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- PDB-7li1: Crystal structure of holo Moraxella catarrhalis ferric binding pr... -

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Basic information

Entry
Database: PDB / ID: 7li1
TitleCrystal structure of holo 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 / CARBONATE ION / : / Fe(3+) ABC transporter substrate-binding protein
Function and homology information
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 20, 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)138,03418
Polymers137,2194
Non-polymers81514
Water6,593366
1
A: Fe(3+) ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4814
Polymers34,3051
Non-polymers1763
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)34,4814
Polymers34,3051
Non-polymers1763
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)34,4814
Polymers34,3051
Non-polymers1763
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)34,5926
Polymers34,3051
Non-polymers2885
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.130, 67.560, 73.770
Angle α, β, γ (deg.)91.020, 92.260, 105.020
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#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
#2: Chemical
ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: CO3
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M lithium sulfate monohydrate, 0.1 M HEPES pH 7.5, 30% v/v polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 26, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→29.71 Å / Num. obs: 110222 / % possible obs: 94.25 % / Redundancy: 2 % / CC1/2: 1 / Rmerge(I) obs: 0.023 / Net I/σ(I): 16.74
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 2 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 0.83 / Num. unique obs: 10935 / CC1/2: 0.424 / % possible all: 93.44

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7LI0

7li0


Resolution: 1.75→29.71 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2000 -Random selection
Rwork0.2311 ---
obs-110042 94.25 %-
Refinement stepCycle: LAST / Resolution: 1.75→29.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9262 0 38 366 9666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069562
X-RAY DIFFRACTIONf_angle_d0.743813097
X-RAY DIFFRACTIONf_chiral_restr0.05061500
X-RAY DIFFRACTIONf_plane_restr0.00561742
X-RAY DIFFRACTIONf_dihedral_angle_d13.13435652
LS refinement shellResolution: 1.75→1.81 Å /
RfactorNum. reflection
Rfree0.4302 205
Rwork0.4171 10906

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