PDB-9hm3: Crystal structure of MnmA from Streptococcus pneumoniae in comple...

ID or keywords:

Entry

Database: PDB / ID: 9hm3

Title

Crystal structure of MnmA from Streptococcus pneumoniae in complex with AMP-PNP

Components

tRNA-specific 2-thiouridylase MnmA

Keywords

TRANSFERASE / tRNA thiolation / sulfur / sulfuration / thiouridylase / RNA

Function / homology

Function and homology information

tRNA-uridine 2-sulfurtransferase / tRNA-uridine 2-sulfurtransferase activity / tRNA wobble position uridine thiolation / cytoplasm
Similarity search - Function

Biological species

Streptococcus pneumoniae TIGR4 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.82 Å

Authors

Gervason, S. / Pecqueur, L. / Golinelli-Pimpaneau, B.

Funding support

France, 2items

Citation

Journal: To Be Published
Title: A [4Fe-4S] cluster, coordinated by two conserved cysteines and one aspartate, is essential for tRNA thiolation by MnmA enzymes from two Gram positive bacteria
Authors: Golinelli-Pimpaneau, B.

History

Deposition	Dec 6, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 17, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9hm3.cif.gz	213 KB	Display	PDBx/mmCIF format
PDB format	pdb9hm3.ent.gz		Display	PDB format
PDBx/mmJSON format	9hm3.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hm/9hm3 ftp://data.pdbj.org/pub/pdb/validation_reports/hm/9hm3	HTTPS FTP

-
Related structure data

Related structure data	9hlnC 9hlvC 9hmjC 9i7rC 2hma 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	#222 - Jun 2018 Proteins and Nanoparticles similarity (1) #108 - Dec 2008 Hsp90 similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #182 - Feb 2015 Insulin receptor similarity (1) #214 - Oct 2017 Chimeric Antigen Receptors similarity (1) #238 - Oct 2019 Ribonucleotide Reductase similarity (1) #43 - Jul 2003 Src Tyrosine Kinase similarity (1) #50 - Feb 2004 Glycolytic Enzymes similarity (1) #60 - Dec 2004 Ubiquitin similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #80 - Aug 2006 AAA+ Proteases similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#222 - Jun 2018
Proteins and Nanoparticles
similarity (1)
#108 - Dec 2008
Hsp90
similarity (1)
#168 - Dec 2013
DNA Helicase
similarity (1)
#182 - Feb 2015
Insulin receptor
similarity (1)
#214 - Oct 2017
Chimeric Antigen Receptors
similarity (1)
#238 - Oct 2019
Ribonucleotide Reductase
similarity (1)
#43 - Jul 2003
Src Tyrosine Kinase
similarity (1)
#50 - Feb 2004
Glycolytic Enzymes
similarity (1)
#60 - Dec 2004
Ubiquitin
similarity (1)
#73 - Jan 2006
Topoisomerase
similarity (1)
#80 - Aug 2006
AAA+ Proteases
similarity (1)
#95 - Nov 2007
Multidrug Resistance Transporters
similarity (1)

Deposited unit

A: tRNA-specific 2-thiouridylase MnmA

hetero molecules

43.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author
Evidence: gel filtration, gel filtration + SEC-MALS

Unit cell

Length a, b, c (Å)	94.182, 94.182, 159.368
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	154
Space group name H-M	P3₂21
Space group name Hall	P3₂2"
Symmetry operation	#1: x,y,z #2: -y,x-y,z+2/3 #3: -x+y,-x,z+1/3 #4: x-y,-y,-z+1/3 #5: -x,-x+y,-z+2/3 #6: y,x,-z

-
Protein , 1 types, 1 molecules A

#1: Protein	tRNA-specific 2-thiouridylase MnmA Mass: 41882.969 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae TIGR4 (bacteria) Gene: mnmA, trmU, SP_0118 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q97T38, tRNA-uridine 2-sulfurtransferase

-
Non-polymers , 6 types, 269 molecules

#2: Chemical	ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400 Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₇ / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical	ChemComp-PG6 / 1-(2-METHOXY-ETHOXY)-2-{2-[2-(2-METHOXY-ETHOXY]-ETHOXY}-ETHANE Mass: 266.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₂H₂₆O₆ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃ / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical	ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER Mass: 506.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₀H₁₇N₆O₁₂P₃ / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: SO₄ / Feature type: SUBJECT OF INVESTIGATION
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H₂O

-
Details

Has ligand of interest	Y
Has protein modification	N

-
Experiment

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

-
Sample preparation

Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 1.85M ammonium sulfate, 5% w/v PEG 400, 0.1M MES pH 6.5

-
Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

SOLEIL

/ Beamline: PROXIMA 1 / Wavelength: 0.978 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 26, 2023

Radiation

Monochromator: Si filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.978 Å / Relative weight: 1

Reflection

Resolution: 1.82→19.88 Å / Num. obs: 57321 / % possible obs: 95.7 % / Redundancy: 20.56 % / CC_1/2: 0.999 / R_merge(I) obs: 0.122 / R_pim(I) all: 0.0275 / R_rim(I) all: 0.1251 / Net I/σ(I): 17.45

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. measured obs	Num. unique all	Num. unique obs	CC_1/2	CC_1/2 anomalous	R_pim(I) all	R_rim(I) all	AbsDiff over sigma anomalous	% possible anomalous	% possible ellipsoidal	% possible ellipsoidal anomalous	% possible spherical	% possible spherical anomalous	Redundancy anomalous	% possible all
5.466-19.833	19.29	0.0398	56.83	55271	55271	2866	2866	0.999	-0.281	0.0092	0.0409	0.775	100	100	100	100	100	10.75	100
4.329-5.465	20.31	0.0468	55.88	58198	58198	2866	2866	1	-0.29	0.0106	0.0479	0.665	100	100	100	100	100	10.93	100
3.769-4.329	21.29	0.0554	52.21	61020	61020	2866	2866	0.999	-0.313	0.0123	0.0568	0.654	100	100	100	100	100	11.34	100
3.42-3.769	21.7	0.0691	43.41	62204	62204	2866	2866	0.999	-0.176	0.0152	0.0708	0.711	100	100	100	100	100	11.45	100
3.171-3.42	20.05	0.093	32.21	57476	57476	2866	2866	0.998	-0.099	0.0212	0.0954	0.739	100	100	100	100	100	10.54	100
2.979-3.171	19.51	0.1298	23.81	55914	55914	2866	2866	0.997	-0.142	0.03	0.1333	0.727	99.8	99.9	99.8	99.9	99.8	10.2	99.9
2.828-2.979	20.29	0.1856	17.75	58137	58137	2866	2866	0.994	-0.065	0.0422	0.1904	0.758	100	100	100	100	100	10.59	100
2.703-2.828	20.74	0.2535	13.59	59430	59430	2866	2866	0.992	-0.05	0.0568	0.2598	0.738	99.8	99.8	99.8	99.8	99.8	10.84	99.8
2.597-2.703	21.08	0.3302	10.5	60407	60407	2866	2866	0.989	-0.065	0.0735	0.3383	0.711	100	100	100	100	100	10.97	100
2.507-2.597	21.25	0.4261	8.38	60916	60916	2867	2867	0.978	-0.047	0.0944	0.4366	0.719	100	100	100	100	100	11.04	100
2.427-2.507	21.42	0.4938	7.2	61392	61392	2866	2866	0.978	-0.016	0.1089	0.5058	0.711	99.9	99.9	99.9	99.9	99.9	11.13	99.9
2.356-2.427	21.52	0.633	5.68	61665	61665	2866	2866	0.957	-0.052	0.1394	0.6483	0.68	100	100	100	100	100	11.16	100
2.293-2.356	21.45	0.7743	4.67	61471	61471	2866	2866	0.932	0.011	0.1706	0.793	0.699	99.9	99.9	99.9	99.9	99.9	11.13	99.9
2.236-2.293	19.87	1.0072	3.77	56936	56936	2866	2866	0.894	-0.038	0.2312	1.0337	0.703	100	100	100	100	100	10.27	100
2.185-2.236	20.58	1.1018	3.26	58977	58977	2866	2866	0.857	-0.03	0.2481	1.1296	0.68	100	100	100	100	100	10.66	100
2.138-2.185	19.28	1.2844	2.66	55244	55244	2866	2866	0.829	-0.039	0.2989	1.319	0.672	100	100	100	100	100	9.96	100
2.094-2.138	20.08	1.7112	2.07	57557	57557	2866	2866	0.703	-0.008	0.3901	1.7555	0.671	100	99.8	100	99.8	100	10.36	99.8
2.05-2.094	20.55	1.9607	1.84	58896	58896	2866	2866	0.644	0.004	0.4417	2.0102	0.691	91.3	90.8	91.3	90.8	91.3	10.57	90.8
1.992-2.05	20.48	2.0556	1.77	58707	58707	2866	2866	0.591	-0.001	0.4642	2.1079	0.68	71.4	71.8	71.4	62.1	61.3	10.62	71.8
1.85-1.992	20.39	2.4688	1.47	58437	58437	2866	2866	0.459	-0.025	0.5583	2.5318	0.678	71.3	70.7	71.3	20.8	20.1	10.66	70.7

-
Processing

Software

Name	Version	Classification
PHENIX	1.21.2_5419	refinement
autoPROC	1.0.5	data processing
XDS	Jun 30, 2024	data reduction
STARANISO	2.4.16	data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.82→19.88 Å / SU ML: 0.1491 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.6414
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2019	2722	5.04 %
R_work	0.1758	51331	-
obs	0.1772	54053	73.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 47.68 Å²

Refinement step

Cycle: LAST / Resolution: 1.82→19.88 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2883	0	106	258	3247

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0061	3056
X-RAY DIFFRACTION	f_angle_d	0.8821	4125
X-RAY DIFFRACTION	f_chiral_restr	0.0487	428
X-RAY DIFFRACTION	f_plane_restr	0.0063	526
X-RAY DIFFRACTION	f_dihedral_angle_d	18.411	1150

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 (%)
1.82-1.85	0.5033	4	0.4008	110	X-RAY DIFFRACTION	2.99
1.85-1.89	0.2707	15	0.3306	268	X-RAY DIFFRACTION	7.47
1.89-1.93	0.3493	25	0.3184	549	X-RAY DIFFRACTION	15.01
1.93-1.97	0.2993	46	0.2943	816	X-RAY DIFFRACTION	22.52
1.97-2.02	0.2161	48	0.2757	1230	X-RAY DIFFRACTION	33.33
2.02-2.07	0.2463	99	0.2811	1647	X-RAY DIFFRACTION	45.71
2.07-2.12	0.3028	106	0.2658	2463	X-RAY DIFFRACTION	66.88
2.12-2.18	0.3027	182	0.2624	3440	X-RAY DIFFRACTION	93.79
2.19-2.26	0.2703	223	0.2335	3630	X-RAY DIFFRACTION	100
2.26-2.34	0.253	196	0.2217	3636	X-RAY DIFFRACTION	100
2.34-2.43	0.2298	201	0.2034	3674	X-RAY DIFFRACTION	100
2.43-2.54	0.2049	215	0.2047	3670	X-RAY DIFFRACTION	99.97
2.54-2.67	0.2041	155	0.1941	3702	X-RAY DIFFRACTION	100
2.67-2.84	0.216	183	0.1899	3718	X-RAY DIFFRACTION	100
2.84-3.06	0.1986	189	0.1841	3679	X-RAY DIFFRACTION	100
3.06-3.37	0.1927	201	0.1694	3721	X-RAY DIFFRACTION	100
3.37-3.85	0.201	197	0.1449	3712	X-RAY DIFFRACTION	100
3.85-4.84	0.1546	192	0.1272	3789	X-RAY DIFFRACTION	100
4.84-19.88	0.1873	245	0.1671	3877	X-RAY DIFFRACTION	99.9

Refinement TLS params.

Method: refined / Origin x: 30.2365345438 Å / Origin y: 24.7651389163 Å / Origin z: 4.11948599105 Å

	11	12	13	21	22	23	31	32	33
T	0.178952028394 Å²	0.0270297264032 Å²	0.00604248395515 Å²	-	0.228524320749 Å²	0.0399805745198 Å²	-	-	0.23752227834 Å²
L	1.07663477773 °²	-0.446658991194 °²	-0.53620555266 °²	-	1.24195752144 °²	1.15793900516 °²	-	-	2.97585461699 °²
S	0.108992219992 Å °	-0.242754491121 Å °	-0.0541480951302 Å °	-0.131657907687 Å °	-0.0128236233691 Å °	-0.12299564451 Å °	0.108201768346 Å °	0.241358538248 Å °	-0.0872241070946 Å °

Refinement TLS group

Selection details: all

-
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

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 6 types, 269 molecules

-
Details

-
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

-Protein , 1 types, 1 molecules A

-Non-polymers , 6 types, 269 molecules

-Details

-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

-
Protein , 1 types, 1 molecules A

-
Non-polymers , 6 types, 269 molecules

-
Details

-
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