpdD

hetero molecules

defined by author&software
30.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	23
Space group name H-M	I222
Space group name Hall	I22
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

ID	Model	Components
1	1	A-428- HOH
2	1	B-419- HOH

#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 interest	N
Has protein modification	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.54 Å³/Da / Density % sol: 51.54 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.1M Tris-Cl pH8.5, 0.2M Magnesium chloride, 30% PEG4K

-
Data collection

Diffraction	Mean temperature: 80 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 9, 2017
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 2→46.42 Å / Num. obs: 21329 / % possible obs: 97.34 % / Redundancy: 2 % / B_iso Wilson estimate: 21.27 Å² / CC_1/2: 1 / Net I/σ(I): 16.94
Reflection shell	Resolution: 2→2.072 Å / Num. unique obs: 2092 / CC_1/2: 0.9

-
Processing

Software

Name	Version	Classification
PHENIX	1.14_3260	refinement
PHENIX	1.14_3260	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method 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

	R_factor	Num. reflection	% reflection
R_free	0.2308	1058	5.09 %
R_work	0.1853	19709	-
obs	0.1877	20767	97.36 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 32.27 Å²

Refinement step

Cycle: LAST / Resolution: 2→46.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1855	0	4	269	2128

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0067	1901
X-RAY DIFFRACTION	f_angle_d	0.7694	2593
X-RAY DIFFRACTION	f_chiral_restr	0.051	312
X-RAY DIFFRACTION	f_plane_restr	0.0048	333
X-RAY DIFFRACTION	f_dihedral_angle_d	2.6693	1331

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2-2.09	0.248	130	0.2003	2441	X-RAY DIFFRACTION	98.54
2.09-2.2	0.2525	133	0.2033	2473	X-RAY DIFFRACTION	99.28
2.2-2.34	0.4231	102	0.3256	2089	X-RAY DIFFRACTION	83.5
2.34-2.52	0.2488	133	0.1906	2499	X-RAY DIFFRACTION	99.32
2.52-2.77	0.2349	143	0.1851	2496	X-RAY DIFFRACTION	99.74
2.77-3.17	0.2375	145	0.1828	2519	X-RAY DIFFRACTION	99.81
3.17-4	0.2187	143	0.1625	2511	X-RAY DIFFRACTION	98.66
4-46.42	0.1681	129	0.1568	2681	X-RAY DIFFRACTION	99.82

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	2.38707991524	-1.60623811754	1.9401863611	3.58239867896	-1.12402674438	2.35698803267	-0.0877540335376	-0.254109743713	-0.127204819264	0.108603090752	0.0228358616373	-0.0688212701685	0.0685257383657	0.0631139359861	0.0650936330686	0.138930388068	0.0203462701503	0.00414637538732	0.0856269350935	-0.0166027051957	0.0908365361009	-21.8387914809	-7.64142744403	-21.7040182278
2	5.84038876255	5.21213589176	1.22483590065	4.68897868283	1.12039569147	2.90968044643	-0.360515752507	0.483869409786	-0.369704170189	-0.606040694098	0.147815122269	-0.213477765858	0.00765169607733	0.0218957091865	0.170283757736	0.214926344979	0.0278966945292	0.015496562283	0.149173204347	-0.0194039174139	0.142292208381	-27.3646738259	-6.71385629951	-37.0041183521
3	0.77044080436	-0.607348225395	-0.0596656623946	5.18290441278	1.31893626134	6.26600778512	0.159060662545	0.739951338831	-0.0992215940372	0.284467913399	-0.252264486394	-2.04719871672	0.48811688989	1.79966007515	0.115135843244	0.383608204406	0.0461679814116	0.0596578110881	0.748895185464	0.0554249691093	0.662317266685	-10.2056152389	-3.33225150353	-34.9176638456
4	4.89984047568	0.706967176803	1.35757582757	2.92334460303	0.264830863283	2.28981367008	0.0952642810309	0.216880181998	-0.305702036057	-0.122397904569	-0.135266841672	-0.136327759101	0.268773906919	0.0818525047526	0.0382023012669	0.204218636738	0.0267088691693	0.00989427082447	0.128624621998	-0.00257532976221	0.114197087415	-25.3915171064	-11.4845433862	-30.5767538844
5	8.20041455468	2.1131827814	-3.1842722842	3.7434465046	-0.528238815992	3.68146468736	-0.48253724087	0.182093917605	-0.062723460438	-0.140707819752	0.266004249375	-0.24985876794	0.494572285973	0.128179047618	0.161219556582	0.212922991963	0.072958643466	-0.0251448384908	0.114527313295	0.049102559452	0.154394095961	-19.2084757036	-15.3763311919	-24.3694224493
6	2.98022382858	0.685517681697	-1.64738473583	2.15304797708	-1.34141573875	3.46846202148	0.148391132619	0.00161809786725	-0.0516480741463	0.112368612791	-0.0466155736626	0.00806439458004	-0.125673856396	0.217012697847	-0.0999788748053	0.133160242586	-0.0228690609888	0.00584900577199	0.131779049588	-0.0372155126721	0.0992572654066	-29.9644203772	-20.215192718	-55.0692259321
7	5.07616288905	0.558190042007	0.708243692311	2.37508378936	2.00072827301	6.94654982689	-0.220208843461	0.0556748490828	0.548246963821	0.0517611453576	-0.367687087275	0.686599975818	-0.315745162958	-1.42248352338	0.522213503013	0.441830316107	0.130654111795	-0.0198713634552	0.609689777263	-0.044784897885	0.505959371617	-42.9998865242	-11.0327541213	-59.2986503517
8	6.01128968966	1.23990028795	-2.23747287446	2.68992919837	2.45588393204	5.4759848841	0.0999711876595	-0.518685211569	0.0506045933608	0.0735604843188	0.087375279449	0.094563129433	-0.501046525063	0.485360835974	-0.0031990548801	0.221269516548	-0.0362058736129	0.0299737974479	0.181317082991	-0.0069386646299	0.14363375064	-27.1096668505	-14.2331256534	-47.2989282212
9	7.8556188071	0.301980268991	-1.9620848893	2.55819780836	-0.0951651452518	3.55107512464	0.151311113422	-0.0127613390558	-0.262625837584	0.0450640620028	-0.0249302070524	0.212573435746	-0.0294753176548	-0.48439020875	-0.0628681439736	0.227063747473	-0.0146628784386	0.0198111453088	0.273852740351	0.0208084007577	0.113681595956	-35.8779530898	-17.9437375896	-55.3152613182
10	8.35422327589	-5.49881506696	1.87727604853	5.56421499776	-0.384523719728	4.72332698946	0.0342822802949	-0.232827071585	-0.0984091451172	0.243959907244	-0.0206832881675	0.000645176034159	0.0360518452144	0.0434001664325	-0.0243195147105	0.188259437166	-0.0787370558775	0.00345636306215	0.1247565139	0.0120458666289	0.0889284326748	-30.5403429802	-22.4449975646	-45.864257648

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid -1 through 37 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 38 through 52 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 53 through 65 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 66 through 89 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 90 through 121 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid -1 through 52 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 53 through 65 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 66 through 77 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 78 through 94 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 95 through 121 )

-
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

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

+
Jul 12, 2017. Major update of PDB

-
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

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

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

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

-
Yorodumi