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- PDB-7emw: Crystal Structure of the HasAp V37G/K59Q Mutant Capturing Iron Te... -

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Basic information

Entry
Database: PDB / ID: 7emw
TitleCrystal Structure of the HasAp V37G/K59Q Mutant Capturing Iron Tetraphenylporphyrin
ComponentsHeme acquisition protein HasAp
KeywordsTRANSPORT PROTEIN / HEME ACQUISITION PROTEIN
Function / homologyHaem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / metal ion binding / Chem-MQP / Heme acquisition protein HasAp
Function and homology information
Biological speciesPseudomonas aeruginosa str. PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsShisaka, Y. / Sakakibara, E. / Sugimoto, H. / Shoji, O.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP18H02084 Japan
Japan Science and TechnologyJPMJCR15P3 Japan
Japan Society for the Promotion of Science (JSPS)JP18J15250 Japan
CitationJournal: Chembiochem / Year: 2022
Title: Tetraphenylporphyrin Enters the Ring: First Example of a Complex between Highly Bulky Porphyrins and a Protein.
Authors: Shisaka, Y. / Sakakibara, E. / Suzuki, K. / Stanfield, J.K. / Onoda, H. / Ueda, G. / Hatano, M. / Sugimoto, H. / Shoji, O.
History
DepositionApr 14, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)19,6923
Polymers18,9311
Non-polymers7612
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-1 kcal/mol
Surface area8030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.700, 58.340, 65.320
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Heme acquisition protein HasAp


Mass: 18931.457 Da / Num. of mol.: 1 / Mutation: V37G/K59Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa str. PAO1 (bacteria)
Gene: hasAp, PA3407 / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: G3XD33
#2: Chemical ChemComp-MQP / [5,10,15,20-tetraphenylporphyrinato(2-)-kappa~4~N~21~,N~22~,N~23~,N~24~]iron / Fe-5,10,15,20-Tetraphenylporphyrin


Mass: 668.565 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H28FeN4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.6 / Details: 50mM Citric acid/NaOH (pH 3.6), 10% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2020
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7 Å / Relative weight: 1
ReflectionResolution: 1.12→43.51 Å / Num. obs: 72261 / % possible obs: 100 % / Redundancy: 39.483 % / Biso Wilson estimate: 22.925 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.071 / Χ2: 0.856 / Net I/σ(I): 24.82 / Num. measured all: 2853115 / Scaling rejects: 1559
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.12-1.1538.8484.391.2205663529752940.4874.44799.9
1.15-1.1840.983.4411.76210350513451330.6583.483100
1.18-1.2139.9662.6722.43200392501450140.7892.706100
1.21-1.2539.8422.113.27193831486548650.8492.137100
1.25-1.2942.061.6514.61197852470447040.9261.671100
1.29-1.3441.7691.1916.57190509456145610.9661.205100
1.34-1.3941.4310.8729.26184657445744570.9830.883100
1.39-1.4540.7860.65612.21171792421242120.9910.664100
1.45-1.5139.3280.46616.46161401410441040.9950.472100
1.51-1.5839.1460.32422.03153767392839280.9970.328100
1.58-1.6740.6270.23728.75151131372037200.9980.24100
1.67-1.7737.8890.17134.87133975353735360.9990.173100
1.77-1.8940.5410.12246.02135365333933390.9990.123100
1.89-2.0439.3370.08955.86122809312231220.9990.09100
2.04-2.2437.8860.07263.2108051285228520.9990.073100
2.24-2.536.3690.06168.5195323262326210.9990.06299.9
2.5-2.8933.9410.05371.65781332310230210.05499.7
2.89-3.5435.2070.04780.07702741996199610.048100
3.54-5.0136.0590.05184.7656576157115690.9990.05299.9
5.01-43.5133.5450.05581.18312649359320.9980.05699.7

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELL

3ell


Resolution: 1.12→43.51 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.001 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.03 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1586 3649 5.1 %RANDOM
Rwork0.1429 ---
obs0.1437 68537 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.67 Å2 / Biso mean: 21.938 Å2 / Biso min: 14.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å2-0 Å20 Å2
2--0.73 Å2-0 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.12→43.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1243 0 55 138 1436
Biso mean--19.72 35.26 -
Num. residues----172
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131687
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181365
X-RAY DIFFRACTIONr_angle_refined_deg1.6121.6732355
X-RAY DIFFRACTIONr_angle_other_deg1.6371.5973205
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4215237
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.47225.07765
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69115216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg37.032151
X-RAY DIFFRACTIONr_chiral_restr0.0780.2214
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022109
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02382
X-RAY DIFFRACTIONr_rigid_bond_restr2.3833051
LS refinement shellResolution: 1.12→1.149 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 266 -
Rwork0.289 5016 -
all-5282 -
obs--99.85 %

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