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- PDB-3waf: X-ray structure of apo-TtFbpA, a ferric ion-binding protein from ... -

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Basic information

Entry
Database: PDB / ID: 3waf
TitleX-ray structure of apo-TtFbpA, a ferric ion-binding protein from thermus thermophilus HB8
ComponentsIron ABC transporter, periplasmic iron-binding protein
KeywordsMETAL BINDING PROTEIN / PERIPLASMIC BINDING PROTEIN / ABC TRANSPORTER / TTHA1628 / PEAMEASES
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
ISOPROPYL ALCOHOL / Iron ABC transporter, periplasmic iron-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsWang, S. / Ogata, M. / Horita, S. / Ohtsuka, J. / Nagata, K. / Tanokura, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: A novel mode of ferric ion coordination by the periplasmic ferric ion-binding subunit FbpA of an ABC-type iron transporter from Thermus thermophilus HB8.
Authors: Wang, S. / Ogata, M. / Horita, S. / Ohtsuka, J. / Nagata, K. / Tanokura, M.
History
DepositionMay 2, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron ABC transporter, periplasmic iron-binding protein
B: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,5084
Polymers72,3882
Non-polymers1202
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2660 Å2
ΔGint1 kcal/mol
Surface area23960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.150, 99.050, 132.230
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 Iron ABC transporter, periplasmic iron-binding protein


Mass: 36193.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA1628 / Plasmid: pRSF vector / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3) / References: UniProt: Q5SHV2
#2: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O

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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: 1.77 Å3/Da / Density % sol: 30.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.2
Details: 0.1M SODIUM CITRATE TRIBASIC DEHYDRATE (PH5.2), 20% (W/V) 2-PROPANOL, 20% (W/V) PEG 4000, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→79.29 Å / Num. obs: 47714 / Redundancy: 13.2 %
Reflection shellResolution: 1.8→1.85 Å / % possible all: 87.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.6.0117refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XVY

1xvy


Resolution: 1.8→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 5.072 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.20959 2414 5.1 %RANDOM
Rwork0.17524 ---
obs0.17697 45298 98.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.144 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å2-0 Å20 Å2
2--0.67 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4792 0 8 292 5092
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194900
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9956654
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8255616
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.95822.673202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27215824
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9911546
X-RAY DIFFRACTIONr_chiral_restr0.090.2756
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213688
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.803→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.154 145 -
Rwork0.116 2781 -
obs--88.45 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1124-0.02680.04120.2560.21030.2163-0.0030.0065-0.0065-0.0188-0.0042-0.0042-0.0251-0.00990.00720.01290.0068-0.00170.0233-0.01020.027133.487752.65874.5753
20.2111-0.07670.09810.08090.06560.2521-0.0293-0.01340.00620.01570.01270.00120.0086-0.00350.01660.0224-0.0059-0.00010.0239-0.00690.012532.536532.013231.5737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A22 - 330
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION1A501 - 652
4X-RAY DIFFRACTION2B22 - 330
5X-RAY DIFFRACTION2B401
6X-RAY DIFFRACTION2A653
7X-RAY DIFFRACTION2B501 - 639

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