[English] 日本語
Yorodumi
- PDB-9hln: Crystal structure of MnmA D100C mutant from Streptococcus pneumon... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9hln
TitleCrystal structure of MnmA D100C mutant from Streptococcus pneumoniae with [4Fe-4S] cluster in complex with formate
ComponentstRNA-specific 2-thiouridylase MnmA
KeywordsTRANSFERASE / iron-sulfur cluster / tRNA thiolation / sulfur / sulfuration / thiouridylase
Function / homology
Function and homology information


tRNA-uridine 2-sulfurtransferase / tRNA-uridine 2-sulfurtransferase activity / tRNA wobble position uridine thiolation / cytoplasm
Similarity search - Function
tRNA-specific 2-thiouridylase / tRNA-specific 2-thiouridylase MnmA-like, central domain superfamily / tRNA-specific 2-thiouridylase MnmA-like, central domain / tRNA-specific 2-thiouridylase MnmA-like, C-terminal domain / tRNA methyl transferase HUP domain / Aminomethyltransferase beta-barrel domain / tRNA methyl transferase PRC-barrel domain / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
FORMIC ACID / IRON/SULFUR CLUSTER / tRNA-specific 2-thiouridylase MnmA
Similarity search - Component
Biological speciesStreptococcus pneumoniae TIGR4 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsGervason, S. / Pecqueur, L. / Golinelli-Pimpaneau, B.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-11-labx-0011 France
Agence Nationale de la Recherche (ANR)ANR-22-CE44-0012 France
CitationJournal: 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
DepositionDec 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2026Group: Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_modification_feature ...pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_atom_coordination / pdbx_nonpoly_atom_coordination_sphere / pdbx_nonpoly_atom_coordination_sphere_order
Item: _pdbx_entry_details.has_protein_modification / Description: Metalloprotein remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA-specific 2-thiouridylase MnmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,07418
Polymers41,8711
Non-polymers1,20317
Water7,458414
1
A: tRNA-specific 2-thiouridylase MnmA
hetero molecules

A: tRNA-specific 2-thiouridylase MnmA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,14836
Polymers83,7422
Non-polymers2,40634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area10410 Å2
ΔGint-77 kcal/mol
Surface area29640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.452, 93.452, 159.020
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"
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

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein tRNA-specific 2-thiouridylase MnmA


Mass: 41871.023 Da / Num. of mol.: 1 / Mutation: D100C
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 , 5 types, 431 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: CH2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 414 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: ANAEROBY (<1.5 ppm O2) 3.5M Sodium formate 0.1M Bis-tris propane pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 8, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.92→19.81 Å / Num. obs: 39900 / % possible obs: 94.8 % / Redundancy: 20.45 % / CC1/2: 0.998 / Rmerge(I) obs: 0.2149 / Rpim(I) all: 0.0485 / Rrim(I) all: 0.2204 / Net I/σ(I): 10.73
Reflection shell

Num. unique all: 1995 / Num. unique obs: 1995

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsCC1/2CC1/2 anomalousRpim(I) allRrim(I) allAbsDiff over sigma anomalous% possible anomalous% possible ellipsoidal% possible ellipsoidal anomalous% possible spherical% possible spherical anomalousRedundancy anomalous% possible all
6.137-19.80920.10.083828.5340103401030.9990.3670.0190.0861.06810010010010010011.45100
4.863-6.13719.930.112423.9239759397590.9980.1110.02580.11540.8510010010010010010.8100
4.24-4.86320.110.101426.2340114401140.998-0.0480.0230.1040.75710010010010010010.8100
3.845-4.2421.080.120923.1542062420620.998-0.0150.02680.12390.76899.999.999.999.999.911.2199.9
3.565-3.84519.40.139819.1138702387020.997-0.0510.03230.14350.78810010010010010010.27100
3.351-3.56519.360.172316.5538629386290.9950.0240.04010.1770.82699.899.899.899.899.810.2399.8
3.181-3.35120.390.212113.9740680406800.993-0.0780.0480.21750.80710010010010010010.74100
3.04-3.18120.920.268511.2141736417360.99-0.0720.05970.27510.78110010010010010010.99100
2.92-3.0420.990.3379.1441884418840.986-0.0850.0750.34530.81610010010010010011.04100
2.818-2.9221.230.42447.2842358423580.9830.0190.09410.43480.80199.999.999.999.999.911.1199.9
2.729-2.81821.310.54245.8542508425080.97-0.0590.11970.55560.78399.999.999.999.999.911.1799.9
2.649-2.72921.520.62215.0242934429340.966-0.0550.13680.63710.76599.999.999.999.999.911.2299.9
2.578-2.64921.50.76964.142886428860.9560.0230.16950.78830.74610010010010010011.21100
2.514-2.57821.610.85323.6643108431080.952-0.030.1870.87360.75599.999.899.999.899.911.2599.8
2.454-2.51420.920.94043.2341744417440.95-0.0010.20960.96370.75498.698.598.698.598.610.8798.5
2.396-2.45418.960.92863.0737819378190.946-0.0720.21780.95410.73588.989.188.989.188.99.8789.1
2.326-2.39619.921.02092.9239735397350.937-0.0620.23341.04760.72778.378.578.367.66710.3978.5
2.238-2.32620.051.0612.8939996399960.922-0.0440.24221.08870.73683.583.783.547.246.310.5183.7
2.133-2.23819.751.12412.6639404394040.906-0.0130.25771.15370.75883.783.583.733.332.110.3983.5
1.922-2.13319.981.41872.1239866398660.888-0.0370.32471.45610.70876.475.876.412.211.310.6875.8

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
autoPROC1.0.5data processing
XDSJun 30, 2024data reduction
STARANISO2.4.16data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.92→19.81 Å / SU ML: 0.1894 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4284
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1896 2012 5.04 %
Rwork0.1622 37878 -
obs0.1636 39890 64.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.61 Å2
Refinement stepCycle: LAST / Resolution: 1.92→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2894 0 63 414 3371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00643030
X-RAY DIFFRACTIONf_angle_d0.83124079
X-RAY DIFFRACTIONf_chiral_restr0.0487430
X-RAY DIFFRACTIONf_plane_restr0.0057532
X-RAY DIFFRACTIONf_dihedral_angle_d17.09251101
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.92-1.970.147780.2458137X-RAY DIFFRACTION3.38
1.97-2.020.2045190.2172433X-RAY DIFFRACTION10.37
2.02-2.080.269340.2206624X-RAY DIFFRACTION15.19
2.08-2.150.3068510.2093970X-RAY DIFFRACTION23.55
2.15-2.230.2148800.21691394X-RAY DIFFRACTION33.6
2.23-2.320.2401950.21681918X-RAY DIFFRACTION46.09
2.32-2.420.23951660.22092895X-RAY DIFFRACTION70.22
2.42-2.550.24552220.21924019X-RAY DIFFRACTION96.78
2.55-2.710.25811980.21624192X-RAY DIFFRACTION100
2.71-2.920.23852020.19744219X-RAY DIFFRACTION100
2.92-3.210.20522250.17214189X-RAY DIFFRACTION100
3.21-3.670.18582140.13394237X-RAY DIFFRACTION100
3.67-4.610.12852210.10974275X-RAY DIFFRACTION100
4.61-19.810.16122770.15124376X-RAY DIFFRACTION99.85
Refinement TLS params.Method: refined / Origin x: 29.9375794645 Å / Origin y: 24.3051739347 Å / Origin z: 2.94020119222 Å
111213212223313233
T0.149277836571 Å20.0239693260284 Å20.00249518922226 Å2-0.168417716238 Å20.0311624103018 Å2--0.191539586672 Å2
L0.744979100836 °2-0.225182705486 °2-0.373597345748 °2-0.882674399292 °20.840790334253 °2--2.54727017334 °2
S0.0413862274918 Å °-0.131771139042 Å °-0.0675352728004 Å °-0.0642951114165 Å °-0.0229416567581 Å °-0.0596228858458 Å °0.184157314067 Å °0.137008475394 Å °-0.0205635593804 Å °
Refinement TLS groupSelection details: all

+
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