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- PDB-3w8o: Crystal Structure of HasAp with Iron Phthalocyanine -

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Basic information

Entry
Database: PDB / ID: 3w8o
TitleCrystal Structure of HasAp with Iron Phthalocyanine
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-WPC / Heme acquisition protein HasAp
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsShirataki, C. / Shoji, O. / Terada, M. / 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 20, 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_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_label_asym_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
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2284
Polymers38,0912
Non-polymers1,1372
Water5,855325
1
A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6142
Polymers19,0461
Non-polymers5681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6142
Polymers19,0461
Non-polymers5681
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)153.868, 153.868, 36.699
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Heme acquisition protein HasAp


Mass: 19045.664 Da / Num. of mol.: 2 / 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-WPC / [29H,31H-phthalocyaninato(2-)-kappa~4~N~29~,N~30~,N~31~,N~32~]iron / Phthalocyanine containing Fe


Mass: 568.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H16FeN8
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 3.29 Å3/Da / Density % sol: 62.64 % / Mosaicity: 0.447 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M MES, 1.6M Magnesium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 13, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 43201 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 20.7 Å2 / Rmerge(I) obs: 0.088 / Χ2: 1.212 / Net I/σ(I): 13.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.85-1.928.20.36642601.187199.9
1.92-1.998.40.26442681.1071100
1.99-2.088.50.19843131.0931100
2.08-2.198.50.15742641.0751100
2.19-2.338.50.13142891.1241100
2.33-2.518.60.10743061.0811100
2.51-2.768.60.08643001.0891100
2.76-3.168.60.07943441.1281100
3.16-3.998.50.09943641.9361100
3.99-508.20.05144931.292199.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ELL

3ell


Resolution: 1.85→19.23 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2381 / WRfactor Rwork: 0.2004 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.876 / SU B: 2.673 / SU ML: 0.081 / SU R Cruickshank DPI: 0.1161 / SU Rfree: 0.1136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.116 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2179 2174 5.1 %RANDOM
Rwork0.1854 ---
obs0.187 43011 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 106.07 Å2 / Biso mean: 24.7156 Å2 / Biso min: 11.57 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→19.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2670 0 82 325 3077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.022900
X-RAY DIFFRACTIONr_bond_other_d0.0010.022514
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.9763986
X-RAY DIFFRACTIONr_angle_other_deg0.53435801
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0145390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.77425.304115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33215383
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.026154
X-RAY DIFFRACTIONr_chiral_restr0.060.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02683
LS refinement shellResolution: 1.847→1.895 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 144 -
Rwork0.241 2945 -
all-3089 -
obs--98.66 %

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