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- PDB-8a9x: Crystal structure of PulM C-ter domain -

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Basic information

Entry
Database: PDB / ID: 8a9x
TitleCrystal structure of PulM C-ter domain
ComponentsType II secretion system protein M
KeywordsSTRUCTURAL PROTEIN / Type II Secretion System / Assembly platform / Klebsiella oxytoca / Ferredoxine-like domain
Function / homologyGeneral secretion pathway protein M, EpsM / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta / :
Function and homology information
Biological speciesKlebsiella oxytoca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.523 Å
AuthorsDazzoni, R. / Li, Y. / Lopez-Castilla, A. / Brier, S. / Mechaly, A. / Cordier, F. / Haouz, A. / Nilges, M. / Francetic, O. / Bardiaux, B. / Izadi-Pruneyre, N.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)19-CE11-0020-01 France
CitationJournal: Structure / Year: 2023
Title: Structure and dynamic association of an assembly platform subcomplex of the bacterial type II secretion system.
Authors: Dazzoni, R. / Li, Y. / Lopez-Castilla, A. / Brier, S. / Mechaly, A. / Cordier, F. / Haouz, A. / Nilges, M. / Francetic, O. / Bardiaux, B. / Izadi-Pruneyre, N.
History
DepositionJun 29, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.year
Revision 1.2Apr 12, 2023Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Type II secretion system protein M
B: Type II secretion system protein M
C: Type II secretion system protein M
D: Type II secretion system protein M
E: Type II secretion system protein M
F: Type II secretion system protein M
G: Type II secretion system protein M


Theoretical massNumber of molelcules
Total (without water)59,9537
Polymers59,9537
Non-polymers00
Water10,016556
1
A: Type II secretion system protein M
C: Type II secretion system protein M


Theoretical massNumber of molelcules
Total (without water)17,1302
Polymers17,1302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-11 kcal/mol
Surface area8130 Å2
MethodPISA
2
B: Type II secretion system protein M

F: Type II secretion system protein M


Theoretical massNumber of molelcules
Total (without water)17,1302
Polymers17,1302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_455x-1/2,-y+1/2,-z1
Buried area1250 Å2
ΔGint-10 kcal/mol
Surface area7990 Å2
MethodPISA
3
D: Type II secretion system protein M

E: Type II secretion system protein M


Theoretical massNumber of molelcules
Total (without water)17,1302
Polymers17,1302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_545x+1/2,y-1/2,z1
Buried area1270 Å2
ΔGint-9 kcal/mol
Surface area8060 Å2
MethodPISA
4
G: Type II secretion system protein M

G: Type II secretion system protein M


Theoretical massNumber of molelcules
Total (without water)17,1302
Polymers17,1302
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area1360 Å2
ΔGint-10 kcal/mol
Surface area7750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.85, 135.529, 109.408
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Type II secretion system protein M / T2SS protein M / General secretion pathway protein M


Mass: 8564.783 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella oxytoca (bacteria) / Gene: DVB85_16620 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8B2TA77
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / Source method: isolated from a natural source / Formula: H2O

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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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 0.1 M HEPES pH 7.5, 0.2 M CaCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.52→67.76 Å / Num. obs: 91712 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.02 / Rrim(I) all: 0.073 / Net I/σ(I): 17.6
Reflection shellResolution: 1.52→1.549 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.951 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4530 / CC1/2: 0.9 / CC star: 0.975 / Rpim(I) all: 0.264 / Rrim(I) all: 0.987 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (8-JUN-2022)refinement
PHASERphasing
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NMR structure

Resolution: 1.523→67.76 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.95 / SU R Cruickshank DPI: 0.083 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.088 / SU Rfree Blow DPI: 0.082 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.2305 4685 -RANDOM
Rwork0.2167 ---
obs0.2174 91712 100 %-
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.2976 Å20 Å20 Å2
2--4.8442 Å20 Å2
3----3.5466 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 1.523→67.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4124 0 0 556 4680
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0114187HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.045727HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1416SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes704HARMONIC5
X-RAY DIFFRACTIONt_it4187HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion591SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact4189SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.98
X-RAY DIFFRACTIONt_other_torsion15.02
LS refinement shellResolution: 1.523→1.53 Å
RfactorNum. reflection% reflection
Rfree0.2696 98 -
Rwork0.2468 --
obs--100 %
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)
10.5909-0.21080.03820.593-0.05440.1576-0.0195-0.059-0.0228-0.0590.00140.0059-0.02280.00590.0181-0.00410.01050.0155-0.014-0.0017-0.00667.828243.545416.562
20.9156-0.37030.19840-0.05261.147-0.00160.03590.02660.0359-0.03360.02460.02660.02460.0351-0.0133-0.0035-0.0154-0.0048-0.0113-0.0147-13.357444.25190.2762
31.1107-0.6353-0.03511.01420.12220.4872-0.02630.01580.02590.0158-0.0042-0.01510.0259-0.01510.0305-0.02780.00980.0145-0.0236-0.01070.014112.371724.539518.3517
41.0396-0.6489-0.19451.6649-0.39190.2993-0.06950.05960.00080.05960.1281-0.03190.0008-0.0319-0.05860.01190.02410.0039-0.03680.0053-0.015823.72516.770818.9157
50.0593-0.31960.11340.71690.053600.0273-0.1055-0.0328-0.1055-0.0150.0264-0.03280.0264-0.01240.0212-0.0094-0.0209-0.01560.0187-0.01-2.877960.943115.3321
61.1651-0.14190.34912.0144-0.06630.6118-0.0572-0.00390.02-0.0039-0.0267-0.04840.02-0.04840.0839-0.03560.00810.00810.0098-0.0116-0.008812.404517.5471-11.693
71.89260.2551-1.268300.10240.53820.27380.06470.13830.0647-0.01230.11490.13830.1149-0.2615-0.1493-0.00340.081-0.0317-0.03350.2547-1.473640.486-17.6112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A79 - 158
2X-RAY DIFFRACTION2{ B|* }B81 - 157
3X-RAY DIFFRACTION3{ C|* }C80 - 157
4X-RAY DIFFRACTION4{ D|* }D80 - 158
5X-RAY DIFFRACTION5{ E|* }E80 - 158
6X-RAY DIFFRACTION6{ F|* }F80 - 157
7X-RAY DIFFRACTION7{ G|* }G81 - 158

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