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- PDB-4rfs: Structure of a pantothenate energy coupling factor transporter -

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Basic information

Entry
Database: PDB / ID: 4rfs
TitleStructure of a pantothenate energy coupling factor transporter
Components
  • Energy-coupling factor transporter ATP-binding protein EcfA1
  • Energy-coupling factor transporter ATP-binding protein EcfA2
  • Energy-coupling factor transporter transmembrane protein EcfT
  • Substrate binding pritein S
KeywordsHYDROLASE / TRANSPORT PROTEIN / Transporter / ECF
Function / homology
Function and homology information


Translocases / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances / transmembrane transporter activity / membrane => GO:0016020 / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
ECF transporter, substrate-specific component / ECF transporter transmembrane protein EcfT / ECF transporter, substrate-specific component / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / Cobalt import ATP-binding protein cbiO. / ABC transporter, CbiO/EcfA subunit ...ECF transporter, substrate-specific component / ECF transporter transmembrane protein EcfT / ECF transporter, substrate-specific component / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1 / ABC/ECF transporter, transmembrane component / Cobalt transport protein / Arp2/3 complex 21 kDa subunit ARPC3 - #20 / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Energy-coupling factor transporter ATP-binding protein EcfA1 / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter transmembrane protein EcfT / Predicted membrane protein
Similarity search - Component
Biological speciesLactobacillus brevis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.232 Å
AuthorsZhang, M. / Bao, Z. / Zhao, Q. / Guo, H. / Xu, K. / Zhang, P.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of a pantothenate transporter and implications for ECF module sharing and energy coupling of group II ECF transporters.
Authors: Zhang, M. / Bao, Z. / Zhao, Q. / Guo, H. / Xu, K. / Wang, C. / Zhang, P.
History
DepositionSep 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 28, 2015Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Energy-coupling factor transporter ATP-binding protein EcfA2
B: Energy-coupling factor transporter ATP-binding protein EcfA1
S: Substrate binding pritein S
T: Energy-coupling factor transporter transmembrane protein EcfT


Theoretical massNumber of molelcules
Total (without water)116,8764
Polymers116,8764
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12320 Å2
ΔGint-96 kcal/mol
Surface area41980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.726, 145.240, 157.141
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 EcfA2 / ECF transporter A component EcfA2


Mass: 32176.533 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: ecfA2 / 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 EcfA1 / ECF transporter A component EcfA1


Mass: 30550.432 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: ecfA1 / 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 Substrate binding pritein S


Mass: 22209.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: LVIS_0658 / Production host: Escherichia coli (E. coli) / References: UniProt: Q03SM0
#4: Protein Energy-coupling factor transporter transmembrane protein EcfT / ECF transporter T component EcfT


Mass: 31939.779 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus brevis (bacteria) / Gene: ecfT / Production host: Escherichia coli (E. coli) / References: UniProt: Q03PY7

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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: 3.81 Å3/Da / Density % sol: 67.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 8.4
Details: 0.1 M Tris, 20% PEG2000, 15% glycerol, 0.2M MgCl2, pH 8.4, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97913 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 3.25→37.5 Å / Num. obs: 28312 / % possible obs: 97.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 21.4
Reflection shellResolution: 3.25→3.37 Å / % possible obs: 97.6 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.884 / Mean I/σ(I) obs: 1.9 / % possible all: 97.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.232→37.5 Å / SU ML: 1.24 / σ(F): 1.34 / Phase error: 30.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2889 1418 5.01 %
Rwork0.2261 --
obs0.2291 28312 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.77 Å2 / ksol: 0.29 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-30.8835 Å20 Å20 Å2
2--51.3715 Å20 Å2
3---34.2712 Å2
Refinement stepCycle: LAST / Resolution: 3.232→37.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7601 0 0 0 7601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017788
X-RAY DIFFRACTIONf_angle_d1.47610588
X-RAY DIFFRACTIONf_dihedral_angle_d19.1882825
X-RAY DIFFRACTIONf_chiral_restr0.0891246
X-RAY DIFFRACTIONf_plane_restr0.0071351
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2322-3.34770.40131180.28742500X-RAY DIFFRACTION92
3.3477-3.48160.36331400.26572634X-RAY DIFFRACTION97
3.4816-3.63990.33971440.23332649X-RAY DIFFRACTION97
3.6399-3.83170.33141300.20682679X-RAY DIFFRACTION97
3.8317-4.07150.25241300.18752692X-RAY DIFFRACTION97
4.0715-4.38540.27711430.1692679X-RAY DIFFRACTION98
4.3854-4.82590.22851480.17092728X-RAY DIFFRACTION99
4.8259-5.52230.2781500.22492776X-RAY DIFFRACTION100
5.5223-6.95030.32191450.26842800X-RAY DIFFRACTION100
6.9503-37.54480.28361700.25042757X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 15.838 Å / Origin y: 170.9193 Å / Origin z: 186.2089 Å
111213212223313233
T0.3387 Å20.0595 Å2-0.0051 Å2-0.5111 Å20.0552 Å2--0.6183 Å2
L1.2559 °20.3254 °2-0.5405 °2-1.0551 °2-0.7975 °2--1.5439 °2
S0.1445 Å °-0.4246 Å °-0.0342 Å °0.1325 Å °-0.1034 Å °-0.0519 Å °0.0139 Å °0.4001 Å °-0.0481 Å °
Refinement TLS groupSelection details: all

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