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- PDB-6iwf: Crystal structure of HitA from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 6iwf
TitleCrystal structure of HitA from Pseudomonas aeruginosa
ComponentsFerric iron-binding protein HitA
KeywordsMETAL BINDING PROTEIN / HitA / ferric iron -binding protein
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / 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
Ferric iron-binding periplasmic protein HitA
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.70662332929 Å
AuthorsGuo, Y. / Zhengrui, Z. / Li, H.
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 5, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 11, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Database references / Structure summary / Category: audit_author / citation / citation_author / Item: _audit_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ferric iron-binding protein HitA
B: Ferric iron-binding protein HitA


Theoretical massNumber of molelcules
Total (without water)66,6472
Polymers66,6472
Non-polymers00
Water5,423301
1
A: Ferric iron-binding protein HitA


Theoretical massNumber of molelcules
Total (without water)33,3241
Polymers33,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ferric iron-binding protein HitA


Theoretical massNumber of molelcules
Total (without water)33,3241
Polymers33,3241
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.324, 105.195, 59.676
Angle α, β, γ (deg.)90.000, 110.361, 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 protein HitA


Mass: 33323.621 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.28 Å3/Da / Density % sol: 46.01 %
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: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→41.41 Å / Num. obs: 62932 / % possible obs: 97.71 % / Redundancy: 3.4 % / Biso Wilson estimate: 12.4437748527 Å2 / CC1/2: 0.98 / Rpim(I) all: 0.023 / Rrim(I) all: 0.043 / Net I/σ(I): 17.3
Reflection shellResolution: 1.707→1.768 Å / Num. unique obs: 6025 / CC1/2: 0.028 / Rpim(I) all: 0.206 / Rrim(I) all: 0.361

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IVY

6ivy


Resolution: 1.70662332929→41.4062347783 Å / SU ML: 0.181665160234 / Cross valid method: FREE R-VALUE / σ(F): 1.36389424381 / Phase error: 23.2146734494
RfactorNum. reflection% reflection
Rfree0.237498765464 3127 4.97130411281 %
Rwork0.19763723608 --
obs0.19963654854 62901 97.6844949683 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 15.7459878243 Å2
Refinement stepCycle: LAST / Resolution: 1.70662332929→41.4062347783 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4639 0 0 301 4940
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006083727800154733
X-RAY DIFFRACTIONf_angle_d0.7881286327266415
X-RAY DIFFRACTIONf_chiral_restr0.0490354839439716
X-RAY DIFFRACTIONf_plane_restr0.00511642372865838
X-RAY DIFFRACTIONf_dihedral_angle_d7.184057332682871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7066-1.73330.3012253848491370.2384185022062465X-RAY DIFFRACTION90.4414320473
1.7333-1.76170.280278064021560.2240552580822700X-RAY DIFFRACTION96.3562753036
1.7617-1.79210.2750714897061420.223641345172686X-RAY DIFFRACTION98.296836983
1.7921-1.82470.2938240063581320.2155396807872767X-RAY DIFFRACTION98.4714673913
1.8247-1.85980.2865717157111360.2118306726972725X-RAY DIFFRACTION98.4176126591
1.8598-1.89770.248721181871490.2071806119872723X-RAY DIFFRACTION98.6602542082
1.8977-1.9390.2356020592821440.2031372371992747X-RAY DIFFRACTION98.5008517888
1.939-1.98410.2744071560721450.2131611053182760X-RAY DIFFRACTION98.1087470449
1.9841-2.03370.2643080606011290.2083558936762671X-RAY DIFFRACTION98.6958054283
2.0337-2.08870.2382582895191410.2068419741462748X-RAY DIFFRACTION98.1651376147
2.0887-2.15020.220640731121340.1994707703512611X-RAY DIFFRACTION93.9103660623
2.1502-2.21960.2284198084181520.2092670825172747X-RAY DIFFRACTION98.7061627511
2.2196-2.29890.2443424319371560.2016580556732744X-RAY DIFFRACTION99.0775538094
2.2989-2.39090.270876133761520.2035680892022747X-RAY DIFFRACTION99.3148338472
2.3909-2.49970.2343009622571340.217638612262768X-RAY DIFFRACTION99.2136752137
2.4997-2.63150.2473279527471420.2110980642432746X-RAY DIFFRACTION98.8026000684
2.6315-2.79630.2434087737141670.2151192525122719X-RAY DIFFRACTION98.6666666667
2.7963-3.01220.2639442280961440.2190819478612728X-RAY DIFFRACTION96.9287883901
3.0122-3.31520.2587596272841230.2086719113122665X-RAY DIFFRACTION95.5776482688
3.3152-3.79460.2232935592511280.1798016324022799X-RAY DIFFRACTION99.727427598
3.7946-4.77970.1791590687591590.1554244811792770X-RAY DIFFRACTION99.4904891304
4.7797-41.41840.1853078070981250.155042269512738X-RAY DIFFRACTION95.5607476636

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