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- PDB-7emq: Crystal Structure of HasAp Capturing Manganese Tetraphenylporphyrin -

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Basic information

Entry
Database: PDB / ID: 7emq
TitleCrystal Structure of HasAp Capturing Manganese 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 / Mn-5,10,15,20-Tetraphenylporphyrin / PHOSPHATE ION / Heme acquisition protein HasAp
Function and homology information
Biological speciesPseudomonas aeruginosa str. PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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
B: Heme acquisition protein HasAp
C: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,01719
Polymers56,7053
Non-polymers4,31316
Water7,386410
1
A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8854
Polymers18,9021
Non-polymers9843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-4 kcal/mol
Surface area8290 Å2
MethodPISA
2
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4406
Polymers18,9021
Non-polymers1,5395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8040 Å2
MethodPISA
3
C: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6929
Polymers18,9021
Non-polymers1,7908
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.802, 84.802, 84.485
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Heme acquisition protein HasAp


Mass: 18901.535 Da / Num. of mol.: 3
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

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Non-polymers , 6 types, 426 molecules

#2: Chemical ChemComp-J7X / Mn-5,10,15,20-Tetraphenylporphyrin


Mass: 667.658 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C44H28MnN4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CXS / 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID


Mass: 221.317 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H19NO3S / Comment: pH buffer*YM
#5: Chemical
ChemComp-NHE / 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID / N-CYCLOHEXYLTAURINE / CHES


Mass: 207.290 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H17NO3S / Comment: pH buffer*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.08 % / Mosaicity: 0.13 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5
Details: 100mM CAPS/NaOH (pH10.5), 1.2M Sodium phosphate monobasic/0.8M pottasium phosphate dibasic, 0.2M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RAYONIX MX225-HS / Detector: CCD / Date: Dec 18, 2018
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→48.9 Å / Num. obs: 95073 / % possible obs: 99.6 % / Redundancy: 14.5 % / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.018 / Rrim(I) all: 0.071 / Net I/σ(I): 24.4 / Num. measured all: 1380059 / Scaling rejects: 5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.5-1.539.41.114087843370.6240.3751.175293
8.22-48.914.10.03387436180.9990.0090.03575.499.3

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELL

3ell


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.436 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1648 4921 5.2 %RANDOM
Rwork0.1209 ---
obs0.1231 90071 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 132.24 Å2 / Biso mean: 19.98 Å2 / Biso min: 11.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å2-0 Å2-0 Å2
2--0.23 Å2-0 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3972 0 291 410 4673
Biso mean--34.61 32.79 -
Num. residues----547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0134668
X-RAY DIFFRACTIONr_bond_other_d0.0020.0183910
X-RAY DIFFRACTIONr_angle_refined_deg1.9341.7146444
X-RAY DIFFRACTIONr_angle_other_deg1.6491.6549149
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365609
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73724.722180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.92815592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.151156
X-RAY DIFFRACTIONr_chiral_restr0.1080.2592
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.025564
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02969
X-RAY DIFFRACTIONr_rigid_bond_restr3.90638578
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 398 -
Rwork0.228 6173 -
all-6571 -
obs--93.43 %

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