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- PDB-5b57: Inward-facing conformation of ABC heme importer BhuUV from Burkho... -

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Basic information

Entry
Database: PDB / ID: 5b57
TitleInward-facing conformation of ABC heme importer BhuUV from Burkholderia cenocepacia
Components
  • Hemin import ATP-binding protein HmuV
  • Putative hemin ABC transport system, membrane protein
KeywordsMETAL TRANSPORT / metal-binding / membrane protein
Function / homology
Function and homology information


transmembrane transporter activity / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
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, BtuC-like / 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. ...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, BtuC-like / 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
Hemin ABC transport system, membrane protein / Hemin ABC transporter ATP-binding protein
Similarity search - Component
Biological speciesBurkholderia cenocepacia J2315 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
Model detailsBacterial heme transporter BhuUV
AuthorsNaoe, Y. / Nakamura, N. / Doi, A. / Shiro, Y. / Sugimoto, H.
Funding support Japan, 4items
OrganizationGrant numberCountry
JSPS23121531 Japan
JSPS24687015 Japan
JSPS25121739 Japan
JSPS15H01655 Japan
CitationJournal: Nat Commun / Year: 2016
Title: Crystal structure of bacterial haem importer complex in the inward-facing conformation
Authors: Naoe, Y. / Nakamura, N. / Doi, A. / Sawabe, M. / Nakamura, H. / Shiro, Y. / Sugimoto, H.
History
DepositionApr 25, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative hemin ABC transport system, membrane protein
B: Putative hemin ABC transport system, membrane protein
C: Hemin import ATP-binding protein HmuV
D: Hemin import ATP-binding protein HmuV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,2258
Polymers136,0684
Non-polymers1,1574
Water39622
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11770 Å2
ΔGint-113 kcal/mol
Surface area47030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.824, 118.283, 142.747
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative hemin ABC transport system, membrane protein / heme importer transmembrane subunit BhuU


Mass: 38801.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia J2315 (bacteria)
Strain: J2315 / Gene: hmuU, BCAM2629 / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): c41(DE3) / References: UniProt: B4EKB4
#2: Protein Hemin import ATP-binding protein HmuV / heme importer ATP-binding subunit BhuV


Mass: 29232.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia J2315 (bacteria)
Strain: J2315 / Gene: hmuV, BCAM2630 / Plasmid: pET-19b / Production host: Escherichia coli (E. coli) / Strain (production host): c41(DE3)
References: UniProt: B4EKB5, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#3: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.44 Å3/Da / Density % sol: 64.22 % / Mosaicity: 0.323 °
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 9.5 / Details: 30% PEG 400, 0.1M CAPSO, 0.1M NaCl, 0.1M Li2SO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 21, 2014 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 46529 / % possible obs: 99.1 % / Redundancy: 7.6 % / Biso Wilson estimate: 40.52 Å2 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.041 / Rrim(I) all: 0.117 / Χ2: 0.943 / Net I/av σ(I): 16.5 / Net I/σ(I): 7 / Num. measured all: 355680
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.8-2.855.90.87821430.7320.3540.9510.81992.5
2.85-2.96.40.76421940.8010.3060.8260.84695.3
2.9-2.966.70.75222550.8430.2980.8110.85697.5
2.96-3.0270.73722830.8160.290.7940.85898.9
3.02-3.087.30.6122910.920.2370.6560.87299
3.08-3.157.50.50323090.9430.1950.540.89999.8
3.15-3.237.60.46923170.9310.1810.5040.885100
3.23-3.327.80.37523450.9670.1430.4010.91100
3.32-3.427.90.30223020.9760.1140.3230.915100
3.42-3.5380.22723250.9870.0860.2430.943100
3.53-3.6580.19223410.9910.0720.2050.918100
3.65-3.880.15623170.9920.0590.1670.926100
3.8-3.9780.12623540.9950.0470.1340.915100
3.97-4.188.10.09323420.9970.0340.0990.868100
4.18-4.448.20.07623520.9980.0280.0810.89100
4.44-4.798.20.07723530.9970.0280.0821.072100
4.79-5.278.10.09123780.9960.0330.0971.487100
5.27-6.038.10.10423830.9950.0380.1111.6100
6.03-7.5980.05824070.9990.0220.0620.886100
7.59-507.60.021253810.0080.0230.35799.5

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155_1692: ???refinement
HKL-2000data scaling
PDB_EXTRACT3.2data extraction
PHASER2.5.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BhuUV-T

Resolution: 2.8→45.539 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 1903 4.99 %Random selection
Rwork0.2123 36226 --
obs0.215 38129 81.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 162.37 Å2 / Biso mean: 43.3546 Å2 / Biso min: 8.73 Å2
Refinement stepCycle: final / Resolution: 2.8→45.539 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8484 0 76 22 8582
Biso mean--71.36 30.47 -
Num. residues----1170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0118776
X-RAY DIFFRACTIONf_angle_d1.2911981
X-RAY DIFFRACTIONf_chiral_restr0.0611482
X-RAY DIFFRACTIONf_plane_restr0.0071520
X-RAY DIFFRACTIONf_dihedral_angle_d14.5165249
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8005-2.87050.3813350.29081036107133
2.8705-2.94810.3156820.26711346142843
2.9481-3.03480.3292940.27521668176254
3.0348-3.13280.31661000.26511986208663
3.1328-3.24470.35421220.26832280240273
3.2447-3.37460.28331280.23692592272082
3.3746-3.52810.28321510.22382873302492
3.5281-3.7140.29341580.21473121327999
3.714-3.94660.26321670.218631913358100
3.9466-4.25110.2491790.19531503329100
4.2511-4.67860.25211680.163831753343100
4.6786-5.35460.2231600.171332243384100
5.3546-6.74280.26231920.227132283420100
6.7428-45.54510.22621670.21093356352399
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)
14.5814-1.3939-2.12941.50393.21867.1054-0.0658-0.27020.01070.3677-0.04280.1614-1.250.4987-0.05870.84270.14910.16460.8922-0.03280.2759-54.400932.2371-25.4261
20.4989-0.16350.34330.0694-0.28070.7218-0.13510.37890.22540.0102-0.10470.1028-0.1668-0.7026-0.02310.04750.1028-0.150.9276-0.1060.2721-50.741129.902-54.9181
35.6895-0.6142-2.56094.9246-1.22841.7749-0.15710.4143-0.1602-0.14020.3364-0.26170.4179-0.5280.06180.3446-0.0996-0.0130.2284-0.0920.3375-29.569316.6367-57.3964
42.45410.12140.17851.63551.15311.7214-0.0281-0.1273-0.71330.69910.2227-0.19511.0340.2653-0.11270.61650.04290.11670.1025-0.1450.6796-25.067910.7356-37.5089
50.92350.72240.10240.64040.14760.0250.09610.1335-0.2028-0.0994-0.2135-0.0868-0.0438-0.1275-0.0350.28140.0346-0.00170.406-0.07740.1578-30.727921.3552-55.5231
65.3429-1.73610.47555.6347-0.5126.6366-0.26340.5166-0.6974-0.0795-0.15570.07560.399-0.45090.39620.2499-0.08440.09280.3835-0.02130.2422-38.57615.8063-27.7015
71.22960.26970.01061.5828-0.27790.8377-0.08380.27050.1852-0.04940.04310.1691-0.1221-0.29950.08570.18470.0908-0.07430.3367-0.06350.1937-41.043931.0195-47.5856
82.5922-0.5380.96693.1559-4.496.4063-0.5051-0.71230.68940.6284-0.25850.6598-1.0493-0.28680.02620.43380.2689-0.08740.6582-0.25820.5331-32.665944.5763-35.2992
95.07366.4899-6.69118.4858-8.70768.9416-0.4390.85780.3305-0.14540.3308-0.08390.5533-0.41420.18210.43360.1119-0.05490.5553-0.12230.37646.655527.2686-24.95
102.3962-0.1416-0.42981.1896-0.25150.468-0.28610.23690.227-0.04570.0058-0.17170.19350.30870.14370.1210.03610.00790.6228-0.04130.31369.926324.9569-53.9045
111.6959-0.2025-1.15890.0568-0.00671.69360.07490.62910.0656-0.00370.0631-0.1185-0.25640.5462-0.17660.1085-0.1280.22060.6271-0.04570.06492.533833.318-53.0849
123.8769-0.60730.04457.8801-3.11222.8401-0.42-0.02480.02020.3581-0.286-0.1859-0.33590.37020.35090.3134-0.0377-0.00340.06480.04560.1912-18.057441.932-55.2961
133.9846-0.1674-0.95884.30250.15082.70020.31890.3640.534-0.1894-0.19080.0895-1.0485-0.1632-0.17730.2551-0.0306-0.0830.03940.08720.4729-16.823748.8345-48.2961
142.02640.03370.46520.64-0.17780.23020.0160.37720.0659-0.2398-0.0394-0.0076-0.35920.2046-0.00120.2205-0.0492-0.03940.32080.01590.1762-14.63939.4585-54.1565
150.6706-0.50830.3871.0411.39386.7305-0.14140.15210.4032-0.13160.03780.0868-0.38550.5629-0.04360.1904-0.0857-0.07530.20420.01720.277-8.40543.6313-33.9777
161.6990.35850.23371.64220.74543.46970.04170.116-0.58490.06010.0081-0.17260.41030.24050.1390.19160.09920.08420.2106-0.00470.2036-5.437924.6102-44.0293
171.14741.2738-1.16952.0369-0.32132.90170.0383-0.00660.71350.13370.1510.4589-0.8331-0.51410.48930.25870.1883-0.08310.1188-0.21150.4646-22.154552.1785-7.3789
182.8344-1.9012-1.11295.32172.64254.04910.09960.09390.3544-0.0545-0.2032-0.0587-0.3040.13780.09770.1752-0.0893-0.03710.24780.03740.1897-6.683845.6858-15.3256
190.09230.2675-0.83630.7727-2.31469.03780.56610.3112-0.2433-0.81580.40221.37570.2201-1.1639-0.85730.63490.3524-0.23061.6827-0.1591.27698.027342.9469-21.6605
205.40761.8811-4.19115.5214-1.74534.8986-0.4236-0.3752-0.39440.17540.2376-0.62490.53710.60210.10330.26160.2412-0.03760.6592-0.31610.32455.893735.8449-9.6371
211.85141.12830.90051.9923-0.0282.1141-0.08860.4289-0.3716-0.00280.1461-0.34851.10960.4779-0.02130.45590.0492-0.00710.21270.00870.1979-4.419331.2916-10.4666
223.2990.2441-0.21981.83530.02231.7719-0.034-0.3113-0.36060.3686-0.09740.11950.07060.0744-0.05460.1626-0.0051-0.15980.2083-0.07960.097-11.16439.2417-0.6223
234.3513-1.0184-1.6882.12990.63811.95710.0626-0.42060.42340.38-0.32820.3686-0.2902-0.6448-0.20130.3815-0.0280.08510.3397-0.22510.3443-23.679345.59356.8167
240.9168-0.33280.04527.5434-0.4883.53220.365-0.64240.50671.02020.2195-0.0724-0.30120.3125-0.08720.27440.03830.11550.671-0.18720.4022-29.43537.715111.1079
252.86870.0524-0.47571.97440.16290.09120.1159-0.4328-0.65810.1429-0.0777-0.31350.3420.02441.02640.8479-0.03310.15990.22330.23950.3644-26.71054.3991-4.4383
263.43550.6055-0.04114.0926-0.31894.30990.1361-0.1216-0.2256-0.0071-0.4858-0.27240.5040.26970.19940.4652-0.0580.04270.13310.07960.3275-26.278111.4231-9.2254
273.3823-0.74230.35371.2508-0.66812.4866-0.39330.1282-0.3951-0.36080.3077-0.31920.799-0.36670.14090.5887-0.18010.09010.24440.04930.2801-36.60618.7611-13.7082
281.89310.3438-0.19344.0101-1.61162.5969-0.08510.04410.38570.51170.23020.9297-0.3648-1.24870.00120.29350.03820.10970.5483-0.05580.3-47.0826.0395-14.6606
292.30440.2173-0.8454.3431.38454.152-0.17520.20140.022-0.10480.04850.17110.1577-0.4961-0.28340.3535-0.08570.16210.32640.11360.2828-37.757920.023-5.8211
300.1953-0.24040.00750.74930.67311.7230.2501-0.12020.11740.2224-0.37360.08910.1523-0.4486-1.08760.3891-0.26930.18790.57120.01320.0771-37.354521.43320.9057
314.7414-0.59771.48722.05810.46342.24780.0787-0.6686-0.58880.5002-0.4254-0.1190.71150.4184-0.20260.6621-0.0417-0.09750.32710.21840.325-22.878815.55526.8976
323.94070.3968-1.21496.92360.96242.9254-0.0821-0.8792-0.1481.38690.31120.79120.3142-0.5453-0.37620.5807-0.0558-0.03820.82530.16130.3939-23.739525.596415.2292
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 24:29)A24 - 29
2X-RAY DIFFRACTION2(chain A and resid 30:112)A30 - 112
3X-RAY DIFFRACTION3(chain A and resid 113:156)A113 - 156
4X-RAY DIFFRACTION4(chain A and resid 157:173)A157 - 173
5X-RAY DIFFRACTION5(chain A and resid 174:237)A174 - 237
6X-RAY DIFFRACTION6(chain A and resid 238:266)A238 - 266
7X-RAY DIFFRACTION7(chain A and resid 267:347)A267 - 347
8X-RAY DIFFRACTION8(chain A and resid 348:359)A348 - 359
9X-RAY DIFFRACTION9(chain B and resid 25:30)B25 - 30
10X-RAY DIFFRACTION10(chain B and resid 31:59)B31 - 59
11X-RAY DIFFRACTION11(chain B and resid 60:112)B60 - 112
12X-RAY DIFFRACTION12(chain B and resid 113:133)B113 - 133
13X-RAY DIFFRACTION13(chain B and resid 140:171)B140 - 171
14X-RAY DIFFRACTION14(chain B and resid 172:237)B172 - 237
15X-RAY DIFFRACTION15(chain B and resid 238:285)B238 - 285
16X-RAY DIFFRACTION16(chain B and resid 286:358)B286 - 358
17X-RAY DIFFRACTION17(chain C and (resid 1:64 or resid 274))C0
18X-RAY DIFFRACTION18(chain C and resid 65:113)C65 - 113
19X-RAY DIFFRACTION19(chain C and resid 114:120)C114 - 120
20X-RAY DIFFRACTION20(chain C and resid 121:131)C121 - 131
21X-RAY DIFFRACTION21(chain C and resid 132:164)C132 - 164
22X-RAY DIFFRACTION22(chain C and resid 165:220)C165 - 220
23X-RAY DIFFRACTION23(chain C and resid 221:246)C221 - 246
24X-RAY DIFFRACTION24(chain C and resid 247:273)C247 - 273
25X-RAY DIFFRACTION25(chain D and resid 1:27)D1 - 27
26X-RAY DIFFRACTION26(chain D and (resid 28:61 or resid 274))D0
27X-RAY DIFFRACTION27(chain D and resid 62:95)D62 - 95
28X-RAY DIFFRACTION28(chain D and resid 96:165)D96 - 165
29X-RAY DIFFRACTION29(chain D and resid 166:189)D166 - 189
30X-RAY DIFFRACTION30(chain D and resid 190:220)D190 - 220
31X-RAY DIFFRACTION31(chain D and resid 221:257)D221 - 257
32X-RAY DIFFRACTION32(chain D and resid 258:273)D258 - 273

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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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