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- PDB-5fwo: Llama nanobody PorM_130 -

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Basic information

Entry
Database: PDB / ID: 5fwo
TitleLlama nanobody PorM_130
ComponentsNANOBODY
KeywordsIMMUNE SYSTEM / TYPE-9 SECRETION SYSTEM (T9SS) / NANOBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesLAMA GLAMA (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLeone, P. / Roussel, A.
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
DepositionFeb 18, 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 1.3Jan 10, 2024Group: 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: NANOBODY


Theoretical massNumber of molelcules
Total (without water)14,9951
Polymers14,9951
Non-polymers00
Water1,946108
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.539, 54.539, 126.725
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-2017-

HOH

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Components

#1: Antibody NANOBODY


Mass: 14994.608 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LAMA GLAMA (llama) / Plasmid: PHEN6 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): ROSETTA PLYSS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 1.96 Å3/Da / Density % sol: 37.2 % / Description: NONE
Crystal growpH: 7 / Details: 0.2M AMMONIUM CITRATE DIBASIC 20% PEG3350, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9801
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 13038 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 21 % / Biso Wilson estimate: 26.78 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 24.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 21.1 % / Rmerge(I) obs: 1.36 / Mean I/σ(I) obs: 2.4 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FHB
Resolution: 1.7→44.26 Å / Cor.coef. Fo:Fc: 0.9578 / Cor.coef. Fo:Fc free: 0.927 / SU R Cruickshank DPI: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.128 / SU Rfree Blow DPI: 0.118 / SU Rfree Cruickshank DPI: 0.11
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2223 679 5.24 %RANDOM
Rwork0.1861 ---
obs0.188 12963 99.95 %-
Displacement parametersBiso mean: 34.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.1419 Å20 Å20 Å2
2---1.1419 Å20 Å2
3---2.2838 Å2
Refine analyzeLuzzati coordinate error obs: 0.229 Å
Refinement stepCycle: LAST / Resolution: 1.7→44.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms981 0 0 108 1089
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011027HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.051394HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d355SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes19HARMONIC2
X-RAY DIFFRACTIONt_gen_planes163HARMONIC5
X-RAY DIFFRACTIONt_it1027HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.74
X-RAY DIFFRACTIONt_other_torsion14.73
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion130SEMIHARMONIC5
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_contact1356SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.84 Å / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2489 133 5.15 %
Rwork0.2375 2451 -
all0.2381 2584 -
obs--99.88 %
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)
10.0350.47868.13260.9842-2.02773.2299-0.1913-0.18170.26640.32520.09520.5010.07630.39240.0961-0.0280.21180.0030.0828-0.1181-0.0902-8.4147-13.944312.1508
27.9607-1.9284-1.43350.4338-0.62244.0859-0.39190.46380.38490.0040.2789-0.4920.33980.95640.113-0.1550.0047-0.03740.1379-0.0715-0.03115.0349-16.4229-2.5838
37.56830.4783-2.11094.19511.20561.0333-0.22540.36580.1390.01360.3076-0.25280.07010.6259-0.0822-0.11560.0181-0.01180.03440.0002-0.08531.5749-20.4936-5.5939
42.03431.2866-0.47270.80782.8764.48340.0237-0.42130.1250.6877-0.43310.18490.53070.1180.40940.20950.05770.085-0.0056-0.0614-0.077-12.5444-19.368110.8929
50.9808-0.224-0.187510.2617-2.43777.28850.0066-0.74320.20070.6724-0.37140.34480.3214-0.20030.3648-0.0491-0.10.0512-0.0396-0.1046-0.1401-17.0006-19.40064.3418
62.5749-2.57530.311.1966-2.14876.757-0.179-0.02340.60970.07860.07420.0634-0.79590.62640.1048-0.0062-0.0874-0.0683-0.10820.0035-0.0055-5.3828-8.3679-4.1059
7-0.2859-0.5034-2.320610.1071-1.51462.4893-0.1510.07490.54610.07310.00140.0947-0.90750.28980.14960.2372-0.1445-0.1565-0.14620.06450.0252-6.6373-2.0583-5.9034
81.6680.4060.87973.44991.83046.4276-0.1631-0.13060.22570.2025-0.32360.31430.0295-0.35910.4867-0.045-0.0194-0.0195-0.0637-0.06010.0249-15.6913-16.8304-4.117
91.4594-1.45610.9230.80622.25566.7645-0.21950.13780.29180.005-0.14770.2731-0.0425-0.15720.3672-0.0721-0.0162-0.0494-0.11380.0009-0.0343-14.1641-18.0157-9.9486
105.05810.47182.88953.2752.37194.1102-0.39930.37330.0921-0.27430.0823-0.02810.05490.4050.317-0.029-0.0158-0.032-0.06640.0073-0.1026-7.2124-19.4979-11.0197
111.11262.53054.80132.8991-2.09610-0.0329-0.7796-0.42180.9939-0.31-0.07191.0752-0.0560.34290.40150.0140.0760.08680.1074-0.0036-12.3558-27.20214.0544
123.29580.1456-0.00057.44974.1452.3295-0.1158-0.37180.14920.69560.14960.19550.6044-0.449-0.0338-0.03840.05790.0011-0.00260.0447-0.1594-8.0206-22.88191.8833
136.36332.2205-4.56445.9322-2.61844.8948-0.0040.26230.1727-0.27110.1927-0.2808-0.38930.701-0.1886-0.0215-0.04390.00040.0590.0025-0.06990.1876-18.5619-11.419
141.4569-2.0486-0.6867.61651.16440.60010.10120.31810.4026-0.60170.0406-0.4127-0.370.5654-0.14170.0863-0.1709-0.03690.18210.04990.07811.1602-9.2731-9.0402
153.81860.7168-0.65821.59252.14746.6855-0.2312-0.41290.27550.041-0.27530.33530.005-0.38310.5064-0.03040.0079-0.0307-0.0578-0.07780.0633-13.5956-13.17311.4318
16-3.30464.53480.95096.3379-3.00790.00420.1896-0.33970.27110.0703-0.44980.6458-0.2753-1.01770.2602-0.1370.0355-0.06310.16-0.18710.276-24.7869-16.0106-2.3836
171.96782.1921-2.37731.8753-7.85595.67220.10410.0355-0.1478-0.1611-0.04940.2936-0.4289-0.0501-0.05470.00980.125-0.13810.0001-0.09980.1651-20.3313-10.6126-8.7896
18-1.951.0904-2.03257.0659-1.65321.2627-0.00670.13870.60760.1138-0.16280.0668-0.4046-0.27340.16950.01130.0746-0.0962-0.0186-0.14180.1677-18.5106-7.3467-0.087
19-0.465-1.7423-3.98718.45675.186118.2468-0.1515-0.5350.31230.54110.03680.17790.1361-0.03040.1147-0.08050.0145-0.0524-0.1463-0.0732-0.0976-10.7493-10.28326.5397
206.1637-2.8853-1.27592.5462-0.48960.2272-0.37710.44660.2453-0.20230.3712-0.7142-0.19910.64510.0059-0.0172-0.1643-0.00830.19730.00210.08174.9353-11.5094-4.7676
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|2 - 6 }
2X-RAY DIFFRACTION2{ A|7 - 14 }
3X-RAY DIFFRACTION3{ A|15 - 22 }
4X-RAY DIFFRACTION4{ A|23 - 29 }
5X-RAY DIFFRACTION5{ A|30 - 36 }
6X-RAY DIFFRACTION6{ A|37 - 42 }
7X-RAY DIFFRACTION7{ A|43 - 47 }
8X-RAY DIFFRACTION8{ A|48 - 54 }
9X-RAY DIFFRACTION9{ A|55 - 65 }
10X-RAY DIFFRACTION10{ A|66 - 72 }
11X-RAY DIFFRACTION11{ A|73 - 77 }
12X-RAY DIFFRACTION12{ A|78 - 82 }
13X-RAY DIFFRACTION13{ A|83 - 88 }
14X-RAY DIFFRACTION14{ A|89 - 94 }
15X-RAY DIFFRACTION15{ A|95 - 103 }
16X-RAY DIFFRACTION16{ A|104 - 108 }
17X-RAY DIFFRACTION17{ A|109 - 113 }
18X-RAY DIFFRACTION18{ A|114 - 118 }
19X-RAY DIFFRACTION19{ A|119 - 124 }
20X-RAY DIFFRACTION20{ A|125 - 130 }

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