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- PDB-7li0: Crystal structure of apo Moraxella catarrhalis ferric binding pro... -

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Basic information

Entry
Database: PDB / ID: 7li0
TitleCrystal structure of apo Moraxella catarrhalis ferric binding protein A in an open conformation
ComponentsFe(3+) ABC transporter substrate-binding protein
KeywordsMETAL TRANSPORT / ferric binding protein A / FbpA
Function / homologyFerric binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / outer membrane-bounded periplasmic space / metal ion binding / CITRIC ACID / CARBONATE ION / DI(HYDROXYETHYL)ETHER / Fe(3+) ABC transporter substrate-binding protein
Function and homology information
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsChan, C. / Ng, D. / Fraser, M.E. / Schryvers, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Biometals / Year: 2022
Title: Structural and functional insights into iron acquisition from lactoferrin and transferrin in Gram-negative bacterial pathogens.
Authors: Chan, C. / Ng, D. / Fraser, M.E. / Schryvers, A.B.
History
DepositionJan 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fe(3+) ABC transporter substrate-binding protein
B: Fe(3+) ABC transporter substrate-binding protein
C: Fe(3+) ABC transporter substrate-binding protein
D: Fe(3+) ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,97315
Polymers137,2194
Non-polymers75411
Water13,025723
1
A: Fe(3+) ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4345
Polymers34,3051
Non-polymers1294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Fe(3+) ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4253
Polymers34,3051
Non-polymers1202
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Fe(3+) ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5264
Polymers34,3051
Non-polymers2213
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Fe(3+) ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5893
Polymers34,3051
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.060, 67.830, 73.530
Angle α, β, γ (deg.)91.280, 91.590, 105.820
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Fe(3+) ABC transporter substrate-binding protein


Mass: 34304.738 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella catarrhalis (bacteria) / Gene: fbpA / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566 / References: UniProt: A0A1E9VR34

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Non-polymers , 6 types, 734 molecules

#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: CO3
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 723 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M ammonium citrate tribasic pH 6.5, 30% v/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.92009 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92009 Å / Relative weight: 1
ReflectionResolution: 1.84→51.61 Å / Num. obs: 96783 / % possible obs: 96.8 % / Redundancy: 1.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.058 / Net I/σ(I): 6.6
Reflection shellResolution: 1.84→1.87 Å / Rmerge(I) obs: 0.416 / Num. unique obs: 4682 / CC1/2: 0.795

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6G7N

6g7n


Resolution: 1.85→51.61 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2229 --Random selection
Rwork0.1932 ---
obs-95165 96.67 %-
Displacement parametersBiso mean: 34.67 Å2
Refinement stepCycle: LAST / Resolution: 1.85→51.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9357 0 48 723 10128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00439636
X-RAY DIFFRACTIONf_angle_d0.652513169
X-RAY DIFFRACTIONf_chiral_restr0.04551500
X-RAY DIFFRACTIONf_plane_restr0.00411736
X-RAY DIFFRACTIONf_dihedral_angle_d12.44315728

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