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- PDB-4hzu: Structure of a bacterial energy-coupling factor transporter -

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Basic information

Entry
Database: PDB / ID: 4hzu
TitleStructure of a bacterial energy-coupling factor transporter
Components
  • Energy-coupling factor transporter ATP-binding protein EcfA 1
  • Energy-coupling factor transporter ATP-binding protein EcfA 2
  • Energy-coupling factor transporter transmembrane protein EcfT
  • Predicted membrane protein
KeywordsHYDROLASE / TRANSPORT PROTEIN / membrane protein / ECF / transporter
Function / homology
Function and homology information


Translocases / ATPase-coupled transmembrane transporter activity / transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / membrane / plasma membrane
Similarity search - Function
ECF transporter, substrate-specific component-like / ECF-type riboflavin transporter, S component / : / ECF transporter transmembrane protein EcfT / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / Cobalt import ATP-binding protein cbiO. ...ECF transporter, substrate-specific component-like / ECF-type riboflavin transporter, S component / : / ECF transporter transmembrane protein EcfT / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / Cobalt import ATP-binding protein cbiO. / : / ABC transporter, CbiO/EcfA subunit / Arp2/3 complex 21 kDa subunit ARPC3 / 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Predicted membrane protein / Energy-coupling factor transporter ATP-binding protein EcfA1 / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter transmembrane protein EcfT
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.53 Å
AuthorsWang, T.L. / Fu, G.B. / Pan, X.J. / Shi, Y.G.
CitationJournal: Nature / Year: 2013
Title: Structure of a bacterial energy-coupling factor transporter.
Authors: Wang, T. / Fu, G. / Pan, X. / Wu, J. / Gong, X. / Wang, J. / Shi, Y.
History
DepositionNov 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Energy-coupling factor transporter ATP-binding protein EcfA 1
A: Energy-coupling factor transporter ATP-binding protein EcfA 2
T: Energy-coupling factor transporter transmembrane protein EcfT
S: Predicted membrane protein


Theoretical massNumber of molelcules
Total (without water)110,4574
Polymers110,4574
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12450 Å2
ΔGint-104 kcal/mol
Surface area41000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.971, 148.690, 154.574
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 Energy-coupling factor transporter ATP-binding protein EcfA 1 / ECF transporter A component EcfA 1


Mass: 32176.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: ecfA1, cbiO1, LVIS_1661 / Production host: Escherichia coli (E. coli)
References: UniProt: Q03PY6, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#2: Protein Energy-coupling factor transporter ATP-binding protein EcfA 2 / ECF transporter A component EcfA 2


Mass: 30550.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: ecfA2, cbiO2, LVIS_1662 / Production host: Escherichia coli (E. coli)
References: UniProt: Q03PY5, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances
#3: Protein Energy-coupling factor transporter transmembrane protein EcfT / ECF transporter T component EcfT


Mass: 30321.086 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: ecfT, LVIS_1660 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03PY7
#4: Protein Predicted membrane protein


Mass: 17409.064 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: LVIS_2151 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03NM0

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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: 4.16 Å3/Da / Density % sol: 70.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.2
Details: 17% (w/v) polyethylene glycol 2000, 16% (v/v) glycerol, 100 mM Tris buffer (pH 8.2), and 100 mM magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97947 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2012
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 3.53→48.685 Å / Num. obs: 22601 / % possible obs: 96.9 % / Redundancy: 3.4 % / Biso Wilson estimate: 124.93 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 13.9
Reflection shellResolution: 3.53→3.66 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.888 / Mean I/σ(I) obs: 1.4 / % possible all: 97.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 3.53→48.685 Å / SU ML: 0.48 / σ(F): 1.35 / Phase error: 32.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2917 1157 5.12 %
Rwork0.2408 --
obs0.2432 22577 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.53→48.685 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7437 0 0 0 7437
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037587
X-RAY DIFFRACTIONf_angle_d0.82310309
X-RAY DIFFRACTIONf_dihedral_angle_d19.0464655
X-RAY DIFFRACTIONf_chiral_restr0.0571217
X-RAY DIFFRACTIONf_plane_restr0.0041306
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5295-3.69010.33881360.27922593X-RAY DIFFRACTION96
3.6901-3.88460.31351250.26172675X-RAY DIFFRACTION98
3.8846-4.12790.32491530.23572638X-RAY DIFFRACTION97
4.1279-4.44640.26471450.20232662X-RAY DIFFRACTION97
4.4464-4.89340.25431670.18612631X-RAY DIFFRACTION98
4.8934-5.60060.27921510.21272729X-RAY DIFFRACTION98
5.6006-7.05280.28711520.30982733X-RAY DIFFRACTION98
7.0528-48.68910.30371280.2442759X-RAY DIFFRACTION94
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)
12.05710.34760.15592.6753-1.4492.94470.2995-0.922-0.03910.5541-0.4696-0.5593-0.07480.35030.15140.9154-0.2385-0.20281.39310.01911.062441.923839.903525.1147
23.66421.8155-1.38066.5902-1.62332.43530.1193-0.03050.27710.1516-0.1040.00740.04150.0432-0.02790.62370.0806-0.00270.94710.00860.725116.427836.73610.4447
33.74912.3595-3.3315.7888-1.44762.75190.501-0.8645-1.04110.7905-0.7476-0.11570.40830.89530.20820.96410.0711-0.12920.86580.27420.972218.44916.513737.9675
41.23471.4157-0.41283.304-0.6941.52420.2208-0.8362-0.11480.7558-0.12650.4852-0.21470.5431-0.13441.0305-0.02090.00961.39630.3270.919611.272516.597249.3733
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain S
4X-RAY DIFFRACTION4chain T

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