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- PDB-3wae: X-ray structure of Fe(III)-bicarbonates-ttfbpa, a ferric ion-bind... -

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Basic information

Entry
Database: PDB / ID: 3wae
TitleX-ray structure of Fe(III)-bicarbonates-ttfbpa, a ferric ion-binding protein from thermus thermophilus HB8
ComponentsIRON ABC TRANSPORTER, PERIPLASMIC IRON-BINDING PROTEIN
KeywordsMETAL BINDING PROTEIN / A FERRIC BINDING PROTEIN / FERRIC ION
Function / homology
Function and homology information


Bacterial extracellular solute-binding protein / Ferric binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BICARBONATE ION / : / Iron ABC transporter, periplasmic iron-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)72,7438
Polymers72,3882
Non-polymers3566
Water9,242513
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-29 kcal/mol
Surface area24150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.170, 101.020, 134.610
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: PRSFDUET-1 VECTOR / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHV2
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-BCT / BICARBONATE ION / Bicarbonate


Mass: 61.017 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.89 Å3/Da / Density % sol: 34.8 %
Crystal growpH: 5.5
Details: 0.1M BIS-TRIS (PH 5.5), 0.2M SODIUM CHLORIDE, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL32XU11
SYNCHROTRONPhoton Factory AR-NE3A21.7209
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDJul 8, 2011
ADSC QUANTUM 2702CCDNov 4, 2011
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.72091
ReflectionResolution: 1.7→45 Å / Num. obs: 62381 / % possible obs: 99.4 % / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5refinement
XDSMEdata reduction
XDSMEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→19.98 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.924 / SU B: 2.574 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24258 3103 5.1 %RANDOM
Rwork0.20133 ---
obs0.20342 58159 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.618 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å2-0 Å20 Å2
2---0.03 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4785 0 18 513 5316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194941
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2921.9986720
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.285629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.49522.745204
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.34415837
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.831546
X-RAY DIFFRACTIONr_chiral_restr0.0790.2765
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213736
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: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 203 -
Rwork0.3 3954 -
obs--100 %

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