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- PDB-9ri2: Crystal structure of bacillithiol methyltransferase NmbA from Chl... -

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Basic information

Entry
Database: PDB / ID: 9ri2
TitleCrystal structure of bacillithiol methyltransferase NmbA from Chlorobaculum tepidum
ComponentsMethyltransferase, putative
KeywordsTRANSFERASE / natural product methyl transferase / low-molecular weight thiol / bacillithiol / SAM
Function / homologyMethyltransferase domain 25 / Methyltransferase domain / methyltransferase activity / methylation / S-adenosyl-L-methionine-dependent methyltransferase superfamily / CITRATE ANION / Methyltransferase, putative
Function and homology information
Biological speciesChlorobaculum tepidum TLS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsHammerstad, M. / Hersleth, H.-P.
Funding support Norway, 1items
OrganizationGrant numberCountry
Norwegian Research Council301584 Norway
CitationJournal: Redox Biol / Year: 2025
Title: The methyltransferase NmbA methylates the low-molecular weight thiol bacillithiol, and displays a specific structural architecture.
Authors: Hammerstad, M. / Steinvik, E. / Hersleth, H.P.
History
DepositionJun 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 10, 2025Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2025Group: Database references / Category: citation
Item: _citation.journal_id_CSD / _citation.page_last ..._citation.journal_id_CSD / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Methyltransferase, putative
B: Methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,6915
Polymers61,0312
Non-polymers6613
Water25214
1
A: Methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,9873
Polymers30,5151
Non-polymers4712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Methyltransferase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7042
Polymers30,5151
Non-polymers1891
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.751, 55.517, 186.017
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 14 through 263 or resid 302))
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ARGARGVALVALAA14 - 26314 - 263
d_12FLCFLCFLCFLCAD302
d_21ARGARGVALVALBB14 - 26314 - 263
d_22FLCFLCFLCFLCBE301

NCS oper: (Code: givenMatrix: (-0.0525192346924, 0.649697344239, 0.75837661546), (0.652675386888, -0.552446011624, 0.51847684962), (0.755815168767, 0.52220375825, -0.395027423771)Vector: 24. ...NCS oper: (Code: given
Matrix: (-0.0525192346924, 0.649697344239, 0.75837661546), (0.652675386888, -0.552446011624, 0.51847684962), (0.755815168767, 0.52220375825, -0.395027423771)
Vector: 24.7869035583, -20.7303103884, -13.3245950978)

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Components

#1: Protein Methyltransferase, putative


Mass: 30515.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobaculum tepidum TLS (bacteria) / Gene: CT1040 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KDK7
#2: Chemical ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H26N2O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 13 mg/mL protein (1:1) 0.03 M citric acid, 0.07 M BIS-TRIS propane, pH = 7.6, 20 % w/v polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Oct 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.7→47.67 Å / Num. obs: 15493 / % possible obs: 97 % / Redundancy: 4.9 % / Biso Wilson estimate: 48.5 Å2 / CC1/2: 0.981 / Rmerge(I) obs: 0.228 / Rpim(I) all: 0.114 / Rrim(I) all: 0.256 / Net I/σ(I): 6.3
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.23 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2017 / CC1/2: 0.455 / Rpim(I) all: 0.617 / Rrim(I) all: 1.382 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
REFMAC5.8.0352refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→47.67 Å / SU ML: 0.4324 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.6312
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2529 778 5.04 %
Rwork0.2127 14649 -
obs0.2147 15427 96.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.68 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.7→47.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3682 0 45 14 3741
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00243812
X-RAY DIFFRACTIONf_angle_d0.55615158
X-RAY DIFFRACTIONf_chiral_restr0.042545
X-RAY DIFFRACTIONf_plane_restr0.0056674
X-RAY DIFFRACTIONf_dihedral_angle_d14.51271413
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 1.21563091958 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.870.37641280.3122367X-RAY DIFFRACTION95.59
2.87-3.090.35031250.29952456X-RAY DIFFRACTION98.47
3.09-3.40.2841380.24622452X-RAY DIFFRACTION99.39
3.4-3.860.24051210.21322348X-RAY DIFFRACTION98.21
3.92-4.90.20511230.16132403X-RAY DIFFRACTION98.48
4.91-47.670.22431430.18792623X-RAY DIFFRACTION98.15
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)
14.887389686070.402952950951-0.8613158056313.664285176330.1636361337015.02659698675-0.282498610128-0.2708511820270.0792988620013-0.06007363512330.3408267965290.298409377110.191218754276-0.128382921883-0.03644170899390.447395116905-0.0191110599438-0.05760165523760.326270357346-0.07391481499180.350603551609-6.2188894447-36.3742644171-37.3848248076
22.64242825617-0.9858699676582.09953834833.690458126922.141271783116.270167757740.01109114053970.141398847652-0.193614352073-0.14100689250.0693204791267-0.7912175674110.2276689193740.3992849237590.004136008480980.3715059999350.01527835983220.0757956526610.3084130943230.06459650746090.50789914836814.2887463227-24.7695286249-40.0577615771
35.17923872191-0.362770420645-3.957173419061.229585480890.2006185798925.43963597902-0.00871614696293-0.302758564613-0.6444914586810.0622320844354-0.166263409382-0.0832853453280.2138917157240.09649054197950.1675494503770.3752093676260.0733564109112-0.02790594848210.2424738334860.02203763245830.32854108574512.668023211-27.7211798922-32.2451251843
42.81879166457-0.0143087159263-1.1013254981.18355279986-0.2768935455821.99295199887-0.31906448756-0.174766994828-0.219602715390.104348821570.185057350672-0.3392460775940.00791022359994-0.02749967569080.08234619465130.352373729662-0.00773814563795-0.04079703221610.4366907155670.04708659548430.39219085873311.5421671569-25.4500033453-25.4515547281
51.471553891570.435366042008-0.6956619219712.01573916870.2996382938581.373668217830.05408841527280.08273114959090.01867332174390.160621478362-0.1874470547810.0750477693712-0.0195673507914-0.1299074652940.1345625745440.3105863081760.03517924553060.001580128266280.3534794793-0.004338208851420.301183861175-2.3859517798-22.5812882291-32.6968694015
62.137397852010.8138497710460.4038162272323.265523894580.5478836462472.12761909956-0.1265738831260.1114153759940.289905495173-0.04276060382870.1398817988150.0366117832887-0.0519724545662-0.0181646438626-0.01801369482830.2967326184910.002150759353630.05111632038930.2487935320320.03454028025940.2942961763860.734976773175-16.2105868592-45.3629377789
72.755716437380.9965355325280.1851038827372.576924329881.466560252515.706444045690.00313245186845-0.02500826579920.17658819804-0.0641680079965-0.2337526370620.542535085012-0.383792548664-0.3627175662370.2869443757580.3431004720220.03384239691610.01046510880180.490755349625-0.007725463321920.531290697919-24.5365315134-21.0884564125-10.4053323981
82.41263515285-0.810600429461-0.7039852743173.157232053931.539626796742.981794057730.00313780131696-0.164571440681-0.09119425862780.0961506402051-0.02947471214020.07378396873850.0981280711291-0.04143022591130.01272777360150.282251939551-0.0308154589184-0.008034487178020.357696798518-0.007535197972390.302326510608-15.8961851816-24.345846831-9.13884590293
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 13 through 36 )AA13 - 361 - 24
22chain 'A' and (resid 37 through 69 )AA37 - 6925 - 57
33chain 'A' and (resid 70 through 88 )AA70 - 8858 - 76
44chain 'A' and (resid 89 through 123 )AA89 - 12377 - 111
55chain 'A' and (resid 124 through 217 )AA124 - 217112 - 181
66chain 'A' and (resid 218 through 265 )AA218 - 265182 - 229
77chain 'B' and (resid 14 through 70 )BD14 - 701 - 57
88chain 'B' and (resid 71 through 263 )BD71 - 26358 - 226

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