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- PDB-3fvq: Crystal structure of the nucleotide binding domain FbpC complexed... -

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Basic information

Entry
Database: PDB / ID: 3fvq
TitleCrystal structure of the nucleotide binding domain FbpC complexed with ATP
ComponentsFe(3+) ions import ATP-binding protein fbpC
KeywordsHYDROLASE / Nucleotide Binding Domain / ABC Motor Domain / Ferric Iron Transport / ATP-binding / Cell inner membrane / Cell membrane / Ion transport / Iron / Iron transport / Membrane / Nucleotide-binding / Transport
Function / homology
Function and homology information


ABC-type Fe3+ transporter / ABC-type ferric iron transporter activity / iron import into cell / ATP hydrolysis activity / ATP binding / plasma membrane
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #450 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #470 / FbpC, C-terminal regulatory nucleotide binding domain / FbpC C-terminal regulatory nucleotide binding domain / Ferric cations import ATP-binding protein fbpC family profile. / ABC transporter, ferric cation import, FbpC / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #450 / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #470 / FbpC, C-terminal regulatory nucleotide binding domain / FbpC C-terminal regulatory nucleotide binding domain / Ferric cations import ATP-binding protein fbpC family profile. / ABC transporter, ferric cation import, FbpC / 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. / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / P-loop containing nucleotide triphosphate hydrolases / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Beta Barrel / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Fe(3+) ions import ATP-binding protein FbpC
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / N? / Resolution: 1.9 Å
AuthorsNewstead, S. / Bilton, P. / Carpenter, E.P. / Campopiano, D. / Iwata, S.
CitationJournal: Structure / Year: 2009
Title: Insights into how nucleotide-binding domains power ABC transport.
Authors: Newstead, S. / Fowler, P.W. / Bilton, P. / Carpenter, E.P. / Sadler, P.J. / Campopiano, D.J. / Sansom, M.S. / Iwata, S.
History
DepositionJan 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fe(3+) ions import ATP-binding protein fbpC
B: Fe(3+) ions import ATP-binding protein fbpC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,9217
Polymers77,7862
Non-polymers1,1355
Water9,404522
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-79 kcal/mol
Surface area30470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.861, 89.095, 149.014
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 Fe(3+) ions import ATP-binding protein fbpC


Mass: 38893.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (bacteria) / Gene: fbpC, NGO0215 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5FA19, EC: 3.6.3.30
#2: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 522 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THESE SEQUENCE CONFLICTS ARE DUE TO THIS GENE HAVING BEEN ISOLATED FROM A ...AUTHORS STATE THAT THESE SEQUENCE CONFLICTS ARE DUE TO THIS GENE HAVING BEEN ISOLATED FROM A CLINICAL ISOLATE OF N. GONORRHEA RATHER THAN THE ONE USED FOR THE SEQUENCING PROJECT. THESE MUTATIONS WERE PRESENT IN THE CLINICAL ISOLATE BUT ARE NOT IN ANY FUNCTIONALLY SIGNIFICANT AREAS OF THE PROTEIN.

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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: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG 6000, 0.1M MES, 0.2M CaCl2, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 190 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9797 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.9→76.4 Å / Num. all: 52525 / Num. obs: 51975 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 4 % / Rmerge(I) obs: 0.104
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 3.4 / % possible all: 92.1

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: N? / Resolution: 1.9→52.27 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.872 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.27 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25646 2624 5.1 %RANDOM
Rwork0.19468 ---
obs0.19784 49321 87.37 %-
all-49323 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.003 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→52.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5249 0 65 522 5836
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225572
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.9977612
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285736
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60323.169243
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0315928
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2271553
X-RAY DIFFRACTIONr_chiral_restr0.1160.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214237
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.22585
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.23696
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1680.2495
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0870.210
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2110.259
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.223
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9141.53511
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.57625649
X-RAY DIFFRACTIONr_scbond_it2.64532061
X-RAY DIFFRACTIONr_scangle_it4.2484.51940
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 201 -
Rwork0.235 3751 -
obs--91.4 %

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