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- PDB-5ovw: Nanobody-bound BtuF, the vitamin B12 binding protein in Escherich... -

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Basic information

Entry
Database: PDB / ID: 5ovw
TitleNanobody-bound BtuF, the vitamin B12 binding protein in Escherichia coli
Components
  • NanobodySingle-domain antibody
  • Vitamin B12-binding protein
KeywordsTRANSPORT PROTEIN / Nanobody / Inhibitor / vitamin B12 / substrate-binding protein
Function / homology
Function and homology information


cobalamin transport / cobalamin binding / outer membrane-bounded periplasmic space / periplasmic space
Similarity search - Function
ABC transporter, vitamin B12-binding protein / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Vitamin B12-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.653 Å
AuthorsMireku, S.A. / Sauer, M.M. / Glockshuber, R. / Locher, K.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science FoundationSNF 310030B_166672 Switzerland
CitationJournal: Sci Rep / Year: 2017
Title: Structural basis of nanobody-mediated blocking of BtuF, the cognate substrate-binding protein of the Escherichia coli vitamin B12 transporter BtuCD.
Authors: Mireku, S.A. / Sauer, M.M. / Glockshuber, R. / Locher, K.P.
History
DepositionAug 30, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Vitamin B12-binding protein
B: Vitamin B12-binding protein
C: Vitamin B12-binding protein
D: Vitamin B12-binding protein
E: Vitamin B12-binding protein
F: Vitamin B12-binding protein
G: Nanobody
H: Nanobody
I: Nanobody
J: Nanobody
K: Nanobody
L: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)291,32217
Polymers290,86112
Non-polymers4605
Water4,756264
1
A: Vitamin B12-binding protein
H: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5693
Polymers48,4772
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-14 kcal/mol
Surface area16110 Å2
MethodPISA
2
B: Vitamin B12-binding protein
I: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5693
Polymers48,4772
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2450 Å2
ΔGint-13 kcal/mol
Surface area16220 Å2
MethodPISA
3
C: Vitamin B12-binding protein
G: Nanobody


Theoretical massNumber of molelcules
Total (without water)48,4772
Polymers48,4772
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-12 kcal/mol
Surface area16310 Å2
MethodPISA
4
D: Vitamin B12-binding protein
J: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5693
Polymers48,4772
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-14 kcal/mol
Surface area16200 Å2
MethodPISA
5
E: Vitamin B12-binding protein
K: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5693
Polymers48,4772
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2480 Å2
ΔGint-13 kcal/mol
Surface area16260 Å2
MethodPISA
6
F: Vitamin B12-binding protein
L: Nanobody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5693
Polymers48,4772
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2610 Å2
ΔGint-12 kcal/mol
Surface area16200 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)83.800, 141.000, 216.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Vitamin B12-binding protein


Mass: 31511.924 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: OmpA-BtuF-3C-His6 / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: btuF, yadT, b0158, JW0154 / Production host: Escherichia coli (E. coli) / References: UniProt: P37028
#2: Antibody
Nanobody / Single-domain antibody


Mass: 16964.984 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: SecretionSignal-Nanobody-His6 / Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: PEG4000, Tris-HCl, Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99984 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 30, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99984 Å / Relative weight: 1
ReflectionResolution: 2.653→19.996 Å / Num. obs: 63910 / % possible obs: 85.33 % / Redundancy: 6.8 % / Net I/σ(I): 1.36

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
Cootmodel building
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.653→19.996 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2594 3239 5.07 %
Rwork0.2232 --
obs0.2251 63910 85.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.653→19.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17058 0 30 264 17352
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317479
X-RAY DIFFRACTIONf_angle_d0.55823797
X-RAY DIFFRACTIONf_dihedral_angle_d12.98710594
X-RAY DIFFRACTIONf_chiral_restr0.0432622
X-RAY DIFFRACTIONf_plane_restr0.0043126
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6533-2.69280.505480.382174X-RAY DIFFRACTION6
2.6928-2.73480.3261290.3829508X-RAY DIFFRACTION17
2.7348-2.77950.4048480.3627927X-RAY DIFFRACTION30
2.7795-2.82730.33871010.34821534X-RAY DIFFRACTION51
2.8273-2.87860.42761280.3412176X-RAY DIFFRACTION71
2.8786-2.93380.35481330.34012632X-RAY DIFFRACTION87
2.9338-2.99350.35131520.33233030X-RAY DIFFRACTION98
2.9935-3.05830.33561720.33523026X-RAY DIFFRACTION100
3.0583-3.12920.34531750.32173059X-RAY DIFFRACTION100
3.1292-3.20710.34211420.29953085X-RAY DIFFRACTION100
3.2071-3.29350.29491500.29953066X-RAY DIFFRACTION100
3.2935-3.390.34511460.29023101X-RAY DIFFRACTION100
3.39-3.49880.29581500.26633115X-RAY DIFFRACTION100
3.4988-3.62320.28591580.24523076X-RAY DIFFRACTION100
3.6232-3.76730.30851740.24453051X-RAY DIFFRACTION100
3.7673-3.93750.28581800.2173074X-RAY DIFFRACTION100
3.9375-4.14340.22841610.19173097X-RAY DIFFRACTION100
4.1434-4.40040.2121670.17273124X-RAY DIFFRACTION100
4.4004-4.7360.21751660.16313091X-RAY DIFFRACTION100
4.736-5.20490.20151750.16213118X-RAY DIFFRACTION100
5.2049-5.94080.21131700.17223146X-RAY DIFFRACTION100
5.9408-7.42060.21371630.18223190X-RAY DIFFRACTION100
7.4206-19.99690.16981910.15043271X-RAY DIFFRACTION100
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)
10.17080.08530.07570.14710.00040.24540.0865-0.06530.03450.16990.09020.2041-0.0247-0.10830.07220.43550.00530.08990.3995-0.02020.52184.9604153.38236.6091
20.107-0.1471-0.03770.1897-0.02420.0560.08350.0350.11660.1325-0.0554-0.08910.0285-0.054400.3814-0.055-0.0340.4025-0.04940.514231.5942149.78255.6018
30.65380.11490.02210.27960.11270.5772-0.36030.13520.2691-0.19530.13960.2694-0.37220.0086-0.41690.6229-0.0854-0.15660.44890.02970.45512.0563122.2943-29.013
40.12080.02840.04130.7057-0.11140.0564-0.05490.2092-0.2876-0.01080.33910.04540.12650.440.47940.31830.1657-0.01180.6449-0.18680.39911.90197.2695-27.5641
50.1713-0.08670.07730.23030.22240.2020.1489-0.15220.09180.1574-0.01530.20370.0062-0.05640.26760.5495-0.03050.19090.486-0.13550.51354.9192157.375728.3533
60.03590.02770.00770.12120.10120.07830.1510.1570.55110.02940.1346-0.1939-0.29220.11910.0230.7671-0.25990.3530.8188-0.10610.943816.2098181.824526.5416
70.16250.07220.22040.1579-0.03340.25030.0007-0.14550.25620.0161-0.12750.2706-0.1105-0.0711-0.18360.36760.0103-0.06350.4194-0.11510.50753.5659125.9294-7.2848
80.12490.1520.07860.2210.04390.0756-0.075-0.02090.1508-0.11960.0603-0.0424-0.14610.0437-0.00070.2941-0.04030.03720.3676-0.06080.420330.4807127.8683-7.731
90.12840.26710.13240.50150.21190.3321-0.0520.096-0.20580.1720.1824-0.01160.2841-0.11540.2420.3834-0.04740.09340.48280.05320.31621.0245101.499943.9537
100.2373-0.12180.02390.2622-0.14780.1497-0.2302-0.24880.05130.49930.2994-0.1043-0.17560.08370.12230.63190.0294-0.06590.4191-0.12020.374635.3883124.423942.2568
110.44020.3465-0.1230.51810.28680.38930.2160.29940.05530.30920.0087-0.06160.2315-0.12310.08470.7213-0.07840.11090.41680.02060.415118.3527102.289665.7283
120.00610.00930.02820.03750.03970.0821-0.45880.06920.2084-0.2940.0720.5410.1755-0.1697-0.15670.85860.0905-0.01140.56020.24550.94290.0944122.088165.1581
130.2391-0.1479-0.06150.1048-0.00270.05080.2941-0.02050.17340.4209-0.3484-0.4244-0.08610.1503-0.00740.824-0.2305-0.10380.9643-0.33290.902731.75160.545741.9097
140.10550.1370.01560.2177-0.10790.1301-0.11890.04430.0748-0.17510.2037-0.16670.0074-0.12290.08480.5429-0.09390.06250.28640.00390.4419.7757172.9447-10.9603
150.419-0.2024-0.51110.14530.13080.6675-0.31760.52490.05520.0189-0.2754-0.065-0.06480.7385-1.09110.3069-0.52190.37682.0021-0.0655-0.0727.7344118.0333-43.8302
160.0899-0.018-0.03280.26830.31870.38480.1422-0.0556-0.2093-0.0730.0095-0.06130.0327-0.01850.23160.2471-0.0323-0.05350.4121-0.01220.389918.0617105.27688.9181
170.0675-0.1175-0.04110.33130.11240.0319-0.1497-0.1916-0.15560.33990.28710.2818-0.0755-0.38030.16090.38860.08490.12010.67590.14810.44038.38123.389627.8456
180.04850.09520.10280.08940.08260.1191-0.0643-0.00580.1127-0.20360.13520.0883-0.0550.10460.10540.8211-0.2830.19840.4981-0.1680.644426.4387127.561479.6433
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 149 )
2X-RAY DIFFRACTION2chain 'A' and (resid 150 through 266 )
3X-RAY DIFFRACTION3chain 'B' and (resid 22 through 149 )
4X-RAY DIFFRACTION4chain 'B' and (resid 150 through 266 )
5X-RAY DIFFRACTION5chain 'C' and (resid 22 through 149 )
6X-RAY DIFFRACTION6chain 'C' and (resid 150 through 266 )
7X-RAY DIFFRACTION7chain 'D' and (resid 22 through 149 )
8X-RAY DIFFRACTION8chain 'D' and (resid 150 through 266 )
9X-RAY DIFFRACTION9chain 'E' and (resid 22 through 149 )
10X-RAY DIFFRACTION10chain 'E' and (resid 150 through 266 )
11X-RAY DIFFRACTION11chain 'F' and (resid 22 through 149 )
12X-RAY DIFFRACTION12chain 'F' and (resid 150 through 266 )
13X-RAY DIFFRACTION13chain 'G' and (resid 24 through 149 )
14X-RAY DIFFRACTION14chain 'H' and (resid 24 through 149 )
15X-RAY DIFFRACTION15chain 'I' and (resid 24 through 149 )
16X-RAY DIFFRACTION16chain 'J' and (resid 24 through 149 )
17X-RAY DIFFRACTION17chain 'K' and (resid 24 through 149 )
18X-RAY DIFFRACTION18chain 'L' and (resid 24 through 149 )

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