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- PDB-3w8m: Crystal Structure of HasAp with Iron Salophen -

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Basic information

Entry
Database: PDB / ID: 3w8m
TitleCrystal Structure of HasAp with Iron Salophen
ComponentsHeme acquisition protein HasAp
KeywordsTRANSPORT 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
Chem-YOM / Heme acquisition protein HasAp
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å
AuthorsShirataki, C. / Shoji, O. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Inhibition of Heme Uptake in Pseudomonas aeruginosa by its Hemophore (HasAp ) Bound to Synthetic Metal Complexes
Authors: Shirataki, C. / Shoji, O. / Terada, M. / Ozaki, S. / Sugimoto, H. / Shiro, Y. / Watanabe, Y.
History
DepositionMar 19, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 9, 2014Group: Database references
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_ref_seq_dif.details / _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: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4162
Polymers19,0461
Non-polymers3701
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.212, 98.212, 32.662
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Protein Heme acquisition protein HasAp


Mass: 19045.664 Da / Num. of mol.: 1 / Fragment: UNP residues 1-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: PAO1 / Gene: hasAp, PA3407 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: G3XD33
#2: Chemical ChemComp-YOM / 2,2'-[1,2-PHENYLENEBIS(NITRILOMETHYLIDYNE)]BIS[PHENOLATO]](2-)-N,N',O,O']-IRON / SALOPHEN IRON CHELATE


Mass: 370.182 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H14FeN2O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.39 Å3/Da / Density % sol: 48.48 % / Mosaicity: 1.247 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.25
Details: 50mM MES, 1.7M Lithium sulfate, 12mM Magnesium sulfate, pH 5.25, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.46→50 Å / Num. obs: 30551 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 6.6 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.051 / Χ2: 1.05 / Net I/σ(I): 31.2
Reflection shellResolution: 1.46→1.51 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.247 / Mean I/σ(I) obs: 3.8 / Num. unique all: 2569 / Χ2: 0.786 / % possible all: 82

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELL

3ell


Resolution: 1.46→19.63 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.2224 / WRfactor Rwork: 0.1953 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8562 / SU B: 1.313 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0725 / SU Rfree: 0.0725 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.072 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2059 1529 5 %RANDOM
Rwork0.1818 ---
obs0.183 28953 96.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 75.4 Å2 / Biso mean: 19.6082 Å2 / Biso min: 10.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.46→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1335 0 25 166 1526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191468
X-RAY DIFFRACTIONr_bond_other_d0.0010.021298
X-RAY DIFFRACTIONr_angle_refined_deg1.2611.9582018
X-RAY DIFFRACTIONr_angle_other_deg0.74133005
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8775204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.67325.08559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85415203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.26152
X-RAY DIFFRACTIONr_chiral_restr0.0710.2219
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021768
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02354
LS refinement shellResolution: 1.461→1.499 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 92 -
Rwork0.281 1767 -
all-1859 -
obs--80.58 %

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