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- PDB-6g7n: Trichodesmium Tery_3377 (IdiA) (FutA) with iron and alanine ligand. -

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Basic information

Entry
Database: PDB / ID: 6g7n
TitleTrichodesmium Tery_3377 (IdiA) (FutA) with iron and alanine ligand.
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
D-ALANINE / D-GLUTAMIC ACID / : / Extracellular solute-binding protein, family 1
Similarity search - Component
Biological speciesTrichodesmium erythraeum IMS101 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 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 2.0Dec 19, 2018Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id ..._atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id
Revision 2.1May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,3438
Polymers69,7592
Non-polymers5846
Water13,547752
1
A: Extracellular solute-binding protein, family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1724
Polymers34,8801
Non-polymers2923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Extracellular solute-binding protein, family 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1724
Polymers34,8801
Non-polymers2923
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.220, 83.190, 65.160
Angle α, β, γ (deg.)90.000, 95.250, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#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 IMS101 (bacteria)
Gene: Tery_3377 / Plasmid: pET3377 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q10Z45
#2: Chemical ChemComp-DAL / D-ALANINE


Type: D-peptide linking / Mass: 89.093 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7NO2
#3: Chemical ChemComp-DGL / D-GLUTAMIC ACID


Type: D-peptide linking / Mass: 147.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO4
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 752 / 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: 2.18 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: L-Na-Glutamate, Alanine (racemic), Glycine, Lysine HCl (racemic), Serine (racemic), Sodium HEPES, MOPS (acid), PEG500MME, PEG20000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 5, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.1→83.19 Å / Num. obs: 239749 / % possible obs: 99.4 % / Redundancy: 3.21 % / Biso Wilson estimate: 15.555 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.047 / Rrim(I) all: 0.056 / Χ2: 1.063 / Net I/σ(I): 11.73 / Num. measured all: 769551
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
1.1-1.133.030.35235361517791176970.7750.42899.5
1.13-1.163.0650.3023.655279517295172250.8310.36799.6
1.16-1.192.9970.2684.125056316926168690.8740.32699.7
1.19-1.233.1490.2344.865143616399163330.9150.28299.6
1.23-1.273.2840.1925.995196715872158250.950.2399.7
1.27-1.313.2360.1716.654958315353153220.9580.20699.8
1.31-1.363.1220.1437.624612014827147740.9710.17399.6
1.36-1.423.2650.1229.044649314274142390.9810.14699.8
1.42-1.483.3890.10210.954639213722136870.9870.12199.7
1.48-1.563.3590.08113.184384413089130520.9910.09699.7
1.56-1.643.2140.06914.843966212440123420.9930.08299.2
1.64-1.743.2180.0616.763762911790116940.9940.07399.2
1.74-1.863.4280.05319.783781911099110310.9950.06399.4
1.86-2.013.3260.04821.733408110343102480.9960.05799.1
2.01-2.23.1830.04422.9829708947193320.9960.05398.5
2.2-2.463.0310.04123.3625650861484620.9960.04998.2
2.46-2.843.3980.03925.325676760975560.9970.04699.3
2.84-3.483.3370.03825.7221285643763780.9970.04599.1
3.48-4.923.1220.03725.4615349498449160.9960.04598.6
4.92-83.193.5720.0427.289884280527670.9960.04898.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→83.19 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.949 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.028 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1512 11859 4.9 %RANDOM
Rwork0.1337 ---
obs0.1346 227890 99.39 %-
Solvent computationSolvent model: BABINET MODEL
Displacement parametersBiso max: 100.25 Å2 / Biso mean: 16.419 Å2 / Biso min: 7.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å2-0.02 Å2
2--0.47 Å20 Å2
3----0.09 Å2
Refinement stepCycle: final / Resolution: 1.1→83.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 34 772 5674
Biso mean--19.51 28.42 -
Num. residues----636
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195420
X-RAY DIFFRACTIONr_bond_other_d0.0010.025161
X-RAY DIFFRACTIONr_angle_refined_deg1.5681.9657383
X-RAY DIFFRACTIONr_angle_other_deg1.71312032
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5675733
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.78423.799229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.27315979
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8741537
X-RAY DIFFRACTIONr_chiral_restr0.0960.2796
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216173
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021128
X-RAY DIFFRACTIONr_rigid_bond_restr1.939310581
X-RAY DIFFRACTIONr_sphericity_free19.9875519
X-RAY DIFFRACTIONr_sphericity_bonded6.124510684
LS refinement shellResolution: 1.1→1.129 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 905 -
Rwork0.238 16772 -
all-17677 -
obs--99.43 %

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