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- PDB-6ey5: C-terminal part (residues 224-515) of PorM -

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Open data


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Basic information

Entry
Database: PDB / ID: 6ey5
TitleC-terminal part (residues 224-515) of PorM
ComponentsT9SS component cytoplasmic membrane protein PorM
KeywordsPROTEIN TRANSPORT / Type IV Secretion System (T9SS) / nanobody
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 Å
AuthorsLeone, P. / Cambillau, C. / Roussel, A.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-15-CE11-0019-01 France
French Infrastructure for Integrated Structural Biology France
Citation
Journal: Nat Commun / Year: 2018
Title: Type IX secretion system PorM and gliding machinery GldM form arches spanning the periplasmic space.
Authors: Leone, P. / Roche, J. / Vincent, M.S. / Tran, Q.H. / Desmyter, A. / Cascales, E. / Kellenberger, C. / Cambillau, C. / Roussel, A.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2015
Title: Crystallization and preliminary X-ray analysis of the C-terminal fragment of PorM, a subunit of the Porphyromonas gingivalis type IX secretion system.
Authors: Stathopulos, J. / Cambillau, C. / Cascales, E. / Roussel, A. / Leone, P.
History
DepositionNov 10, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2May 8, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T9SS component cytoplasmic membrane protein PorM
B: T9SS component cytoplasmic membrane protein PorM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5506
Polymers65,2882
Non-polymers2624
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: assay for oligomerization, dimerization confirmed by SEC-MALS and bacterial two-hybrid on isolated domains
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10080 Å2
ΔGint-152 kcal/mol
Surface area29720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.004, 77.004, 228.557
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein T9SS component cytoplasmic membrane protein PorM


Mass: 32644.225 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: porM, PGIN_15-9_01458 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1R4DSC1, UniProt: B2RLE8*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.02 M sodium acetate pH 4.8-5.8 0.2 M zinc acetate 15-25%(w/v) PEG 3350
PH range: 4.8 - 5.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97888,0.979109,0.979336,0.976256
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978881
20.9791091
30.9793361
40.9762561
ReflectionResolution: 2.85→40 Å / Num. obs: 16929 / % possible obs: 99.9 % / Redundancy: 8 % / Biso Wilson estimate: 102.19 Å2 / Rrim(I) all: 0.081 / Net I/σ(I): 14.8
Reflection shellResolution: 2.85→3 Å / Redundancy: 8 % / Mean I/σ(I) obs: 2.2 / CC1/2: 0.854 / Rpim(I) all: 0.276 / Rrim(I) all: 0.815 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.85→39.42 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.906 / Rfactor Rfree error: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.368
RfactorNum. reflection% reflectionSelection details
Rfree0.249 902 5.35 %RANDOM
Rwork0.217 ---
obs0.219 16861 99.9 %-
Displacement parametersBiso mean: 109.13 Å2
Baniso -1Baniso -2Baniso -3
1--9.514 Å20 Å20 Å2
2---9.514 Å20 Å2
3---19.028 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: 1 / Resolution: 2.85→39.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4197 0 4 60 4261
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014541HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.236154HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1600SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes118HARMONIC2
X-RAY DIFFRACTIONt_gen_planes658HARMONIC5
X-RAY DIFFRACTIONt_it4541HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion18.38
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion619SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4828SEMIHARMONIC4
LS refinement shellResolution: 2.85→3.05 Å / Rfactor Rfree error: 0 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.305 159 5.34 %
Rwork0.266 2818 -
all0.268 2977 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.1646-2.8748-4.45440.9102-0.65777.11710.05080.1340.0696-0.0065-0.2759-0.2676-0.46270.67220.2251-0.11960.0224-0.02530.13580.1911-0.3855-5.071827.750618.9955
22.1458-3.67122.84812.9841-4.19066.3359-0.01520.00030.01660.0660.0760.1246-0.1689-0.24-0.06070.0008-0.0415-0.13340.3525-0.0518-0.1116-24.77717.130815.6254
36.5145-2.70671.44720.30534.63294.87880.04120.0960.1333-0.4486-0.1676-0.0655-0.51410.29020.1263-0.2130.08-0.00490.150.0651-0.3352-6.957524.504119.554
47.62785.6134-6.18358.3194-3.51192.1965-0.03360.22530.226-0.1238-0.1713-0.0444-0.1795-0.0690.20490.1303-0.00070.17360.1584-0.1656-0.0662-3.880632.39912.8986
513.98194.4969-3.79760.28640.54982.1409-0.05520.63190.70130.35530.27290.2979-0.353-0.3354-0.2177-0.10390.1457-0.002-0.0186-0.0425-0.4179-15.822228.47270.7627
69.3693-5.5778-6.20145.70495.89543.4024-0.0576-0.0995-0.19650.2212-0.0933-0.5785-0.1410.28610.15090.0255-0.13560.02620.13770.1063-0.06914.525328.0054.7603
70.145-4.6290.02120.0560.1583.0790.01080.1063-0.1654-0.1582-0.065-0.0430.3317-0.18840.0542-0.26880.08080.19770.2581-0.27410.2112-2.233821.472.9898
80.01484.8433-1.770311.58933.83385.24440.01980.1969-0.15510.21930.08450.2402-0.0601-0.7017-0.1042-0.09430.06470.16660.2457-0.134-0.1756-23.546618.1082-0.1816
95.147-3.18680.43345.28991.03713.50030.10571.0141-0.5881-0.22930.4912-0.06170.44570.7799-0.5969-0.45340.1136-0.2211-0.2759-0.1048-0.4286-41.04175.46319.1988
100.00530.7997-2.85720.62480.69280.43020.002-0.07440.0927-0.0176-0.02930.02320.008-0.030.02740.2656-0.11330.25620.3275-0.28720.0239-27.72653.72621.5292
115.3779-0.1412-0.6488.64982.791700.1334-0.2636-0.8548-0.48160.1418-0.76690.38090.6699-0.2752-0.42420.3121-0.2395-0.3993-0.0598-0.4527-35.2458-2.089211.9445
121.19010.70210.37630.39482.06052.5123-0.00370.2025-0.0155-0.0388-0.0277-0.1188-0.04150.18090.03140.14060.0875-0.04410.5722-0.07290.5694-20.28389.25037.9529
133.34241.9129-1.36044.02611.83611.71960.01570.0753-0.21250.5510.14530.03620.80690.3239-0.161-0.32640.0745-0.1309-0.5280.189-0.4547-49.1984-2.230216.4797
141.7631-0.41314.05843.23763.60942.1875-0.01730.5569-0.0941-0.1942-0.03630.2911-0.0585-0.38790.05370.11040.05350.0210.3202-0.19570.5752-75.5712-10.91826.8734
150.15470.6835-1.15241.9472-2.2120.41010.00040.15970.02690.0419-0.0150.19380.27960.02060.01470.1138-0.12220.1849-0.1109-0.24550.4617-72.5667-18.02669.719
1611.79424.23520.00831.58551.99212.19060.03870.1129-0.75220.78140.20950.98750.8955-0.4262-0.24810.19130.11840.2331-0.5286-0.09870.0965-66.3763-15.858718.6303
171.013.92265.12285.94780.93286.2973-0.0077-0.2112-0.06710.09810.14640.11690.0585-0.219-0.13870.4498-0.16140.216-0.1523-0.02990.626-74.5507-26.416416.7546
180.22083.2968-5.2955.16133.41020.64770.0285-0.1664-0.09140.1711-0.0033-0.1270.0804-0.3417-0.02520.1292-0.21380.2826-0.3656-0.17650.464-78.8084-16.182622.2826
190.27090.4045-1.90113.07860.93630.03650.0375-0.0197-0.09540.08860.0038-0.11760.2102-0.0446-0.04130.2609-0.10870.2356-0.53330.2199-0.0736-59.6516-17.618519.6705
200.30755.443-2.5754.8818-3.51793.3933-0.0068-0.1116-0.3370.7527-0.28020.05870.4317-0.37290.2870.3534-0.0115-0.0959-0.4354-0.1343-0.0396-64.4202-13.505218.6929
215.8686-0.95081.32356.6978-0.91310.7651-0.1279-0.2262-0.7531-0.04870.17080.08930.0455-0.2223-0.0429-0.00330.10630.24960.041-0.0413-0.2477-11.337522.997210.1891
225.1711-0.5689-3.49223.81051.4120.04830.0145-0.0494-0.09540.08690.04590.09350.20960.5328-0.0604-0.0316-0.0134-0.08860.03420.0606-0.1533-9.56518.072730.9075
230.19291.45692.10221.90260.84542.4687-0.06680.0955-0.2216-0.0896-0.04490.0413-0.2211-0.10610.1117-0.29660.0020.0004-0.0048-0.0052-0.3854-15.79323.134624.0935
242.6381-1.15972.43336.65460.25644.22190.18340.2963-0.2973-0.2366-0.0966-0.23480.36410.8173-0.0868-0.39640.2352-0.0517-0.03660.1031-0.4598-49.127111.829511.9062
253.17733.05270.10170.0671-0.89071.122-0.01160.0513-0.05280.0924-0.046-0.0749-0.1228-0.00550.0576-0.05280.1755-0.03290.44160.19620.5261-36.217827.079710.0854
260.5757-0.7299-0.08182.75013.20087.70840.10770.35520.7751-0.2843-0.18-0.1446-0.95810.11890.0723-0.25940.1168-0.0205-0.15890.1641-0.2681-50.000222.668411.0476
2700.47-2.99490.1661-1.05030-0.08490.1894-0.1275-0.20290.0286-0.12960.1067-0.01110.0564-0.18650.2732-0.13990.50560.0599-0.1669-60.605512.36714.628
287.3298-2.8948-2.24933.6981.56270.04730.02540.06410.2994-0.17670.0637-0.4451-0.2670.1353-0.089-0.25420.2939-0.0652-0.0210.3388-0.4133-46.841220.67232.5434
294.8946-1.1253-0.45415.72111.07386.78050.02710.62320.039-0.3636-0.0657-0.2451-0.17080.1430.0386-0.17210.1984-0.1003-0.0630.0351-0.147-51.205713.57928.2847
304.699-3.9758-2.65013.57440.93747.051-0.0213-0.0898-0.06270.2395-0.0822-0.11880.17810.21870.10350.6054-0.0780.0269-0.24090.1862-0.2442-60.7076-6.393238.5388
311.03540.57440.23911.78671.77773.1525-0.0204-0.21270.17820.12140.08270.00730.06080.0774-0.06230.5667-0.22710.2917-0.0970.0305-0.0672-68.3302-3.654140.0909
3205.852.10217.28121.96143.41870.0961-0.1707-0.65150.21220.2002-0.20230.58660.3447-0.2963-0.17580.02110.1887-0.51760.0749-0.5051-59.30764.137124.7597
332.5307-3.1957-4.62030.71124.67214.7441-0.0176-0.16090.03630.0268-0.0424-0.0004-0.0584-0.08210.060.2719-0.26420.30640.06590.04430.1331-77.3181-2.86729.9723
340.2142-0.4578-0.69441.60520.85550.4532-0.00370.043-0.0404-0.0132-0.01090.0063-0.0277-0.00380.01450.4397-0.13770.1949-0.17570.14370.1237-85.804-17.234331.4694
350.3027-0.9555-2.48830.76370.1860.93910.0167-0.07090.0942-0.02780.0038-0.07760.08180.0495-0.02050.2931-0.23410.2813-0.1474-0.17450.2525-82.7123-5.716231.2518
360.00511.8141-4.176703.23540-0.0031-0.1655-0.07950.08360.01180.0905-0.0598-0.2152-0.00860.3752-0.21540.3783-0.2682-0.0558-0.3864-78.19741.227636.9296
370.1366-1.5431-4.88047.2869-4.6762.5425-0.0172-0.2285-0.0577-0.0815-0.1169-0.05170.0350.00750.1340.631-0.27570.3467-0.19970.3065-0.0546-76.3625-11.156738.549
385.55012.5743-0.65271.76665.47825.1806-0.04990.094-0.09620.0743-0.08220.22930.03220.03210.1321-0.1948-0.04340.3129-0.15110.1396-0.015-70.86723.611323.1994
390-0.739-3.3840-1.393600.01810.11410.04350.09710.0610.0426-0.1564-0.049-0.0791-0.2805-0.048-0.0056-0.5166-0.03440.0004-70.68146.047818.602
400-2.4667-3.00522.3827-1.119400.0111-0.1389-0.11740.2049-0.03350.00090.28580.08230.02240.599-0.18150.0237-0.43710.2666-0.3214-68.9156-10.782931.1942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|225 - 236 }
2X-RAY DIFFRACTION2{ A|237 - 244 }
3X-RAY DIFFRACTION3{ A|245 - 256 }
4X-RAY DIFFRACTION4{ A|257 - 267 }
5X-RAY DIFFRACTION5{ A|268 - 289 }
6X-RAY DIFFRACTION6{ A|290 - 303 }
7X-RAY DIFFRACTION7{ A|304 - 308 }
8X-RAY DIFFRACTION8{ A|309 - 316 }
9X-RAY DIFFRACTION9{ A|317 - 344 }
10X-RAY DIFFRACTION10{ A|345 - 350 }
11X-RAY DIFFRACTION11{ A|351 - 381 }
12X-RAY DIFFRACTION12{ A|382 - 389 }
13X-RAY DIFFRACTION13{ A|390 - 407 }
14X-RAY DIFFRACTION14{ A|408 - 426 }
15X-RAY DIFFRACTION15{ A|427 - 437 }
16X-RAY DIFFRACTION16{ A|438 - 466 }
17X-RAY DIFFRACTION17{ A|467 - 486 }
18X-RAY DIFFRACTION18{ A|487 - 494 }
19X-RAY DIFFRACTION19{ A|495 - 499 }
20X-RAY DIFFRACTION20{ A|500 - 516 }
21X-RAY DIFFRACTION21{ B|224 - 257 }
22X-RAY DIFFRACTION22{ B|258 - 273 }
23X-RAY DIFFRACTION23{ B|274 - 320 }
24X-RAY DIFFRACTION24{ B|321 - 340 }
25X-RAY DIFFRACTION25{ B|341 - 346 }
26X-RAY DIFFRACTION26{ B|347 - 368 }
27X-RAY DIFFRACTION27{ B|369 - 374 }
28X-RAY DIFFRACTION28{ B|375 - 381 }
29X-RAY DIFFRACTION29{ B|382 - 406 }
30X-RAY DIFFRACTION30{ B|407 - 426 }
31X-RAY DIFFRACTION31{ B|427 - 435 }
32X-RAY DIFFRACTION32{ B|436 - 450 }
33X-RAY DIFFRACTION33{ B|451 - 457 }
34X-RAY DIFFRACTION34{ B|458 - 463 }
35X-RAY DIFFRACTION35{ B|464 - 469 }
36X-RAY DIFFRACTION36{ B|470 - 477 }
37X-RAY DIFFRACTION37{ B|478 - 492 }
38X-RAY DIFFRACTION38{ B|493 - 502 }
39X-RAY DIFFRACTION39{ B|503 - 507 }
40X-RAY DIFFRACTION40{ B|508 - 516 }

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  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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