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- PDB-6g7q: Trichodesmium Tery_3377 (IdiA) (FutA) in complex with iron and ci... -

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Basic information

Entry
Database: PDB / ID: 6g7q
TitleTrichodesmium Tery_3377 (IdiA) (FutA) in complex with iron and citrate ligands.
ComponentsExtracellular solute-binding protein, family 1
KeywordsMETAL BINDING PROTEIN / Iron / IdiA / FutA / ABC-Transporter
Function / homology
Function and homology information


iron ion transport / 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
: / CITRATE ANION / Extracellular solute-binding protein, family 1
Similarity search - Component
Biological speciesTrichodesmium erythraeum
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.2 Å
AuthorsMachelett, M.M. / Tews, I.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural and functional characterization of IdiA/FutA (Tery_3377), an iron-binding protein from the ocean diazotrophTrichodesmium erythraeum.
Authors: Polyviou, D. / Machelett, M.M. / Hitchcock, A. / Baylay, A.J. / MacMillan, F. / Moore, C.M. / Bibby, T.S. / Tews, I.
History
DepositionApr 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3May 8, 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
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Extracellular solute-binding protein, family 1
A: Extracellular solute-binding protein, family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,63211
Polymers69,7592
Non-polymers8739
Water15,349852
1
B: Extracellular solute-binding protein, family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1915
Polymers34,8801
Non-polymers3124
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Extracellular solute-binding protein, family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4416
Polymers34,8801
Non-polymers5625
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.330, 102.010, 57.670
Angle α, β, γ (deg.)90.000, 112.850, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 0 / Auth seq-ID: 4 - 318 / Label seq-ID: 1 - 315

Dom-IDAuth asym-IDLabel asym-ID
1BA
2AB

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Components

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Protein , 1 types, 2 molecules BA

#1: Protein Extracellular solute-binding protein, family 1


Mass: 34879.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichodesmium erythraeum (strain IMS101) (bacteria)
Strain: IMS101 / Gene: Tery_3377 / Plasmid: pET21a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q10Z45

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Non-polymers , 5 types, 861 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 852 / 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: 2.19 Å3/Da / Density % sol: 43.81 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG500MME, PEG20000, Sodium formate, Ammonium acetate, Sodium citrate tribasic dihydrate, Sodium potassium tartrate tetrahydrate, Sodium oxamate, Sodium HEPES, MOPS (acid).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.97625 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 183781 / % possible obs: 98.3 % / Redundancy: 5.826 % / Biso Wilson estimate: 17.471 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Rrim(I) all: 0.08 / Χ2: 0.948 / Net I/σ(I): 11.63 / Num. measured all: 1070779 / Scaling rejects: 65
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.2-1.235.5520.8711.557574013757136410.6790.96399.2
1.23-1.265.6970.7171.967558713417132690.7740.79198.9
1.26-1.35.6570.6392.237292613086128920.8040.70498.5
1.3-1.345.5160.5342.676802412764123330.8720.59196.6
1.34-1.395.7870.4623.266912012230119450.8950.50897.7
1.39-1.435.9080.3834.017017911948118790.920.42199.4
1.43-1.495.8540.3055.046648911466113580.9470.33699.1
1.49-1.555.8450.2386.576353911049108700.9640.26298.4
1.55-1.625.7350.1998.045961810672103960.9750.21997.4
1.62-1.75.7690.1669.77565331015197990.9810.18396.5
1.7-1.796.1030.13412.3858689963996160.9880.14799.8
1.79-1.96.0340.10415.4554721913490690.9920.11499.3
1.9-2.035.9180.08119.2850577860785460.9940.08999.3
2.03-2.195.7760.06623.245304799078430.9960.07398.2
2.19-2.45.6570.05626.2239901737070530.9970.06295.7
2.4-2.686.3850.05230.8342468668166510.9970.05699.6
2.68-3.16.2860.04634.7136731587458430.9980.0599.5
3.1-3.795.9740.04138.5329398501649210.9980.04598.1
3.79-5.375.8360.03741.2821726387137230.9980.04196.2
5.37-306.330.03743.4713509216421340.9980.04198.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→30 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.538 / SU ML: 0.029 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.036 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1648 1991 1.1 %RANDOM
Rwork0.1355 ---
obs0.1358 181790 98.43 %-
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso max: 97.67 Å2 / Biso mean: 17.882 Å2 / Biso min: 8.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20.27 Å2
2---0.61 Å20 Å2
3---0.05 Å2
Refinement stepCycle: final / Resolution: 1.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4885 0 53 863 5801
Biso mean--29.57 31.66 -
Num. residues----634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195327
X-RAY DIFFRACTIONr_bond_other_d0.0030.024970
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9657258
X-RAY DIFFRACTIONr_angle_other_deg1.07311625
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6745718
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.13424.706238
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75315942
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.61530
X-RAY DIFFRACTIONr_chiral_restr0.120.2782
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216058
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021072
X-RAY DIFFRACTIONr_rigid_bond_restr2.887310297
X-RAY DIFFRACTIONr_sphericity_free27.1715565
X-RAY DIFFRACTIONr_sphericity_bonded10.305510455
Refine LS restraints NCS

Ens-ID: 1 / Number: 21918 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1B
2A
LS refinement shellResolution: 1.2→1.231 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 147 -
Rwork0.263 13467 -
all-13614 -
obs--99.19 %

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