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- PDB-5lmj: Llama nanobody PorM_19 -

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Open data


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Basic information

Entry
Database: PDB / ID: 5lmj
TitleLlama nanobody PorM_19
Componentsnanobody
KeywordsIMMUNE SYSTEM / nanobody / Porphyromonas gingivalis / Type-9 Secretion System (T9SS)
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLeone, P. / Cambillau, C. / Roussel, A.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research Agency France
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Camelid nanobodies used as crystallization chaperones for different constructs of PorM, a component of the type IX secretion system from Porphyromonas gingivalis.
Authors: Duhoo, Y. / Roche, J. / Trinh, T.T.N. / Desmyter, A. / Gaubert, A. / Kellenberger, C. / Cambillau, C. / Roussel, A. / Leone, P.
History
DepositionAug 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 3, 2017Provider: repository / Type: Initial release
Revision 1.1May 10, 2017Group: Database references
Revision 1.2May 17, 2017Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Apr 10, 2019Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_variant
Revision 1.5Jan 10, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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: nanobody
B: nanobody
C: nanobody
D: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,43315
Polymers58,3884
Non-polymers1,04511
Water7,278404
1
A: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0726
Polymers14,5971
Non-polymers4755
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7873
Polymers14,5971
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6922
Polymers14,5971
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8824
Polymers14,5971
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.258, 113.258, 153.486
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Antibody
nanobody


Mass: 14597.071 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pHEN6 / Production host: Escherichia coli (E. coli) / Variant (production host): WK6
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 4.21 Å3/Da / Density % sol: 70.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1M Hepes pH4.5-5.5 0.4-1.2M NaH2PO4 0.4-1.2M KH2PO4
PH range: 4.5-5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07224 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07224 Å / Relative weight: 1
ReflectionResolution: 2.1→48.1 Å / Num. obs: 58799 / % possible obs: 99.9 % / Redundancy: 8.7 % / Biso Wilson estimate: 54.06 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 8.2 % / Rmerge(I) obs: 1.353 / Mean I/σ(I) obs: 1.7 / CC1/2: 0.652 / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HEM
Resolution: 2.1→46.63 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.94 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.135 / SU Rfree Blow DPI: 0.124 / SU Rfree Cruickshank DPI: 0.119
RfactorNum. reflection% reflectionSelection details
Rfree0.21 2966 5.05 %RANDOM
Rwork0.188 ---
obs0.189 58723 99.8 %-
Displacement parametersBiso mean: 69.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.8657 Å20 Å20 Å2
2--3.8657 Å20 Å2
3----7.7315 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å
Refinement stepCycle: 1 / Resolution: 2.1→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3741 0 55 404 4200
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013969HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.115388HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1324SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes84HARMONIC2
X-RAY DIFFRACTIONt_gen_planes597HARMONIC5
X-RAY DIFFRACTIONt_it3969HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion4.04
X-RAY DIFFRACTIONt_other_torsion15.94
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion488SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4509SEMIHARMONIC4
LS refinement shellResolution: 2.1→2.15 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 196 4.61 %
Rwork0.228 4056 -
all0.229 4252 -
obs--99.74 %
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)
18.6693-4.98671.11070.00121.15810.61130.063-0.5937-0.14750.14280.0247-0.40690.0845-0.2662-0.0876-0.1566-0.0738-0.04270.10420.15710.03299.597-31.7585-20.223
200.0797-0.79541.9132-1.53724.07770.0515-0.7135-1.1589-0.0403-0.04730.0020.8546-0.2943-0.00420.0283-0.174-0.05530.27370.29920.4797.8058-45.0938-18.384
30-2.029-0.00880.02820.86192.88710.1194-0.05070.12070.0325-0.1104-0.0588-0.0609-0.4075-0.009-0.1983-0.03350.03160.22580.1311-0.0535-0.9795-24.4583-25.9627
46.0868-2.451-0.80273.4371-0.86655.0531-0.0453-0.0048-0.7333-0.23770.006-0.05790.3884-0.32710.0394-0.2874-0.1139-0.0342-0.09560.0948-0.01868.3803-36.7823-30.5204
50-4.5897-3.52713.41181.976100.018-0.1432-0.3842-0.8034-0.3522-0.24710.61270.1850.3342-0.14790.0130.0512-0.02860.03450.288816.7089-40.2333-34.8572
60.28592.65551.05554.29311.05073.03320.12250.2824-0.956-0.02790.05540.17450.3972-0.6314-0.178-0.2948-0.1627-0.0740.05970.09650.0119-1.1651-39.5577-32.6968
71.2905-3.75752.08353.58822.36383.51420.12460.0191-0.659-0.20880.2038-0.11710.6348-0.0697-0.3285-0.0872-0.2285-0.1227-0.07110.03540.4094.7894-49.0502-30.5406
83.26081.18820.24760-1.54721.78120.1454-0.2704-0.7387-0.14140.00620.09140.2808-0.5396-0.1516-0.2277-0.1574-0.03710.13870.20480.03990.2039-38.5824-22.2736
91.4481.72070.41792.5219-1.42433.99620.01730.0075-0.6531-0.30460.0576-0.24550.4753-0.2318-0.0748-0.1874-0.08530.0032-0.05250.04070.017410.1285-38.0548-33.4973
103.43690.19440.26135.7761-1.75544.6096-0.0641-0.1909-0.79330.00960.1539-0.20270.0937-0.2769-0.0898-0.3347-0.09410.02-0.1020.088-0.025411.3243-35.8811-29.4003
110.1952-4.63297.53766.98620.6120.57040.2704-0.4682-0.6474-0.5692-0.28080.08540.3130.0060.0104-0.3062-0.0404-0.0375-0.05630.25680.064724.6471-40.7728-21.2741
121.2252-0.7885-1.13250.75831.13213.6704-0.0386-1.5993-0.80990.46780.18070.30130.3589-0.2158-0.1421-0.1492-0.06390.01630.76160.62330.175121.9108-42.726-3.2677
1300.9914-1.47160-0.000800.01430.2521-0.0706-0.54210.1353-0.22360.29020.2095-0.1496-0.295-0.0312-0.1170.26610.23950.431930.8809-46.5757-24.7113
147.2835-0.46331.90720-2.65430.10370.0386-1.3287-0.83550.19960.0279-0.02780.2170.2231-0.0664-0.5089-0.0646-0.02720.25720.3268-0.302730.993-34.2376-11.8851
153.9855-1.498-0.9034.1177-1.46020.05270.1875-0.3929-0.81030.0276-0.0101-0.11460.4840.2213-0.1775-0.26270.001-0.06950.44040.50850.049140.0157-41.9664-9.6271
168.84170.24711.09710.46530.47475.27740.0351-1.6906-1.0460.1605-0.18330.0650.19810.37290.1482-0.3824-0.021-0.09630.39660.5892-0.09733.5241-42.2544-6.1994
174.8547-0.69932.34263.8054-0.95750.0262-0.0105-1.0918-1.2454-0.00080.22370.07690.40530.0066-0.2132-0.471-0.0588-0.05130.28330.66730.001928.4228-45.4911-7.6334
180.55083.1933-0.10340-0.81973.4439-0.0006-0.1618-0.17840.2030.0474-0.04940.0848-0.0579-0.0468-0.328-0.0199-0.04850.96810.3473-0.455226.4476-34.25514.1526
1910.0958-0.6298-1.86720-0.20832.67610.08280.154-0.3150.05140.07940.04020.56020.1299-0.1621-0.4813-0.0083-0.00840.11830.2566-0.267531.7703-32.7566-18.8396
203.1508-0.66361.50121.4408-1.66965.50430.0598-1.0002-0.55610.2024-0.08710.02630.0194-0.0570.0273-0.3869-0.0628-0.02330.1550.2368-0.209726.9588-33.6568-13.4094
212.80071.78294.09342.50343.16682.04160.22520.4026-0.09130.1094-0.2331-0.12680.36440.02540.0079-0.35360.0815-0.06340.12740.0274-0.237759.8771-39.3883-25.2625
226.2137-0.5097-7.73550.7566-1.68283.356-0.04030.0255-0.0103-0.60530.061-0.00010.01790.0926-0.0207-0.18110.07970.04570.94360.3703-0.285664.546-25.1474-44.0128
238.508-3.82993.17415.0082-0.08040.0480.11810.6132-0.5065-0.20870.0510.38320.12370.0359-0.1691-0.39340.0427-0.08490.2785-0.0873-0.331157.5334-39.9492-31.6661
243.2611-2.52392.36473.20512.31783.85430.21971.0198-0.2773-0.5132-0.1272-0.23060.1354-0.2605-0.0924-0.43250.0985-0.01840.34170.1866-0.277354.0516-31.3944-27.784
2500.4801-2.267504.50057.44870.10060.33080.6581-0.25570.12590.1585-0.0395-0.2828-0.2265-0.47410.1319-0.01470.31550.362-0.143954.6068-21.5013-26.1376
269.8471.04730.69010.3232-1.56074.68290.35131.66920.0083-0.5455-0.121-0.018-0.1914-0.6778-0.2304-0.50470.0897-0.050.60180.1834-0.432145.8122-31.6422-33.5641
276.2403-1.091.37971.3789-0.05592.25010.22921.4233-0.0411-0.37780.11620.18360.1909-0.5876-0.3454-0.4940.1011-0.08490.75560.0998-0.468151.0938-34.9391-37.812
282.9576-0.32352.433601.6132.95760.18151.383-0.1028-0.2206-0.00150.1604-0.11070.0704-0.18-0.46590.1282-0.03980.60070.0736-0.43455.5265-34.7046-38.6516
291.74171.8461-1.07680-3.76630.7635-0.04530.0678-0.0414-0.12060.0416-0.1183-0.33890.11530.0037-0.29010.09830.05340.58920.4991-0.138558.9801-19.7334-39.252
305.7909-0.57812.000900.1760.99710.21430.80090.0005-0.17780.03740.0570.1007-0.2238-0.2517-0.46890.0459-0.00620.08550.1898-0.31654.4923-30.9856-23.893
316.6186-2.2019-2.3420.46420.326700.0712-0.8093-0.35030.0995-0.14710.33860.0236-0.01490.076-0.1207-0.07650.02460.20650.0693-0.095817.6871-25.1128-17.9779
320.83890.77770.09851.4434-0.35862.52310.2138-1.36720.29990.6256-0.2260.2241-0.30360.21470.0123-0.019-0.1630.03170.5924-0.14870.022119.4146-14.9704-9.2458
334.89240.1942-0.26352.2446-0.46452.44220.223-0.5120.21910.0364-0.0814-0.0902-0.18590.1011-0.1416-0.192-0.0778-0.00340.0530.0274-0.134222.5709-20.3134-24.9893
341.5940.5356-1.58630.0029-4.88274.7287-0.06190.08980.37470.22440.20890.4518-0.5281-0.1903-0.147-0.0819-0.00840.09990.1795-0.05850.10314.3727-9.9459-25.6477
354.57478.85090.57525.69571.65166.06330.0482-0.51360.52290.51340.1333-0.7383-0.47370.4127-0.1815-0.1874-0.14660.00360.0880.0026-0.069230.2115-12.218-23.9867
364.0378-0.155-1.20996.00040.01372.34680.3627-0.86310.62750.3984-0.31670.1446-0.56370.5133-0.0461-0.1695-0.17070.00480.1823-0.0768-0.116326.7962-14.4619-18.0014
375.25490.80210.07311.3273-0.07714.21410.3746-1.12130.85330.2912-0.07720.0592-0.44970.0676-0.2974-0.1698-0.12740.09320.135-0.1582-0.105916.5667-11.1169-14.4655
382.44351.0634-1.90520.0021-3.28863.713-0.1149-0.3355-0.0547-0.25830.0134-0.04990.06530.25280.1014-0.0707-0.07680.0367-0.17790.0078-0.148225.7807-15.9613-38.0666
393.22912.2153-1.25225.40920.14022.9890.0772-0.43150.2441-0.21080.23630.145-0.25030.0332-0.3134-0.2144-0.04430.0116-0.08880.0231-0.170819.8725-19.4-30.9989
402.7452-0.0997-0.74570-3.68893.9358-0.0527-0.70550.45240.42190.09590.2026-0.3153-0.0992-0.0432-0.17-0.06270.06760.3421-0.12920.003810.6088-13.5813-11.3934
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - 12 }
2X-RAY DIFFRACTION2{ A|13 - 22 }
3X-RAY DIFFRACTION3{ A|23 - 31 }
4X-RAY DIFFRACTION4{ A|32 - 41 }
5X-RAY DIFFRACTION5{ A|42 - 46 }
6X-RAY DIFFRACTION6{ A|47 - 60 }
7X-RAY DIFFRACTION7{ A|61 - 69 }
8X-RAY DIFFRACTION8{ A|70 - 86 }
9X-RAY DIFFRACTION9{ A|87 - 106 }
10X-RAY DIFFRACTION10{ A|107 - 113 }
11X-RAY DIFFRACTION11{ B|1 - 6 }
12X-RAY DIFFRACTION12{ B|7 - 24 }
13X-RAY DIFFRACTION13{ B|25 - 30 }
14X-RAY DIFFRACTION14{ B|31 - 53 }
15X-RAY DIFFRACTION15{ B|54 - 60 }
16X-RAY DIFFRACTION16{ B|61 - 76 }
17X-RAY DIFFRACTION17{ B|77 - 84 }
18X-RAY DIFFRACTION18{ B|85 - 90 }
19X-RAY DIFFRACTION19{ B|91 - 106 }
20X-RAY DIFFRACTION20{ B|107 - 113 }
21X-RAY DIFFRACTION21{ C|1 - 7 }
22X-RAY DIFFRACTION22{ C|8 - 16 }
23X-RAY DIFFRACTION23{ C|17 - 29 }
24X-RAY DIFFRACTION24{ C|30 - 42 }
25X-RAY DIFFRACTION25{ C|43 - 47 }
26X-RAY DIFFRACTION26{ C|48 - 63 }
27X-RAY DIFFRACTION27{ C|64 - 76 }
28X-RAY DIFFRACTION28{ C|77 - 85 }
29X-RAY DIFFRACTION29{ C|86 - 92 }
30X-RAY DIFFRACTION30{ C|93 - 113 }
31X-RAY DIFFRACTION31{ D|1 - 12 }
32X-RAY DIFFRACTION32{ D|13 - 22 }
33X-RAY DIFFRACTION33{ D|23 - 42 }
34X-RAY DIFFRACTION34{ D|43 - 48 }
35X-RAY DIFFRACTION35{ D|49 - 60 }
36X-RAY DIFFRACTION36{ D|61 - 80 }
37X-RAY DIFFRACTION37{ D|81 - 96 }
38X-RAY DIFFRACTION38{ D|97 - 100 }
39X-RAY DIFFRACTION39{ D|101 - 105 }
40X-RAY DIFFRACTION40{ D|106 - 113 }

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