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- PDB-4elr: Ferric binding protein with iron and carbonate -

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Basic information

Entry
Database: PDB / ID: 4elr
TitleFerric binding protein with iron and carbonate
ComponentsIron ABC transporter, periplasmic iron-binding protein
KeywordsMETAL TRANSPORT / beta sheet surrounded by alpha helices
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 / : / Iron ABC transporter, periplasmic iron-binding protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsWang, Q. / Liu, X.Q. / Wang, X.Q.
CitationJournal: To be Published
Title: Crystal structure of ferric binding protein A
Authors: Wang, Q. / Liu, X.Q. / Wang, X.Q.
History
DepositionApr 11, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 17, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _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)74,2776
Polymers74,0452
Non-polymers2324
Water4,360242
1
A: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1393
Polymers37,0231
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Iron ABC transporter, periplasmic iron-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1393
Polymers37,0231
Non-polymers1162
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.602, 63.602, 266.701
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 23 - 330 / Label seq-ID: 23 - 330

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain A and (resseq 23:330 )AA
2chain B and (resseq 23:330 )BB

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Components

#1: Protein Iron ABC transporter, periplasmic iron-binding protein / ferric binding protein


Mass: 37022.711 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1628 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHV2
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.1 Å3/Da / Density % sol: 41.51 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2M MgCl2, 0.1M Hepes pH 7.5, 26% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→42.465 Å / Num. all: 22672 / Num. obs: 22650 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 24.44 Å2

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: dev_596)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.502→42.465 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8421 / SU ML: 0.31 / σ(F): 0 / σ(I): 0 / Phase error: 21.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1133 5.05 %random
Rwork0.1686 ---
all0.171 22672 --
obs0.1712 22428 99.11 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.216 Å2 / ksol: 0.354 e/Å3
Displacement parametersBiso max: 111.44 Å2 / Biso mean: 25.3665 Å2 / Biso min: 7.29 Å2
Baniso -1Baniso -2Baniso -3
1-4.3906 Å20 Å2-0 Å2
2--4.3906 Å20 Å2
3----8.7811 Å2
Refinement stepCycle: LAST / Resolution: 2.502→42.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4802 0 10 242 5054
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084914
X-RAY DIFFRACTIONf_angle_d1.056665
X-RAY DIFFRACTIONf_dihedral_angle_d15.1381834
X-RAY DIFFRACTIONf_chiral_restr0.072758
X-RAY DIFFRACTIONf_plane_restr0.005859
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A2387X-RAY DIFFRACTIONPOSITIONAL0.035
12B2387X-RAY DIFFRACTIONPOSITIONAL0.035
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.502-2.61590.30211330.21052545267897
2.6159-2.75380.26221560.18962583273999
2.7538-2.92630.24841350.17672595273099
2.9263-3.15210.25551500.18126462796100
3.1521-3.46920.23311340.1732640277499
3.4692-3.97090.18681310.160927052836100
3.9709-5.00160.19391440.137927152859100
5.0016-42.4710.17361500.17012866301699

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