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- PDB-1si0: Crystal Structure of Mannheimia haemolytica Ferric iron-Binding P... -

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Basic information

Entry
Database: PDB / ID: 1si0
TitleCrystal Structure of Mannheimia haemolytica Ferric iron-Binding Protein A in a closed conformation
Componentsiron binding protein FbpA
KeywordsMETAL BINDING PROTEIN
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
Bacterial extracellular solute-binding protein / Ferric binding protein / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / : / Fe(3+) ABC transporter substrate-binding protein
Similarity search - Component
Biological speciesMannheimia haemolytica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsShouldice, S.R. / Skene, R.J. / Dougan, D.R. / Snell, G. / McRee, D.E. / Schryvers, A.B. / Tari, L.W.
CitationJournal: J.Bacteriol. / Year: 2004
Title: Structural basis for iron binding and release by a novel class of periplasmic iron-binding proteins found in gram-negative pathogens.
Authors: Shouldice, S.R. / Skene, R.J. / Dougan, D.R. / Snell, G. / McRee, D.E. / Schryvers, A.B. / Tari, L.W.
History
DepositionFeb 26, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: iron binding protein FbpA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0734
Polymers35,8951
Non-polymers1783
Water9,170509
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.670, 192.941, 43.352
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-714-

HOH

21A-775-

HOH

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Components

#1: Protein iron binding protein FbpA


Mass: 35894.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mannheimia haemolytica (bacteria) / Gene: fbpA / Plasmid: pT7-7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)/pLysS / References: UniProt: Q9Z4N6
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O
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: 2.84 Å3/Da / Density % sol: 56.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, isopropanol, PEG 4000, glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 21, 2003
RadiationMonochromator: osmic / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→95.35 Å / Num. all: 90250 / Num. obs: 85709 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.35→1.4 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q35

1q35


Resolution: 1.35→95.35 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.638 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17416 4526 5 %RANDOM
Rwork0.15913 ---
all0.1599 90250 --
obs0.15989 85709 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 11.398 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2---0.72 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.35→95.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2526 0 9 509 3044
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222576
X-RAY DIFFRACTIONr_bond_other_d0.0020.022319
X-RAY DIFFRACTIONr_angle_refined_deg1.0961.9653480
X-RAY DIFFRACTIONr_angle_other_deg0.71835436
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5425315
X-RAY DIFFRACTIONr_chiral_restr0.0630.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022844
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02492
X-RAY DIFFRACTIONr_nbd_refined0.210.2553
X-RAY DIFFRACTIONr_nbd_other0.2360.22912
X-RAY DIFFRACTIONr_nbtor_other0.0820.21506
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.2378
X-RAY DIFFRACTIONr_metal_ion_refined0.0060.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.080.249
X-RAY DIFFRACTIONr_mcbond_it1.53421579
X-RAY DIFFRACTIONr_mcangle_it2.4432543
X-RAY DIFFRACTIONr_scbond_it3.032993
X-RAY DIFFRACTIONr_scangle_it4.8863929
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.24 312
Rwork0.221 6169

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