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- PDB-9hmz: Structure of Corynebacterium glutamicum SteA, a cell division reg... -

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Basic information

Entry
Database: PDB / ID: 9hmz
TitleStructure of Corynebacterium glutamicum SteA, a cell division regulator
ComponentsSteA-like C-terminal domain-containing protein
KeywordsCELL CYCLE / Cell division regulator
Function / homology
Function and homology information


thiamine diphosphokinase activity / thiamine diphosphate biosynthetic process / kinase activity / ATP binding / membrane
Similarity search - Function
SteA-like C-terminal / : / SteA-like C-terminal domain / Thiamin pyrophosphokinase, catalytic domain superfamily
Similarity search - Domain/homology
SteA-like C-terminal domain-containing protein
Similarity search - Component
Biological speciesCorynebacterium glutamicum ATCC 13032 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsGaday, Q. / Carloni, 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

Downloads & links

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Assembly

Deposited unit
A: SteA-like C-terminal domain-containing protein
B: SteA-like C-terminal domain-containing protein
C: SteA-like C-terminal domain-containing protein
D: SteA-like C-terminal domain-containing protein
E: SteA-like C-terminal domain-containing protein
F: SteA-like C-terminal domain-containing protein
G: SteA-like C-terminal domain-containing protein
H: SteA-like C-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)280,5418
Polymers280,5418
Non-polymers00
Water23,5461307
1
A: SteA-like C-terminal domain-containing protein
H: SteA-like C-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)70,1352
Polymers70,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-35 kcal/mol
Surface area28050 Å2
2
B: SteA-like C-terminal domain-containing protein
G: SteA-like C-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)70,1352
Polymers70,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-34 kcal/mol
Surface area28120 Å2
3
C: SteA-like C-terminal domain-containing protein

F: SteA-like C-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)70,1352
Polymers70,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x+1/2,-y,z+1/21
Buried area4340 Å2
ΔGint-34 kcal/mol
Surface area28400 Å2
4
D: SteA-like C-terminal domain-containing protein
E: SteA-like C-terminal domain-containing protein


Theoretical massNumber of molelcules
Total (without water)70,1352
Polymers70,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-32 kcal/mol
Surface area27910 Å2
Unit cell
Length a, b, c (Å)126.506, 128.72, 211.85
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
SteA-like C-terminal domain-containing protein


Mass: 35067.598 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum ATCC 13032 (bacteria)
Gene: Cgl1415 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8NQL9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1307 / Source method: isolated from a natural source / Formula: H2O
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: 3.08 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 10 %w/v PEG 8K 0.1 M Imidazole 8 pH 0.2 M Calcium Acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.05→105.925 Å / Num. obs: 126836 / % possible obs: 95.6 % / Redundancy: 13.6 % / CC1/2: 0.992 / Net I/σ(I): 9.2
Reflection shellResolution: 2.05→2.333 Å / Redundancy: 12.3 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 6342 / CC1/2: 0.703 / % possible all: 73.9

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Processing

Software
NameVersionClassification
autoPROCdata processing
XDSdata reduction
STARANISOdata scaling
PHASERphasing
BUSTER2.10.4refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→105.92 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.347 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.359 / SU Rfree Blow DPI: 0.236 / SU Rfree Cruickshank DPI: 0.236
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 6204 -RANDOM
Rwork0.2052 ---
obs0.2068 126836 58.7 %-
Displacement parametersBiso mean: 63.52 Å2
Baniso -1Baniso -2Baniso -3
1-2.8541 Å20 Å20 Å2
2--2.7327 Å20 Å2
3----5.5868 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.05→105.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19495 0 0 1307 20802
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00819804HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.926872HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d6829SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes3455HARMONIC5
X-RAY DIFFRACTIONt_it19804HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion2622SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact15577SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion16.2
LS refinement shellResolution: 2.05→2.23 Å
RfactorNum. reflection% reflection
Rfree0.2698 120 -
Rwork0.2809 --
obs0.2803 2537 5.17 %
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)
15.44261.19511.18157.6786-1.91158.33020.23010.48410.18730.4841-0.41.21110.18731.21110.17-0.0183-0.1081-0.03280.01520.0767-0.036451.8878-25.284127.6156
21.647-4.58620.445514.1897-0.31970.8957-0.0496-0.36220.1446-0.36220.0742-0.40340.1446-0.4034-0.02470.0137-0.06670.013-0.0208-0.033-0.004126.5215-5.436817.5232
31.9579-0.6458-0.71481.83531.30774.1411-0.0842-0.0763-0.1814-0.07630.02180.1683-0.18140.16830.06250.0552-0.0461-0.0293-0.11980.0026-0.148338.031217.004525.563
45.39810.84322.01778.33444.84799.42970.2365-0.8597-0.2999-0.8597-0.8319-1.2408-0.2999-1.24080.59550.02790.2073-0.18090.0136-0.13820.010812.4027-89.532539.1035
50.31532.97280.772410.56390.62220.7867-0.0058-0.00970.1521-0.00970.03820.34250.15210.3425-0.0324-0.0370.05760.0915-0.00860.0450.100537.2407-69.524550.1649
62.17870.886-0.87472.151-1.17164.16450.0032-0.0215-0.164-0.02150.0181-0.158-0.164-0.158-0.02130.01910.03850.0411-0.12670.0354-0.123625.9847-47.190941.57
710.1015-2.39885.23624.785-1.25149.23470.4212-0.24290.9121-0.24290.02220.19990.91210.1999-0.4433-0.12140.0047-0.05180.0087-0.1572-0.238410.9141-13.220739.8289
87.81537.7225.513410.70135.71675.94350.42380.51440.87860.51440.23570.9150.87860.915-0.6595-0.06270.2176-0.1333-0.0263-0.0496-0.058237.0766-9.113960.4323
93.02110.9901-0.71242.6203-1.54384.31770.06850.1622-0.27290.16220.01130.3059-0.27290.3059-0.0798-0.01990.007-0.1-0.0366-0.0508-0.158337.00217.16958.2939
1010.26960.83675.80846.4693-0.591815.6707-0.22791.27450.17271.27450.1691.56240.17271.56240.0589-0.19480.1625-0.17180.36560.2448-0.414752.764-77.607627.1712
116.1674-4.22752.29536.3784-3.21944.62750.1547-0.60811.1744-0.60810.2199-1.1231.1744-1.123-0.3745-0.1221-0.1436-0.0339-0.21920.04920.094226.8131-73.59346.947
123.6164-1.1053-1.20752.61251.28864.52060.0834-0.0768-0.258-0.0768-0.0005-0.4103-0.258-0.4103-0.083-0.05450.0209-0.0173-0.04360.0705-0.106727.5414-47.55688.738
134.02970.9717-1.30047.247-1.03338.88480.3538-0.876-0.8415-0.876-0.1284-0.694-0.8415-0.694-0.2254-0.30260.3709-0.12080.51160.0509-0.158516.8249-49.1059-26.4801
149.9606-4.8222.71214.1309-2.40884.81310.644-0.34151.2573-0.3415-0.1033-1.05281.2573-1.0528-0.5407-0.1275-0.087-0.1284-0.225-0.090.132724.6242-71.8311-5.2359
152.8438-0.6207-0.93712.41730.2874.38150.1206-0.03650.3576-0.0365-0.07530.32190.35760.3219-0.0453-0.0660.0586-0.09920.0160.0054-0.123149.072-63.7301-7.1312
167.61841.8472-6.92228.2116-7.087418.128-0.52150.00651.33310.0065-0.18571.09111.33311.09110.7072-0.16890.22340.2623-0.04180.0449-0.227510.6154-16.8484-13.748
1712.77227.6105-6.51335.3655-4.66086.19650.5590.5196-0.97360.51960.2807-0.7773-0.9736-0.7773-0.8397-0.00790.12530.1915-0.11130.0417-0.025623.49887.0741-33.75
183.10330.83411.34492.53770.05044.7360.10380.0779-0.15630.0779-0.03930.6252-0.15630.6252-0.0646-0.0889-0.00480.12080.054-0.0056-0.217748.1897-1.6005-31.6772
196.1601-0.8081.776515.58544.51947.5327-0.25760.8919-0.42110.89190.0522-0.2205-0.4211-0.22050.2053-0.18080.0035-0.2585-0.1721-0.00090.013444.2579-31.219169.5185
203.37035.1887-0.301810.31040.5571.02530.13150.63470.32580.6347-0.03590.24060.32580.2406-0.0956-0.02830.1065-0.0421-0.09310.06170.110240.3641-62.93560.0391
211.27930.3141-0.52881.8421-0.9013.5122-0.03530.0388-0.03670.03880.1162-0.1585-0.0367-0.1585-0.0809-0.02850.05510.03610.00360.0241-0.134414.9297-62.78566.2481
226.48321.81631.64417.881-8.051110.2713-0.2017-1.3583-0.3261-1.3583-0.01370.3878-0.32610.38780.21540.0847-0.0391-0.419-0.31050.0841-0.056819.18432.8601-1.3644
234.029-4.55171.53869.1338-2.23391.5236-0.1094-0.55330.371-0.55330.1018-0.16340.371-0.16340.00760.0465-0.1208-0.0871-0.114-0.0410.00922.97961.24167.759
241.5262-0.3578-0.57682.40561.37744.5013-0.0685-0.05380.0403-0.05380.10610.49720.04030.4972-0.0376-0.0281-0.03850.01880.02470.0158-0.225848.30930.93430.8648
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|12 - 128 }A12 - 128
2X-RAY DIFFRACTION2{ A|129 - 168 }A129 - 168
3X-RAY DIFFRACTION3{ A|169 - 342 }A169 - 342
4X-RAY DIFFRACTION4{ B|12 - 128 }B12 - 128
5X-RAY DIFFRACTION5{ B|129 - 168 }B129 - 168
6X-RAY DIFFRACTION6{ B|169 - 342 }B169 - 342
7X-RAY DIFFRACTION7{ C|12 - 128 }C12 - 128
8X-RAY DIFFRACTION8{ C|129 - 168 }C129 - 168
9X-RAY DIFFRACTION9{ C|169 - 342 }C169 - 342
10X-RAY DIFFRACTION10{ D|16 - 128 }D16 - 128
11X-RAY DIFFRACTION11{ D|129 - 168 }D129 - 168
12X-RAY DIFFRACTION12{ D|169 - 342 }D169 - 342
13X-RAY DIFFRACTION13{ E|16 - 128 }E16 - 128
14X-RAY DIFFRACTION14{ E|129 - 168 }E129 - 168
15X-RAY DIFFRACTION15{ E|169 - 342 }E169 - 342
16X-RAY DIFFRACTION16{ F|12 - 128 }F12 - 128
17X-RAY DIFFRACTION17{ F|129 - 168 }F129 - 168
18X-RAY DIFFRACTION18{ F|169 - 342 }F169 - 342
19X-RAY DIFFRACTION19{ G|13 - 128 }G13 - 128
20X-RAY DIFFRACTION20{ G|129 - 168 }G129 - 168
21X-RAY DIFFRACTION21{ G|169 - 342 }G169 - 342
22X-RAY DIFFRACTION22{ H|16 - 128 }H16 - 128
23X-RAY DIFFRACTION23{ H|129 - 168 }H129 - 168
24X-RAY DIFFRACTION24{ H|169 - 342 }H169 - 342

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