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- PDB-7cmg: The Structure of the periplasmic domain of PorM -

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Basic information

Entry
Database: PDB / ID: 7cmg
TitleThe Structure of the periplasmic domain of PorM
ComponentsPor secretion system protein porM/gldM
KeywordsPROTEIN TRANSPORT / Type IX secretion system / trans-periplasmic core complex
Function / homology
Function and homology information


: / : / GldM second domain / GldM third domain / Gliding motility-associated protein GldM / Gliding motility-associated protein GldM, C-terminal / Gliding motility-associated protein GldM, N-terminal / GldM C-terminal domain / GldM N-terminal domain
Similarity search - Domain/homology
Por secretion system protein porM/gldM
Similarity search - Component
Biological speciesPorphyromonas gingivalis ATCC 33277 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsSato, K. / Okada, K. / Nakayam, K. / Imada, K.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)16K11450 Japan
Japan Society for the Promotion of Science (JSPS)19K10091 Japan
Japan Society for the Promotion of Science (JSPS)16K11450 Japan
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: PorM, a core component of bacterial type IX secretion system, forms a dimer with a unique kinked-rod shape.
Authors: Sato, K. / Okada, K. / Nakayama, K. / Imada, K.
History
DepositionJul 27, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 2, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 9, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 7, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Por secretion system protein porM/gldM
B: Por secretion system protein porM/gldM


Theoretical massNumber of molelcules
Total (without water)117,2802
Polymers117,2802
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13570 Å2
ΔGint-95 kcal/mol
Surface area46080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.140, 98.280, 209.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Por secretion system protein porM/gldM


Mass: 58639.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis ATCC 33277 (bacteria)
Strain: ATCC 33277 / Gene: porM, PGN_1674 / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2RLE8

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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: 3.83 Å3/Da / Density % sol: 67.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 14.6% (w/v) ethanol, 0.1 M Tris-HCl pH8.5, 150 mM NaCl, and 1mM taurine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 5, 2012
RadiationMonochromator: Double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.7→88.99 Å / Num. obs: 19679 / % possible obs: 99 % / Redundancy: 3.8 % / Biso Wilson estimate: 46.81 Å2 / CC1/2: 0.974 / Rpim(I) all: 0.103 / Net I/σ(I): 6.4
Reflection shellResolution: 3.7→4.05 Å / Mean I/σ(I) obs: 4.2 / Num. unique obs: 4681 / CC1/2: 0.884 / Rpim(I) all: 0.18

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Processing

Software
NameVersionClassification
BSSdata collection
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ey5

6ey5


Resolution: 3.7→80.47 Å / SU ML: 0.2673 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.6222
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2582 1961 9.99 %
Rwork0.213 17665 -
obs0.2177 19626 98.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.51 Å2
Refinement stepCycle: LAST / Resolution: 3.7→80.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7435 0 0 0 7435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027536
X-RAY DIFFRACTIONf_angle_d0.449510192
X-RAY DIFFRACTIONf_chiral_restr0.04091194
X-RAY DIFFRACTIONf_plane_restr0.00391321
X-RAY DIFFRACTIONf_dihedral_angle_d9.27844648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.790.2871410.25361273X-RAY DIFFRACTION99.93
3.79-3.90.29621380.24911241X-RAY DIFFRACTION99.78
3.9-4.010.28841400.21971252X-RAY DIFFRACTION99.93
4.01-4.140.27571400.21941270X-RAY DIFFRACTION99.58
4.14-4.290.24741390.22141245X-RAY DIFFRACTION99.86
4.29-4.460.2461400.19591258X-RAY DIFFRACTION99.64
4.46-4.660.24151400.19161257X-RAY DIFFRACTION99.5
4.66-4.910.24161390.18631262X-RAY DIFFRACTION99.5
4.91-5.210.25511400.20321254X-RAY DIFFRACTION98.94
5.21-5.620.27871390.21911252X-RAY DIFFRACTION99.07
5.62-6.180.27521420.23921278X-RAY DIFFRACTION98.13
6.18-7.080.32371400.24171262X-RAY DIFFRACTION97.91
7.08-8.910.19471400.20171274X-RAY DIFFRACTION96.52
8.91-80.470.22831430.18991287X-RAY DIFFRACTION92.02
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)
12.92438511484-0.0807436266581.001934162873.99359281052-0.2513454559562.61493447150.3223108699680.177455134560.2532236454710.1339066741760.0365465872383-0.187660931713-0.7213222532230.466131327241-0.1124442764860.493267297255-0.05986810215810.1961898618530.109575281859-0.07366805764630.88461386439336.949841367837.7171796581-50.1696385114
22.970060055410.482927635559-1.9471514710.109972139959-0.05510196936191.981393353720.4356481014770.001304660513550.8072431198680.3530469650160.1355201142420.105908456313-0.822503599018-0.44924122403-0.5403128666540.287631205290.09829628958120.08425972969310.4074475646730.04828933184730.464515811463-9.3770226828613.3131804994-19.2949376075
34.71412112771-0.818545931622-4.859445872390.5375930575771.525997070687.037896234340.2003006994350.5056287938250.316449068717-0.01240348974570.134518350734-0.202622917125-0.36578913592-0.326117985683-0.3188031625830.2311871929460.01750013824540.02166031524260.4914957118150.07943366322170.118784718032-37.5522972753-1.851234386618.85722469667
42.85819518993-0.428551501979-0.9048161654592.86877470597-0.2837342516646.52909026781-0.06448572228550.8498917237850.164253861989-0.176631815493-0.2398821251120.184597442417-0.0999239127661-0.7001866108610.1096925560030.0808377700811-0.106125787607-0.006337242964680.5175245843470.04394279050950.08689200374-55.3650771368-1.4345458422930.7665757475
54.75893586036-0.0744522809137-0.9664604737881.65895217010.4344711542463.141246557490.0843788690712-0.05791221232330.4654338905740.0818980079466-0.193990288973-0.390197456189-0.3735623293970.0533961052750.0423076847086-0.0428722441733-0.1491168916660.111457060864-0.05595914227090.06357347996720.26637530363539.477860217515.7929360071-51.312580814
64.89625008222-0.504645918551-1.319832408944.53297076830.3086337066451.632164431470.06878457341580.2332839812360.203134140793-0.09848032193750.09408685479560.234768349782-0.0983214466696-0.104323804118-0.1761516081440.1320367973860.0711062170053-0.0342129540350.3797285744320.08793077575910.0353721829681-2.596835367663.15920422621-28.106340533
72.3933003860.640917628973-1.995199506121.5920868682-1.024770639153.306158676150.2361585389160.4645321858150.0409675792547-0.439053125263-0.357269151987-0.374395892550.2435730073090.9968924026950.01250931358520.235618452821-0.02322408572550.0629616261131.005588406830.02771829162760.215821367907-19.90960021253.3062049805413.4992218971
85.417611134511.42603989352-0.7768929368043.465290895-0.7680393678843.901727175970.001503243862810.181941180849-0.5428289986190.429682023915-0.263511800282-0.1950853717680.5113349978780.0162010808672-0.1974438421130.24596983031-0.136103263063-0.09819563123290.145464062597-0.1722366170020.0112362958316-40.7478838814-9.1043870517541.5260286742
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 217 )
2X-RAY DIFFRACTION2chain 'A' and (resid 218 through 336 )
3X-RAY DIFFRACTION3chain 'A' and (resid 337 through 431 )
4X-RAY DIFFRACTION4chain 'A' and (resid 432 through 518 )
5X-RAY DIFFRACTION5chain 'B' and (resid 30 through 219 )
6X-RAY DIFFRACTION6chain 'B' and (resid 220 through 313 )
7X-RAY DIFFRACTION7chain 'B' and (resid 314 through 409 )
8X-RAY DIFFRACTION8chain 'B' and (resid 410 through 517 )

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