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- PDB-6ivy: Crystal structure of iron-bound HitA from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6ivy
TitleCrystal structure of iron-bound HitA from Pseudomonas aeruginosa
ComponentsPeriplasmic Ferric iron-binding Protein HitA
KeywordsSTRUCTURAL PROTEIN / HitA / ferric-iron binding protein / Pseudomonas aeruginosa / transporter.
Function / homology
Function and homology information


extracellular space / metal ion binding
Similarity search - Function
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
: / PHOSPHATE ION / Ferric iron-binding periplasmic protein HitA
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99999941515 Å
AuthorsZhang, Z.R. / Li, H.Y.
CitationJournal: Acs Infect Dis. / Year: 2019
Title: Identification and Characterization of a Metalloprotein Involved in Gallium Internalization in Pseudomonas aeruginosa.
Authors: Guo, Y. / Li, W. / Li, H. / Xia, W.
History
DepositionDec 4, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 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 / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Periplasmic Ferric iron-binding Protein HitA
B: Periplasmic Ferric iron-binding Protein HitA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7196
Polymers66,4172
Non-polymers3024
Water5,657314
1
A: Periplasmic Ferric iron-binding Protein HitA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3593
Polymers33,2091
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-23 kcal/mol
Surface area13110 Å2
MethodPISA
2
B: Periplasmic Ferric iron-binding Protein HitA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3593
Polymers33,2091
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area120 Å2
ΔGint-10 kcal/mol
Surface area12900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.577, 104.600, 58.758
Angle α, β, γ (deg.)90.000, 110.192, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Periplasmic Ferric iron-binding Protein HitA


Mass: 33208.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria)
Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1
Gene: hitA, PA4687 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HVA8
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-FE / FE (III) ION


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


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.24 Å3/Da / Density % sol: 45.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: PEG 3350, sodium cacodylate, magnesium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Mar 5, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→25.075 Å / Num. obs: 39097 / % possible obs: 98.99 % / Redundancy: 5 % / Biso Wilson estimate: 13.712096523 Å2 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.047 / Rrim(I) all: 0.11 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.4 / CC1/2: 0.754 / Rpim(I) all: 0.293 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
CrysalisProdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OD7

3od7


Resolution: 1.99999941515→25.0749871935 Å / SU ML: 0.211319251483 / Cross valid method: FREE R-VALUE / σ(F): 1.34117430845 / Phase error: 21.2183335948
RfactorNum. reflection% reflection
Rfree0.221228827531 2025 5.17995549075 %
Rwork0.175198893819 --
obs0.177544416044 39093 98.9821496392 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 14.4352477322 Å2
Refinement stepCycle: LAST / Resolution: 1.99999941515→25.0749871935 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4663 0 12 314 4989
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007650737764474765
X-RAY DIFFRACTIONf_angle_d0.8699094568486455
X-RAY DIFFRACTIONf_chiral_restr0.0491151844844715
X-RAY DIFFRACTIONf_plane_restr0.00550779770594843
X-RAY DIFFRACTIONf_dihedral_angle_d4.335354121532889
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.272682352881360.2173327435132511X-RAY DIFFRACTION93.6659589526
2.05-2.10540.2606039949371350.1990167956572558X-RAY DIFFRACTION95.5981540646
2.1054-2.16730.2571030375781390.1923637135742584X-RAY DIFFRACTION97.9496402878
2.1673-2.23720.2538184403741670.1880281794692622X-RAY DIFFRACTION99.2526690391
2.2372-2.31710.2789764900581310.1873125004392690X-RAY DIFFRACTION100
2.3171-2.40980.217068263311630.1858065596332642X-RAY DIFFRACTION100
2.4098-2.51940.2474227724791400.1920283235172671X-RAY DIFFRACTION99.9644381223
2.5194-2.65210.2408076224791720.1952235830072672X-RAY DIFFRACTION100
2.6521-2.81810.2792175170041600.1928357403792639X-RAY DIFFRACTION100
2.8181-3.03530.2585742869351290.1945156183312695X-RAY DIFFRACTION100
3.0353-3.34010.2006073717351400.1915353467432679X-RAY DIFFRACTION100
3.3401-3.8220.1958451925131420.1542824653052678X-RAY DIFFRACTION100
3.822-4.80970.1576473139311340.1333352609822712X-RAY DIFFRACTION100
4.8097-25.07690.1502011736641370.140950809362715X-RAY DIFFRACTION99.3036211699

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