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- PDB-8y4y: Crystal structure of ferric iron-binding protein (FecB) from Vibr... -

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Basic information

Entry
Database: PDB / ID: 8y4y
TitleCrystal structure of ferric iron-binding protein (FecB) from Vibrio alginolyticus in complex with ferric citrate
ComponentsABC transporter substrate-binding protein
KeywordsMETAL BINDING PROTEIN / Vibrio alginolyticus / periplasmic binding protein / ferric citrate
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile.
Similarity search - Domain/homology
: / CITRATE ANION / DI(HYDROXYETHYL)ETHER / ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesVibrio alginolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsJiang, J.Y. / Lu, P. / Nagata, K.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)19H05771 Japan
Japan Society for the Promotion of Science (JSPS)JP20K22561 Japan
Japan Science and TechnologyJPMJSP2108 Japan
Other privateJapan Science Society 2023-4016
CitationJournal: To Be Published
Title: Crystal structure of ferric iron-binding protein (FecB) from Vibrio alginolyticus in complex with ferric citrate
Authors: Jiang, J.Y. / Lu, P. / Nagata, K.
History
DepositionJan 31, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ABC transporter substrate-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0578
Polymers30,2411
Non-polymers8167
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.497, 100.497, 205.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ABC transporter substrate-binding protein


Mass: 30240.568 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio alginolyticus (bacteria) / Gene: HKB16_09180 / Production host: Escherichia coli KRX (bacteria) / References: UniProt: A0A7Y0SGI3

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Non-polymers , 5 types, 22 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 4.25 Å3/Da / Density % sol: 71.06 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1M HEPES pH7.5, 20% w/v Polyethylene glycol 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 23, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.51→45.16 Å / Num. obs: 18412 / % possible obs: 99.5 % / Redundancy: 6.86 % / Biso Wilson estimate: 61.62 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 1.23
Reflection shellResolution: 2.51→2.67 Å / Rmerge(I) obs: 1.457 / Mean I/σ(I) obs: 1.23 / Num. unique obs: 18412

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Processing

Software
NameVersionClassification
PHENIX(1.21RC1_5058: ???)refinement
HKL-2000data reduction
REFMACphasing
HKL-2000data collection
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→33.06 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.262 850 4.62 %
Rwork0.224 --
obs0.226 18412 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 68.45 Å2
Refinement stepCycle: LAST / Resolution: 2.51→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2129 0 51 15 2195
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.618
X-RAY DIFFRACTIONf_dihedral_angle_d15.334836
X-RAY DIFFRACTIONf_chiral_restr0.041339
X-RAY DIFFRACTIONf_plane_restr0.004388
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.670.33911200.3162815X-RAY DIFFRACTION97
2.67-2.870.40461430.3142887X-RAY DIFFRACTION100
2.87-3.160.34561640.28862860X-RAY DIFFRACTION100
3.16-3.620.28021290.25572938X-RAY DIFFRACTION100
3.62-4.550.25091380.19662962X-RAY DIFFRACTION100
4.56-33.060.21471560.19023100X-RAY DIFFRACTION100

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