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- PDB-4dbl: Crystal structure of E159Q mutant of BtuCDF -

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Basic information

Entry
Database: PDB / ID: 4dbl
TitleCrystal structure of E159Q mutant of BtuCDF
Components
  • Vitamin B12 import ATP-binding protein BtuD
  • Vitamin B12 import system permease protein BtuC
  • Vitamin B12-binding protein
KeywordsTRANSPORT PROTEIN / ABC transporter for vitamin B12 / ATP binding / inner membrane
Function / homology
Function and homology information


ABC-type vitamin B12 transporter / BtuCD complex / cobalamin transport complex / ABC-type vitamin B12 transporter activity / cobalamin transport / cobalamin binding / extrinsic component of membrane / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex ...ABC-type vitamin B12 transporter / BtuCD complex / cobalamin transport complex / ABC-type vitamin B12 transporter activity / cobalamin transport / cobalamin binding / extrinsic component of membrane / transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / outer membrane-bounded periplasmic space / periplasmic space / ATP hydrolysis activity / ATP binding / membrane / identical protein binding / plasma membrane
Similarity search - Function
ABC transporter, vitamin B12 import, permease protein BtuC / ABC transporter, vitamin B12, BtuD / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter, vitamin B12-binding protein / ABC transporter, BtuC-like / ABC transporter periplasmic binding domain / Periplasmic binding protein ...ABC transporter, vitamin B12 import, permease protein BtuC / ABC transporter, vitamin B12, BtuD / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter involved in vitamin B12 uptake, BtuC / ABC transporter, permease protein, BtuC-like / FecCD transport family / ABC transporter, vitamin B12-binding protein / ABC transporter, BtuC-like / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Vitamin B12 import system permease protein BtuC / Vitamin B12 import ATP-binding protein BtuD / Vitamin B12-binding protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.493 Å
AuthorsKorkhov, V.M. / Mireku, S.M. / Hvorup, R.N. / Locher, K.P.
CitationJournal: Febs Lett. / Year: 2012
Title: Asymmetric states of vitamin B12 transporter BtuCD are not discriminated by its cognate substrate binding protein BtuF.
Authors: Korkhov, V.M. / Mireku, S.A. / Hvorup, R.N. / Locher, K.P.
History
DepositionJan 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 7, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Vitamin B12 import system permease protein BtuC
B: Vitamin B12 import system permease protein BtuC
C: Vitamin B12 import ATP-binding protein BtuD
D: Vitamin B12 import ATP-binding protein BtuD
E: Vitamin B12-binding protein
F: Vitamin B12 import system permease protein BtuC
G: Vitamin B12 import system permease protein BtuC
H: Vitamin B12 import ATP-binding protein BtuD
I: Vitamin B12 import ATP-binding protein BtuD
J: Vitamin B12-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)317,00026
Polymers315,46710
Non-polymers1,53316
Water0
1
A: Vitamin B12 import system permease protein BtuC
B: Vitamin B12 import system permease protein BtuC
C: Vitamin B12 import ATP-binding protein BtuD
D: Vitamin B12 import ATP-binding protein BtuD
E: Vitamin B12-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,50013
Polymers157,7345
Non-polymers7668
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: Vitamin B12 import system permease protein BtuC
G: Vitamin B12 import system permease protein BtuC
H: Vitamin B12 import ATP-binding protein BtuD
I: Vitamin B12 import ATP-binding protein BtuD
J: Vitamin B12-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)158,50013
Polymers157,7345
Non-polymers7668
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)133.650, 166.930, 132.820
Angle α, β, γ (deg.)90.00, 119.76, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
33
43
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A'
211chain 'F'
112chain 'B'
212chain 'G'
113chain 'D'
213chain 'C'
313chain 'H'
413chain 'I'
114chain 'E'
214chain 'J'

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Vitamin B12 import system permease protein BtuC


Mass: 37650.617 Da / Num. of mol.: 4 / Mutation: C18S, C32S, C120S, C156S, C205S, C206S, C267S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET-based / Cell line (production host): Bl21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P06609
#2: Protein
Vitamin B12 import ATP-binding protein BtuD / Vitamin B12-transporting ATPase


Mass: 27097.135 Da / Num. of mol.: 4 / Mutation: C180S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET-based / Cell line (production host): Bl21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P06611, EC: 3.6.3.33
#3: Protein Vitamin B12-binding protein


Mass: 28238.096 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pET-based / Cell line (production host): Bl21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: P37028
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4

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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: 4.08 Å3/Da / Density % sol: 69.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4
Details: 0.1M sodium citrate, pH 5.4, 0.3-0.4M ammonium sulphate, 30-35% PEG-400, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 12, 2010
RadiationMonochromator: Si 111 MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→30 Å / Num. all: 63780 / Num. obs: 59380 / % possible obs: 93.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 3.5→3.58 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.957 / Num. unique all: 3463 / Rsym value: 0.719 / % possible all: 88.2

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Processing

Software
NameVersionClassification
DENZOdata reduction
PHENIX(phenix.refine: 1.7.2_869)model building
PHENIX(phenix.refine: 1.7.2_869)refinement
SCALEPACKdata scaling
PHENIX1.7.2_869phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.493→30.015 Å / SU ML: 1.21 / σ(F): 1.34 / Phase error: 24.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2513 2014 3.4 %RANDOM
Rwork0.214 ---
obs0.2153 59310 92.53 %-
all-59380 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.176 Å2 / ksol: 0.281 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.7828 Å20 Å21.5121 Å2
2--11.7562 Å2-0 Å2
3---7.8238 Å2
Refinement stepCycle: LAST / Resolution: 3.493→30.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21150 0 80 0 21230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00421658
X-RAY DIFFRACTIONf_angle_d0.78429506
X-RAY DIFFRACTIONf_dihedral_angle_d13.9737788
X-RAY DIFFRACTIONf_chiral_restr0.053466
X-RAY DIFFRACTIONf_plane_restr0.0033710
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2441X-RAY DIFFRACTIONPOSITIONAL
12F2441X-RAY DIFFRACTIONPOSITIONAL0.029
21B2441X-RAY DIFFRACTIONPOSITIONAL
22G2441X-RAY DIFFRACTIONPOSITIONAL0.004
31D1893X-RAY DIFFRACTIONPOSITIONAL
32C1893X-RAY DIFFRACTIONPOSITIONAL0.041
33H1893X-RAY DIFFRACTIONPOSITIONAL0.041
34I1893X-RAY DIFFRACTIONPOSITIONAL0.005
41E1908X-RAY DIFFRACTIONPOSITIONAL
42J1908X-RAY DIFFRACTIONPOSITIONAL0.003
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4927-3.61740.37311800.31335201X-RAY DIFFRACTION84
3.6174-3.76190.31921960.2555832X-RAY DIFFRACTION95
3.7619-3.93280.27412090.22755823X-RAY DIFFRACTION94
3.9328-4.13960.2712010.20555857X-RAY DIFFRACTION95
4.1396-4.39820.20952100.19455800X-RAY DIFFRACTION94
4.3982-4.73660.21252110.17625810X-RAY DIFFRACTION94
4.7366-5.21110.22641930.18895809X-RAY DIFFRACTION93
5.2111-5.960.29582080.24445752X-RAY DIFFRACTION93
5.96-7.48960.27622070.25765752X-RAY DIFFRACTION92
7.4896-30.01660.20461990.18125660X-RAY DIFFRACTION90
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)
11.42090.05730.22611.46190.07471.5623-0.0030.12170.07450.08310.08340.04340.0786-0.1222-0.02090.3488-0.08980.01340.3619-0.00780.0837-65.6259-46.6967127.1317
21.39970.35210.36521.31820.57271.55350.06330.25540.0999-0.1254-0.0218-0.15940.1401-0.1697-0.0320.2263-0.09560.04520.30840.04180.2618-86.1333-36.9996153.6973
32.1602-0.2761-0.11043.07361.80442.16770.01460.36790.357-0.4599-0.09490.0008-0.46740.05910.02620.3713-0.0402-0.0070.20420.08340.2574-38.4572-17.9497147.0265
43.5833-0.22381.00761.77810.04011.06450.076-0.1116-0.00950.0689-0.1187-0.2240.0481-0.063500.1844-0.0069-0.02720.0408-0.01030.2838-48.5268-25.7523173.6454
50.829-0.0248-0.57240.87971.07841.2433-0.07890.4766-0.2854-0.2306-0.33770.2690.323-0.8229-0.11490.5829-0.2783-0.06461.2224-0.25450.5502-103.6147-58.3084123.5716
61.60120.0980.27451.2930.15281.3106-0.0153-0.09710.00920.10740.1010.03580.02930.1884-0.03070.1806-0.03810.12040.3498-0.05460.2837-109.1927-36.3567178.7471
71.9390.51370.33651.005-0.23541.39530.09940.03650.0718-0.1386-0.01730.01320.05310.2895-0.06330.3019-0.01630.00910.3021-0.12740.17-121.7167-46.0677209.8462
81.57741.2605-0.05213.3301-1.06342.0983-0.02010.2208-0.438-0.3131-0.0636-0.33730.29890.2431-0.02490.27540.0540.06360.2176-0.07470.3733-140.0885-65.0996165.3384
92.35490.10571.64161.5448-0.24212.13160.0714-0.13660.054-0.1532-0.15360.2264-0.0206-0.0682-0.00370.2512-0.0189-0.05150.02330.03020.2424-157.9993-57.3052187.4956
100.31040.7475-0.7650.6322-1.04181.60410.3271-0.5260.26250.0963-0.2988-0.2442-0.39210.7722-0.05770.5498-0.35410.04161.2666-0.13850.6882-86.8776-24.7647209.6769
110.7055-0.4473-0.06660.0592-0.11170.4480.0201-0.17650.02220.0072-0.03860.0391-0.01840.0131-0.00950.5030.095-0.02690.0086-0.16340.113-96.3497-41.5196168.3909
120.8618-0.07990.1085-0.09720.19480.22940.2774-0.4148-0.26750.0778-0.3499-0.034-0.0028-0.00650.00011.92160.0278-0.13971.6382-0.11931.4514-96.2263-41.5533168.117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:324 )A1 - 324
2X-RAY DIFFRACTION2( CHAIN B AND RESID 1:324 )B1 - 324
3X-RAY DIFFRACTION3( CHAIN C AND RESID 2:249 )C2 - 249
4X-RAY DIFFRACTION4( CHAIN D AND RESID 2:249 )D2 - 249
5X-RAY DIFFRACTION5( CHAIN E AND RESID 22:266 )E22 - 266
6X-RAY DIFFRACTION6( CHAIN F AND RESID 1:324 )F1 - 324
7X-RAY DIFFRACTION7( CHAIN G AND RESID 1:324 )G1 - 324
8X-RAY DIFFRACTION8( CHAIN H AND RESID 2:249 )H2 - 249
9X-RAY DIFFRACTION9( CHAIN I AND RESID 2:249 )I2 - 249
10X-RAY DIFFRACTION10( CHAIN J AND RESID 22:266 )J22 - 266
11X-RAY DIFFRACTION11( CHAIN I AND RESID 301:301 ) OR ( CHAIN H AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 )I301
12X-RAY DIFFRACTION11( CHAIN I AND RESID 301:301 ) OR ( CHAIN H AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 )H301
13X-RAY DIFFRACTION11( CHAIN I AND RESID 301:301 ) OR ( CHAIN H AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 )C301
14X-RAY DIFFRACTION11( CHAIN I AND RESID 301:301 ) OR ( CHAIN H AND RESID 301:301 ) OR ( CHAIN C AND RESID 301:301 ) OR ( CHAIN D AND RESID 301:301 )D301
15X-RAY DIFFRACTION12( CHAIN I AND RESID 302:304 ) OR ( CHAIN H AND RESID 302:304 ) OR ( CHAIN C AND RESID 302:304 ) OR ( CHAIN D AND RESID 302:304 )I302 - 304
16X-RAY DIFFRACTION12( CHAIN I AND RESID 302:304 ) OR ( CHAIN H AND RESID 302:304 ) OR ( CHAIN C AND RESID 302:304 ) OR ( CHAIN D AND RESID 302:304 )H302 - 304
17X-RAY DIFFRACTION12( CHAIN I AND RESID 302:304 ) OR ( CHAIN H AND RESID 302:304 ) OR ( CHAIN C AND RESID 302:304 ) OR ( CHAIN D AND RESID 302:304 )C302 - 304
18X-RAY DIFFRACTION12( CHAIN I AND RESID 302:304 ) OR ( CHAIN H AND RESID 302:304 ) OR ( CHAIN C AND RESID 302:304 ) OR ( CHAIN D AND RESID 302:304 )D302 - 304

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