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- PDB-9hmx: Structure of SteB-RipA complex from Mycobacterium tuberculosis -

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Basic information

Entry
Database: PDB / ID: 9hmx
TitleStructure of SteB-RipA complex from Mycobacterium tuberculosis
Components
  • Copper transporter MctB
  • Peptidoglycan endopeptidase RipA
KeywordsCELL CYCLE / Complex / Peptidoglycan hydrolase / Cell division
Function / homology
Function and homology information


cell wall organization or biogenesis / copper ion homeostasis / N-acetylmuramoyl-L-alanine amidase activity / Hydrolases; Acting on peptide bonds (peptidases) / porin activity / pore complex / monoatomic ion transport / cysteine-type peptidase activity / peptidoglycan-based cell wall / cell outer membrane ...cell wall organization or biogenesis / copper ion homeostasis / N-acetylmuramoyl-L-alanine amidase activity / Hydrolases; Acting on peptide bonds (peptidases) / porin activity / pore complex / monoatomic ion transport / cysteine-type peptidase activity / peptidoglycan-based cell wall / cell outer membrane / cell wall organization / proteolysis / extracellular region
Similarity search - Function
Copper transporter MctB / Copper transport outer membrane protein, MctB / : / : / NlpC/P60 family / NlpC/P60 domain profile. / Endopeptidase, NLPC/P60 domain / Papain-like cysteine peptidase superfamily
Similarity search - Domain/homology
HEXANE-1,6-DIOL / Peptidoglycan endopeptidase RipA / Copper transporter MctB
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsCarloni, G. / Wehenkel, A.M. / Alzari, P.M.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-21-CE11-0003 France
CitationJournal: Biorxiv / Year: 2025
Title: Mechanistic insights into the allosteric regulation of cell wall hydrolase RipA in Mycobacterium tuberculosis.
Authors: Carloni, G. / Gaday, Q. / Petit, J. / Martinez, M. / Megrian, D. / Sogues, A. / Ben Assaya, M. / Kakonyi, M. / Haouz, A. / Alzari, P.M. / Wehenkel, A.M.
History
DepositionDec 9, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidoglycan endopeptidase RipA
B: Copper transporter MctB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8374
Polymers51,6012
Non-polymers2362
Water5,242291
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint4 kcal/mol
Surface area24130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.844, 225.049, 70.295
Angle α, β, γ (deg.)90, 124.36, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptidoglycan endopeptidase RipA / Macrophage invasion and intracellular persistence protein A / Resuscitation-promoting factor ...Macrophage invasion and intracellular persistence protein A / Resuscitation-promoting factor interaction partner A / Rpf-interacting protein A


Mass: 22985.221 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: ripA, Rv1477 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: O53168, Hydrolases; Acting on peptide bonds (peptidases)
#2: Protein Copper transporter MctB / Mycobacterial copper transport protein B


Mass: 28615.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: mctB, Rv1698, MTCI125.20 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P9WJ83
#3: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 5.07 Å3/Da / Density % sol: 76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M CdCl2 0.1 M Na Acet pH 4.6 30 %v/v PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.59281 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.59281 Å / Relative weight: 1
ReflectionResolution: 2.217→63.02 Å / Num. obs: 31204 / % possible obs: 88.5 % / Redundancy: 5.19 %
Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last ...Details: Some remarks regarding the mmCIF items written, the PDB Exchange Dictionary (PDBx/mmCIF) Version 5.0 supporting the data files in the current PDB archive (dictionary version 5.325, last updated 2020-04-13: http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Index/) and the actual quantities provided by MRFANA (https://github.com/githubgphl/MRFANA) from the autoPROC package (https://www.globalphasing.com/autoproc/). In general, the mmCIF categories here should provide items that are currently used in the PDB archive. If there are alternatives, the one recommended by the PDB developers has been selected. The distinction between *_all and *_obs quantities is not always clear: often only one version is actively used within the PDB archive (or is the one recommended by PDB developers). The intention of distinguishing between classes of reflections before and after some kind of observation criterion was applied, can in principle be useful - but such criteria change in various ways throughout the data processing steps (rejection of overloaded or too partial reflections, outlier/misfit rejections during scaling etc) and there is no retrospect computation of data scaling/merging statistics for the reflections used in the final refinement (where another observation criterion might have been applied). Typical data processing will usually only provide one version of statistics at various stages and these are given in the recommended item here, irrespective of the "_all" and "_obs" connotation, see e.g. the use of _reflns.pdbx_Rmerge_I_obs, _reflns.pdbx_Rrim_I_all and _reflns.pdbx_Rpim_I_all. Please note that all statistics related to "merged intensities" (or "merging") are based on inverse-variance weighting of the individual measurements making up a symmetry-unique reflection. This is standard for several decades now, even if some of the dictionary definitions seem to suggest that a simple "mean" or "average" intensity is being used instead. R-values are always given for all symmetry-equivalent reflections following Friedel's law, i.e. Bijvoet pairs are not treated separately (since we want to describe the overall mean intensity and not the mean I(+) and I(-) here). The Rrim metric is identical to the Rmeas R-value and only differs in name. _reflns.pdbx_number_measured_all is the number of measured intensities just before the final merging step (at which point no additional rejection takes place). _reflns.number_obs is the number of symmetry-unique observations, i.e. the result of merging those measurements via inverse-variance weighting. _reflns.pdbx_netI_over_sigmaI is based on the merged intensities (_reflns.number_obs) as expected. _reflns.pdbx_redundancy is synonymous with "multiplicity". The per-shell item _reflns_shell.number_measured_all corresponds to the overall value _reflns.pdbx_number_measured_all. The per-shell item _reflns_shell.number_unique_all corresponds to the overall value _reflns.number_obs. The per-shell item _reflns_shell.percent_possible_all corresponds to the overall value _reflns.percent_possible_obs. The per-shell item _reflns_shell.meanI_over_sigI_obs corresponds to the overall value given as _reflns.pdbx_netI_over_sigmaI. But be aware of the incorrect definition of the former in the current dictionary!
CC1/2: 0.996 / CC1/2 anomalous: -0.097 / Rmerge(I) obs: 0.0962 / Rpim(I) all: 0.0461 / Rrim(I) all: 0.1069 / AbsDiff over sigma anomalous: 0.742 / Baniso tensor eigenvalue 1: 91.4167 Å2 / Baniso tensor eigenvalue 2: 0 Å2 / Baniso tensor eigenvalue 3: 9.0403 Å2 / Baniso tensor eigenvector 1 ortho1: 0.8381 / Baniso tensor eigenvector 1 ortho2: 0 / Baniso tensor eigenvector 1 ortho3: 0.5455 / Baniso tensor eigenvector 2 ortho1: 0 / Baniso tensor eigenvector 2 ortho2: 1 / Baniso tensor eigenvector 2 ortho3: 0 / Baniso tensor eigenvector 3 ortho1: -0.5455 / Baniso tensor eigenvector 3 ortho2: 0 / Baniso tensor eigenvector 3 ortho3: 0.8381 / Aniso diffraction limit 1: 3.235 Å / Aniso diffraction limit 2: 2.133 Å / Aniso diffraction limit 3: 2.241 Å / Aniso diffraction limit axis 1 ortho1: 0.83397 / Aniso diffraction limit axis 1 ortho2: 0 / Aniso diffraction limit axis 1 ortho3: 0.55178 / Aniso diffraction limit axis 2 ortho1: 0 / Aniso diffraction limit axis 2 ortho2: 1 / Aniso diffraction limit axis 2 ortho3: 0 / Aniso diffraction limit axis 3 ortho1: -0.55178 / Aniso diffraction limit axis 3 ortho2: 0 / Aniso diffraction limit axis 3 ortho3: 0.83397 / Net I/σ(I): 9.45 / Num. measured all: 162070 / Observed signal threshold: 1.2 / Orthogonalization convention: pdb / % possible anomalous: 86.6 / % possible ellipsoidal: 88.5 / % possible ellipsoidal anomalous: 86.6 / % possible spherical: 61.8 / % possible spherical anomalous: 60.5 / Redundancy anomalous: 2.66 / Signal type: local
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. measured obsNum. unique allNum. unique 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
7.096-63.024.950.050923.1277237723156015600.995-0.1720.02610.05750.67298.799.798.799.798.72.5699.7
5.632-7.0955.050.064917.7478837883156015600.9960.0550.03170.07240.7699.310099.310099.32.58100
4.911-5.6325.260.061916.9782148214156115610.998-0.1070.02850.06830.75499.599.999.599.999.52.6899.9
4.461-4.915.370.064717.7583768376156015600.997-0.1210.02950.07120.75199.799.999.799.999.72.7299.9
4.136-4.4615.010.070815.878107810156015600.995-0.0820.03390.07870.77298.699.798.699.798.62.5599.7
3.894-4.1364.70.079814.0973367336156015600.9940.0670.03910.08910.75997.299.597.299.597.22.4199.5
3.696-3.8944.950.094812.2977287728156015600.994-0.0360.04610.10570.78298.599.598.599.598.52.5299.5
3.534-3.6965.090.110711.0879497949156115610.991-0.1310.05310.12310.76397.599.597.599.597.52.699.5
3.394-3.5345.190.13279.4980928092156015600.990.0520.06330.14730.77395.296.495.296.495.22.6496.4
3.268-3.3945.280.15548.3282428242156015600.9870.0120.07330.17220.79691.192.491.192.491.12.6992.4
3.153-3.2685.390.1817.4284058405156015600.985-0.080.08390.19980.77187.788.487.786.886.32.7388.4
3.043-3.1535.470.20156.6585288528156015600.9810.0070.09240.2220.76686.987.386.98079.72.7687.3
2.941-3.0435.210.23715.7281338133156115610.973-0.060.1120.26260.76584.686.784.674.873.22.6686.7
2.845-2.9415.10.27784.9279587958156015600.96500.13450.30940.75184.486.884.468.7672.6186.8
2.754-2.8455.360.32454.4883598359156015600.9540.0070.15180.35890.7784.586.484.563.1622.7486.4
2.666-2.7535.50.39653.8385828582156015600.9330.0210.18360.43770.73985.687.185.658.557.62.7987.1
2.579-2.6665.560.4763.1886728672156015600.9210.010.21780.52440.68283.88683.851.850.82.8486
2.491-2.5795.60.6112.6687438743156115610.8530.0310.27830.67280.68780.983.480.944.743.62.8783.4
2.401-2.4915.420.79851.9584588458156015600.813-0.0020.36820.88160.66576.681.276.637.235.22.8381.2
2.217-2.4014.410.96341.5368796879156015600.664-0.0460.50621.09350.64946.95146.914.613.52.3451

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Processing

Software
NameVersionClassification
autoPROC1.0.5 20221121data processing
XDSJan 10, 2022data reduction
STARANISO2.3.90data scaling
PHASERphasing
BUSTER2.10.4refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→58.03 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.904 / SU R Cruickshank DPI: 0.252 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.256 / SU Rfree Blow DPI: 0.212 / SU Rfree Cruickshank DPI: 0.212
RfactorNum. reflection% reflectionSelection details
Rfree0.2372 1612 -RANDOM
Rwork0.2056 ---
obs0.2072 31165 62 %-
Displacement parametersBiso mean: 54.17 Å2
Baniso -1Baniso -2Baniso -3
1-8.3461 Å20 Å212.9835 Å2
2---6.3549 Å20 Å2
3----1.9912 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å
Refinement stepCycle: LAST / Resolution: 2.22→58.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 16 291 3642
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0073397HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.884606HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1207SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes611HARMONIC5
X-RAY DIFFRACTIONt_it3397HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion483SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact3154SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.68
X-RAY DIFFRACTIONt_other_torsion16.62
LS refinement shellResolution: 2.22→2.33 Å
RfactorNum. reflection% reflection
Rfree0.2974 29 -
Rwork0.2656 --
obs0.2669 624 9.1 %
Refinement TLS params.

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)
13.28279.20910.305227.41231.31190.25510.18830.5002-0.00770.5002-0.21510.0376-0.00770.03760.0267-0.0293-0.01180.0596-0.2965-0.0268-0.1282-1.13187.188451.3503
20.4533-0.264-0.53042.36851.63343.02840.0303-0.1616-0.0806-0.16160.10040.3176-0.08060.3176-0.1307-0.0816-0.0260.2435-0.25110.0185-0.1024-2.0135-32.214621.2725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A43 - 239
2X-RAY DIFFRACTION2{ B|* }B41 - 313

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