PDB-9g5l: Stapylococcus aureus MazF in complex with nanobody 10

ID or keywords:

Entry

Database: PDB / ID: 9g5l

Title

Stapylococcus aureus MazF in complex with nanobody 10

Components

Endoribonuclease MazF
Nanobody 10

Keywords

TOXIN / Toxin-antitoxin system / Ribonuclease / Nanobody

Function / homology

Function and homology information

rRNA catabolic process / mRNA catabolic process / RNA endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / RNA binding
Similarity search - Function

Biological species

Staphylococcus aureus (bacteria)

Lama glama (llama)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.82220379062 Å

Authors

Prolic-Kalinsek, M. / Haesaerts, S. / Loris, R.

Funding support

Belgium, 1items

Citation

Journal: To Be Published
Title: Nanobody-mediated activation and inhibition of Staphylococcus aureus MazF
Authors: Prolic-Kalinsek, M. / Zorzini, V. / Haesaerts, S. / De Bruyn, P. / Loris, R.

History

Deposition	Jul 17, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 24, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9g5l.cif.gz	134.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9g5l.ent.gz	86.9 KB	Display	PDB format
PDBx/mmJSON format	9g5l.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	9g5l_validation.pdf.gz	438 KB	Display	wwPDB validaton report
Full document	9g5l_full_validation.pdf.gz	439.3 KB	Display
Data in XML	9g5l_validation.xml.gz	11.9 KB	Display
Data in CIF	9g5l_validation.cif.gz	16.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/g5/9g5l ftp://data.pdbj.org/pub/pdb/validation_reports/g5/9g5l	HTTPS FTP

-
Related structure data

Related structure data	9g1yC 9g2gC 9g48C 9g4gC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#136 - Apr 2011 Nanobodies similarity (1) #21 - Sep 2001 Antibodies similarity (1) #256 - Apr 2021 SARS-CoV-2 Spike and Antibodies similarity (1)

Deposited unit

A: Endoribonuclease MazF

B: Nanobody 10

hetero molecules

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

1

A: Endoribonuclease MazF

B: Nanobody 10

hetero molecules

A: Endoribonuclease MazF

B: Nanobody 10

hetero molecules

defined by author&software
Evidence: gel filtration
60.9 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	99.040, 99.040, 70.260
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	92
Space group name H-M	P4₁2₁2
Space group name Hall	P4abw2nw
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+1/4 #3: y+1/2,-x+1/2,z+3/4 #4: x+1/2,-y+1/2,-z+3/4 #5: -x+1/2,y+1/2,-z+1/4 #6: -x,-y,z+1/2 #7: y,x,-z #8: -y,-x,-z+1/2

#1: Protein	Endoribonuclease MazF / SaMazF / Toxin MazF / mRNA interferase MazF Mass: 14952.206 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: mazF, SA1873 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q7A4G9, Hydrolases; Acting on ester bonds
#2: Antibody	Nanobody 10 Mass: 15442.874 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.83 Å³/Da / Density % sol: 56.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion / Details: 0.1 M TRIS-HCl pH 8.5, 8% (w/v) PEG-8000

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.978 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 6, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.978 Å / Relative weight: 1
Reflection	Resolution: 1.819→49.6004644649 Å / Num. obs: 31690 / % possible obs: 99.8 % / Redundancy: 13.2 % / B_iso Wilson estimate: 38.7455481474 Å² / CC_1/2: 1 / Net I/σ(I): 20.27
Reflection shell	Resolution: 1.819→1.89 Å / Num. unique obs: 3391 / CC_1/2: 0.856 / % possible all: 99

-
Processing

Software

Name	Version	Classification
PHENIX	1.11.1_2575	refinement
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.82220379062→49.6004644649 Å / SU ML: 0.215843308439 / Cross valid method: FREE R-VALUE / σ(F): 1.35584641567 / Phase error: 28.508258586
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.22814003521	1581	5.01093467719 %
R_work	0.200938685354	29970	-
obs	0.202336255612	31551	99.23570485 %

Solvent computation

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

Displacement parameters

B_iso mean: 53.9475000594 Å²

Refinement step

Cycle: LAST / Resolution: 1.82220379062→49.6004644649 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1880	0	2	93	1975

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0150990235666	1916
X-RAY DIFFRACTION	f_angle_d	1.37397399336	2606
X-RAY DIFFRACTION	f_chiral_restr	0.0838570185354	297
X-RAY DIFFRACTION	f_plane_restr	0.00881901675497	337
X-RAY DIFFRACTION	f_dihedral_angle_d	12.1034311159	1144

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 (%)
1.82220379062-1.881	0.337638716312	136	0.312072542165	2568	X-RAY DIFFRACTION	95.9545777147
1.881-1.9483	0.334409635934	142	0.265681707404	2687	X-RAY DIFFRACTION	98.8124345093
1.9483-2.0263	0.338105130506	142	0.23562863401	2680	X-RAY DIFFRACTION	99.2962702322
2.0263-2.1185	0.25247523257	142	0.214742902378	2676	X-RAY DIFFRACTION	98.9813839129
2.1185-2.2302	0.24778678958	141	0.202909519458	2679	X-RAY DIFFRACTION	99.5059985886
2.2302-2.3699	0.249908779968	144	0.207180021582	2733	X-RAY DIFFRACTION	99.8265093685
2.3699-2.5529	0.259296988132	142	0.219204519434	2712	X-RAY DIFFRACTION	99.546564353
2.5529-2.8098	0.259549268036	144	0.230955275394	2735	X-RAY DIFFRACTION	99.7574497574
2.8098-3.2163	0.247868745549	145	0.227980097812	2761	X-RAY DIFFRACTION	100
3.2163-4.0519	0.217523260049	147	0.182441996126	2791	X-RAY DIFFRACTION	100
4.0519-49.6004644649	0.192594391604	156	0.180397780755	2948	X-RAY DIFFRACTION	99.8391765841

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	3.48824728977	0.808636633012	-1.45576769313	5.52588941997	0.729827711553	4.40697710998	-0.115186615919	-0.775137312334	-0.297743229816	0.450512453307	0.204609842195	-0.150961492474	0.912305280724	0.567936770725	0.0210699325605	0.645226095238	0.176916193712	-0.0989974053886	0.551261282211	0.0556324246547	0.494828926454	30.620331753	17.1745232382	81.5986303377
2	8.8197313612	-0.53856002636	-1.72761737778	5.72506676399	0.478197010173	8.80609818887	0.526079771491	0.899648561886	-0.976668117002	-0.24244255975	-0.252545481093	-0.426598333476	0.719807560518	-0.53543547336	-0.256637119309	0.772347876172	-0.10681101364	-0.0206260653791	0.695925803552	-0.0794682408087	0.675973929726	20.3491700863	12.9104410697	66.3091318374
3	2.33831797033	-1.34807164373	-1.36946866227	2.78477637259	1.41664175169	4.66081678178	-0.161084051985	-0.147516977304	-0.0951256785105	0.449380208525	0.115441811468	-0.206885270504	0.640463010668	0.166544570469	-0.0597874106602	0.474723066766	0.0975029080343	-0.0383830903093	0.455789534275	0.0195099537951	0.403656068652	27.8411377569	21.1986621825	78.4758472297
4	5.78799121586	-0.46335390201	-2.04583900777	1.86854919725	-2.03118197741	9.46777367993	-0.437627749909	-0.149612333648	-0.536652530355	0.155529840463	0.524252828602	-0.406861831425	1.14529350881	0.594543318679	-0.0626468734677	0.494165756986	0.116824625486	-0.0636371044852	0.443933534527	-0.0396630510785	0.449641105389	36.540305416	14.2399618723	61.4832496191
5	1.40225145858	-1.83429750366	0.388847520116	4.99939367354	-1.6748631702	6.52547580208	-0.285105258545	-0.487346296458	0.281346397272	0.623990414309	-0.00884300934935	-1.0318243686	1.3960286627	1.11303038231	0.182048656885	0.785923006626	0.259482574084	-0.0904290347922	0.635874632085	-0.0251657146132	0.62256872931	40.740484334	11.1681354643	71.4206369047
6	3.13207860157	-0.811474465781	-3.69049875925	1.52272824101	1.1499440124	5.72374290604	-0.210320032684	0.213095952329	-0.100877903842	0.0717845275808	0.0911944054848	0.190394064516	0.862419208336	-0.398772746278	0.0861938013393	0.505865366545	0.0353367430802	-0.037469863849	0.482758927156	0.00687915856439	0.441124611976	26.5646908804	18.1504157648	72.3001571769
7	2.79126498472	0.912203998741	-4.67425039852	6.19990311247	-2.67496534948	8.13535077396	-0.328972917084	-1.00598462109	-0.851348517582	0.777552907174	-0.088863012033	-1.0923188315	1.41211284412	1.47999441177	0.266658952164	0.763802905237	0.239144186918	-0.106360163782	0.618508145012	0.0662162691449	0.522083489562	34.6027300914	13.6149369336	81.4021019545
8	3.85483236175	-4.75753681595	2.89214497481	8.2839899262	-2.54451925971	2.87620384259	-0.210905405981	-0.736118674534	0.881020640124	0.274395772577	0.199871672113	-1.08862717611	-0.451864534892	0.692487698953	-0.115794631604	0.416053416281	0.00815985407056	0.0108196189745	0.589793870596	-0.021664429631	0.533749267176	37.9417980498	27.6589956376	69.6173634695
9	2.53860129785	0.918794699782	-2.05773381507	2.91274333811	-3.23300955195	8.52032646163	0.0838793013014	0.376940605043	-0.168347389532	-0.328257934029	-0.126321482179	-0.00763487172344	0.926418999472	-0.256705124812	-0.0109418360409	0.447820614262	0.0138287929899	-0.0993128273604	0.456465753225	-0.0492603602614	0.445711827983	33.8656769198	9.15780886021	37.750447084
10	2.93479406263	-0.402043072357	-0.145217424644	1.32152256137	-0.42038821623	4.87904828845	0.116739938512	0.151412053513	0.066129417915	0.0473415794737	0.00236117079537	0.0375427898933	-0.0976304841392	-0.290420723934	-0.138232455282	0.393532886399	0.0639441204357	-0.0374283583916	0.397227257701	0.0260759863493	0.416386268573	34.7410711622	18.0745861967	41.4475144685
11	0.0991250396438	0.116902299527	-0.205509062069	0.145558056753	-0.22814460485	0.376359605409	0.179116599948	-0.426957339313	1.11126986273	0.657786323732	0.00294667202254	-2.54471446796	-1.91469760392	1.94934972326	-0.0122614517179	0.903336709894	-0.273070813324	-0.149632346909	0.955718549236	-0.105428606302	1.25604335251	43.465317124	20.637827356	53.0257131492
12	6.28126751616	2.00724750005	-3.787271841	3.9864774943	-4.05061389741	5.35929241465	-0.0329060375369	1.30442721425	-0.0438644925746	-0.809982642501	0.244642174722	0.05392020904	1.34341573062	-0.404362378913	-0.237155800259	0.450017725119	0.113062803075	-0.0636258566187	0.584390068294	-0.0345679215071	0.420539673169	43.5900085007	13.2578785618	32.3660837805

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 0 through 11 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 12 through 22 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 23 through 47 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 48 through 57 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 58 through 71 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 72 through 86 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 87 through 95 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 96 through 114 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 4 through 33 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 34 through 110 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 111 through 122 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 123 through 142 )

-
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://pdbjlvh1.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