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- PDB-3tlk: Crystal structure of holo FepB -

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Basic information

Entry
Database: PDB / ID: 3tlk
TitleCrystal structure of holo FepB
ComponentsFerrienterobactin-binding periplasmic protein
KeywordsMETAL TRANSPORT / Ferric-enterobactin / trimer / siderophore transport / Periplasmic space
Function / homology
Function and homology information


ferric-enterobactin import into cell / iron import into cell / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / DNA damage response / membrane
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Chem-EB4 / : / Ferric enterobactin-binding periplasmic protein FepB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.853 Å
AuthorsLi, N. / Gu, L.
CitationJournal: To be Published
Title: Crystal structure of holo FepB
Authors: Li, N. / Gu, L.
History
DepositionAug 30, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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 / pdbx_struct_conn_angle / struct_conn / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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.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.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_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: Ferrienterobactin-binding periplasmic protein
B: Ferrienterobactin-binding periplasmic protein
C: Ferrienterobactin-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,32114
Polymers106,1553
Non-polymers3,16611
Water11,097616
1
A: Ferrienterobactin-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8685
Polymers35,3851
Non-polymers1,4834
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ferrienterobactin-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2545
Polymers35,3851
Non-polymers8694
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Ferrienterobactin-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1994
Polymers35,3851
Non-polymers8133
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.024, 131.591, 196.113
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-464-

HOH

21C-395-

HOH

31C-400-

HOH

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Components

#1: Protein Ferrienterobactin-binding periplasmic protein / Periplasmic transport protein


Mass: 35385.043 Da / Num. of mol.: 3 / Fragment: periplasmic transport domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b0592, fepB, JW0584 / Plasmid: pET-21b / Production host: Escherichia coli (E. coli) / Strain (production host): DE3 / References: UniProt: P0AEL6
#2: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-EB4 / N,N',N''-[(3S,7S,11S)-2,6,10-trioxo-1,5,9-trioxacyclododecane-3,7,11-triyl]tris(2,3-dihydroxybenzamide) / Enterobactin


Mass: 669.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C30H27N3O15
#4: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 616 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.0M Succinic acid pH 7.0, 0.1M HEPES, 1% w/v Polyethylene glycol monomethyl ether 2000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9792 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jan 31, 2010
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 79154 / Num. obs: 79154 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 19.17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allRsym value% possible all
1.85-1.925.20.4213.0772550.42190.1
3.99-507.20.05236.2684720.05299.9

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3R5T

3r5t


Resolution: 1.853→39.314 Å / SU ML: 0.21 / σ(F): 0.04 / Phase error: 21.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2168 1859 2.5 %RANDOM
Rwork0.1793 ---
all0.1802 74245 --
obs0.1802 74245 91.11 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.687 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso mean: 28.108 Å2
Baniso -1Baniso -2Baniso -3
1-9.9525 Å2-0 Å2-0 Å2
2---7.2166 Å20 Å2
3----2.7359 Å2
Refinement stepCycle: LAST / Resolution: 1.853→39.314 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6742 0 214 616 7572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087101
X-RAY DIFFRACTIONf_angle_d1.289667
X-RAY DIFFRACTIONf_dihedral_angle_d25.8672606
X-RAY DIFFRACTIONf_chiral_restr0.1061093
X-RAY DIFFRACTIONf_plane_restr0.0131262
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8526-1.90260.25311130.1993456376
1.9026-1.95860.26451270.1959488181
1.9586-2.02180.27451290.2015505484
2.0218-2.09410.24571440.1868526587
2.0941-2.17790.19791440.1852533988
2.1779-2.27710.24291450.1809554391
2.2771-2.39710.23031370.1968564793
2.3971-2.54730.25241550.1933574794
2.5473-2.74390.23961490.1919586896
2.7439-3.01990.22861550.1908596097
3.0199-3.45670.2031460.1789601798
3.4567-4.35420.19711570.1555613799
4.3542-39.32260.16661580.1658636599

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