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- PDB-3ell: Structure of the hemophore from Pseudomonas aeruginosa (HasAp) -

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Basic information

Entry
Database: PDB / ID: 3ell
TitleStructure of the hemophore from Pseudomonas aeruginosa (HasAp)
ComponentsHasAp (Heme acquisition protein HasAp)
KeywordsHEME BINDING PROTEIN / alpha beta protein / heme-binding protein
Function / homology
Function and homology information


Heme-binding Protein A; Chain: A; / Haem-binding HasA / Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / HasAp
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchonbrunn, E. / Rivera, M.
CitationJournal: Biochemistry / Year: 2009
Title: Structural characterization of the hemophore HasAp from Pseudomonas aeruginosa: NMR spectroscopy reveals protein-protein interactions between Holo-HasAp and hemoglobin.
Authors: Alontaga, A.Y. / Rodriguez, J.C. / Schonbrunn, E. / Becker, A. / Funke, T. / Yukl, E.T. / Hayashi, T. / Stobaugh, J. / Moenne-Loccoz, P. / Rivera, M.
History
DepositionSep 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HasAp (Heme acquisition protein HasAp)
B: HasAp (Heme acquisition protein HasAp)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0364
Polymers37,8032
Non-polymers1,2332
Water4,504250
1
A: HasAp (Heme acquisition protein HasAp)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5182
Polymers18,9021
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HasAp (Heme acquisition protein HasAp)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5182
Polymers18,9021
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.700, 47.700, 141.290
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein HasAp (Heme acquisition protein HasAp)


Mass: 18901.535 Da / Num. of mol.: 2 / Fragment: HasAp (UNP residues 1 - 184)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: hasAp, PA3407 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: O69756
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.45 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES buffer (pH 6.0), 100 mM NH4Cl, and 80% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Oct 1, 2007 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. all: 36833 / Num. obs: 36833 / % possible obs: 93.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rmerge(I) obs: 0.031 / Net I/σ(I): 22.2
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.063 / Mean I/σ(I) obs: 12.7 / Num. unique all: 5430 / % possible all: 87.6

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
CrystalCleardata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1B2V

1b2v


Resolution: 1.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.1894 1105 -random
Rwork0.1658 ---
obs0.1658 36833 93.1 %-
all-36833 --
Refine analyze
FreeObs
Luzzati coordinate error0.17 Å0.14 Å
Luzzati d res low-5 Å
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2682 0 86 250 3018
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.62

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