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- PDB-4zir: Crystal structure of EcfAA' heterodimer bound to AMPPNP -

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Basic information

Entry
Database: PDB / ID: 4zir
TitleCrystal structure of EcfAA' heterodimer bound to AMPPNP
Components(Energy-coupling factor transporter ATP-binding protein ...) x 2
KeywordsTRANSPORT PROTEIN / HYDROLASE/INHIBITOR / ATPase / transmembrane transport / vitamin uptake / ABC transporter / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


Translocases / riboflavin transport / riboflavin transmembrane transporter activity / ATPase-coupled transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
Cobalt import ATP-binding protein cbiO. / ABC transporter, CbiO/EcfA subunit / 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 ...Cobalt import ATP-binding protein cbiO. / ABC transporter, CbiO/EcfA subunit / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Energy-coupling factor transporter ATP-binding protein EcfA2 / Energy-coupling factor transporter ATP-binding protein EcfA1
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsKarpowich, N.K. / Cocco, N. / Song, J.M. / Wang, D.N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL091618 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: ATP binding drives substrate capture in an ECF transporter by a release-and-catch mechanism.
Authors: Karpowich, N.K. / Song, J.M. / Cocco, N. / Wang, D.N.
History
DepositionApr 28, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 17, 2015Group: Database references
Revision 1.2Jun 24, 2015Group: Database references
Revision 1.3Jul 22, 2015Group: Database references
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3609
Polymers60,1932
Non-polymers1,1677
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-70 kcal/mol
Surface area21520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.275, 107.275, 96.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

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Energy-coupling factor transporter ATP-binding protein ... , 2 types, 2 molecules AB

#1: Protein Energy-coupling factor transporter ATP-binding protein EcfA2 / ECF transporter A component EcfA2 / TmEcfA


Mass: 30333.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: ecfA2, ecfA, ecfA', TM_0222 / Plasmid: pACYC-Duet / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9WY65, 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 / TmEcfA'


Mass: 29859.945 Da / Num. of mol.: 1 / Mutation: K2R, T4E, E53A, E55A, E125A, K126A, E127A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099) (bacteria)
Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099 / Gene: ecfA1, cbiO, ecfA', TM_1663 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9X1Z1, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to catalyse transmembrane movement of substances

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Non-polymers , 4 types, 27 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 100 mM Tris, pH 8.5, 50% MPD, 200 mM monoammonium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 8, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→25.3 Å / Num. obs: 10892 / % possible obs: 93 % / Redundancy: 23.8 % / Rsym value: 0.084 / Net I/σ(I): 33.1
Reflection shellResolution: 3.14→3.2 Å / Redundancy: 23.6 % / Mean I/σ(I) obs: 2.67 / Rsym value: 0.82 / % possible all: 80

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4HLU

4hlu


Resolution: 3→25.285 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 2.62 / Phase error: 24.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2465 1085 9.96 %
Rwork0.1925 --
obs0.1979 10892 92.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→25.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4015 0 67 20 4102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064161
X-RAY DIFFRACTIONf_angle_d1.0835629
X-RAY DIFFRACTIONf_dihedral_angle_d16.6851548
X-RAY DIFFRACTIONf_chiral_restr0.039637
X-RAY DIFFRACTIONf_plane_restr0.004714
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0005-3.13680.2961140.22951021X-RAY DIFFRACTION80
3.1368-3.30180.30141270.24261078X-RAY DIFFRACTION84
3.3018-3.50820.31031260.22141164X-RAY DIFFRACTION90
3.5082-3.77820.27321310.19311229X-RAY DIFFRACTION94
3.7782-4.1570.23731420.18531281X-RAY DIFFRACTION97
4.157-4.7550.24081420.16611306X-RAY DIFFRACTION98
4.755-5.97770.25731450.21081319X-RAY DIFFRACTION98
5.9777-25.28580.21221580.18041409X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 26.3719 Å / Origin y: 14.022 Å / Origin z: 19.1817 Å
111213212223313233
T0.3997 Å2-0.0073 Å20.0371 Å2-0.4038 Å2-0.081 Å2--0.3865 Å2
L1.4044 °20.1553 °20.2695 °2-2.0191 °2-0.7888 °2--1.9156 °2
S0.1308 Å °-0.0437 Å °-0.1517 Å °0.2866 Å °-0.1086 Å °0.0737 Å °-0.0099 Å °-0.236 Å °0.5793 Å °
Refinement TLS groupSelection details: all

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