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- PDB-6j2s: Structure of HitA bound to gallium from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6j2s
TitleStructure of HitA bound to gallium from Pseudomonas aeruginosa
ComponentsFerric iron-binding periplasmic protein
KeywordsMETAL BINDING PROTEIN / HitA / Gallium / metal-drug / ferric iron binding protein / 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
GALLIUM (III) ION / PHOSPHATE ION / Ferric iron ABC transporter iron-binding protein / Ferric iron-binding periplasmic protein HitA
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73005117666 Å
AuthorsGuo, Y. / Li, H.Y. / Sun, H.Z. / Xia, W.
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
DepositionJan 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 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: Ferric iron-binding periplasmic protein
B: Ferric iron-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7466
Polymers66,4172
Non-polymers3294
Water3,603200
1
A: Ferric iron-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3733
Polymers33,2091
Non-polymers1652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferric iron-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3733
Polymers33,2091
Non-polymers1652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.930, 100.460, 58.540
Angle α, β, γ (deg.)90.000, 109.550, 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 Ferric iron-binding periplasmic protein / Iron ABC transporter substrate-binding protein / Iron-utilization periplasmic protein / Major ...Iron ABC transporter substrate-binding protein / Iron-utilization periplasmic protein / Major ferric iron-binding protein


Mass: 33208.535 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria)
Gene: fbpA, C8257_29030, CAZ10_24620, CGU42_22375, DZ940_19785, DZ962_30390, NCTC13719_05161, PAERUG_E15_London_28_01_14_01851, RW109_RW109_06267
Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZDH2, UniProt: Q9HVA8*PLUS
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 69.723 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ga / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
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: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.73→48.4 Å / Num. obs: 51047 / % possible obs: 88 % / Redundancy: 3.1 % / Biso Wilson estimate: 20.061810712 Å2 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.082 / Rrim(I) all: 0.12 / Net I/σ(I): 9.3
Reflection shellResolution: 1.73→1.79 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.45 / Rpim(I) all: 0.423 / Rrim(I) all: 0.616

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IVY

6ivy


Resolution: 1.73005117666→48.3544326644 Å / SU ML: 0.208585883619 / Cross valid method: FREE R-VALUE / σ(F): 1.4188773503 / Phase error: 24.112282637
RfactorNum. reflection% reflection
Rfree0.208927913513 2453 4.80848394558 %
Rwork0.176099720572 --
obs0.177681264117 51014 88.1862812889 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.1618825616 Å2
Refinement stepCycle: LAST / Resolution: 1.73005117666→48.3544326644 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4669 0 12 200 4881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006841824498924771
X-RAY DIFFRACTIONf_angle_d0.8438428020736464
X-RAY DIFFRACTIONf_chiral_restr0.0513152890631718
X-RAY DIFFRACTIONf_plane_restr0.0059701020545843
X-RAY DIFFRACTIONf_dihedral_angle_d5.422079320292894
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7301-1.76330.337102196566720.2692771414251532X-RAY DIFFRACTION49.2326580724
1.7633-1.79930.308733072521770.2651221739981767X-RAY DIFFRACTION58.5396825397
1.7993-1.83840.3184309843941000.2643950687512005X-RAY DIFFRACTION65.5763239875
1.8384-1.88120.2809385108681090.2650682189252319X-RAY DIFFRACTION74.8228043143
1.8812-1.92830.3377314826511220.2618360884182473X-RAY DIFFRACTION82.5644288896
1.9283-1.98040.2642365535741600.2234094739352862X-RAY DIFFRACTION93.7635743096
1.9804-2.03870.2522168507121780.1916855640842991X-RAY DIFFRACTION98.3550589696
2.0387-2.10450.2739780593111590.1846973444762924X-RAY DIFFRACTION97.1329552615
2.1045-2.17970.2243075985161410.1745345456323028X-RAY DIFFRACTION98.5692068429
2.1797-2.2670.2185293298451670.1794372457842905X-RAY DIFFRACTION96.2104603821
2.267-2.37010.2175797718941570.1679094642092979X-RAY DIFFRACTION97.7251480212
2.3701-2.49510.2030322955051360.1846201711532957X-RAY DIFFRACTION96.6864645202
2.4951-2.65140.2182236446681360.1779035135853056X-RAY DIFFRACTION98.4881209503
2.6514-2.85610.2057900913731410.1801779846323003X-RAY DIFFRACTION98.4037558685
2.8561-3.14350.1936615799191730.176132391182978X-RAY DIFFRACTION97.463656047
3.1435-3.59820.1978628454971340.1655218902542898X-RAY DIFFRACTION94.396014944
3.5982-4.53280.1689857539531490.1442544263982911X-RAY DIFFRACTION94.3861813695
4.5328-48.37330.1583652060561420.1499884744962973X-RAY DIFFRACTION95.1726245035

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