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- PDB-7ems: Crystal Structure of the HasAp L85A Mutant Capturing Iron Tetraph... -

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Basic information

Entry
Database: PDB / ID: 7ems
TitleCrystal Structure of the HasAp L85A 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: 1.85 Å
AuthorsShisaka, Y. / 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)58,9878
Polymers56,7983
Non-polymers2,1905
Water6,467359
1
A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6933
Polymers18,9331
Non-polymers7612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6933
Polymers18,9331
Non-polymers7612
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6012
Polymers18,9331
Non-polymers6691
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)31.119, 125.104, 66.176
Angle α, β, γ (deg.)90.000, 99.450, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heme acquisition protein HasAp


Mass: 18932.506 Da / Num. of mol.: 3 / Mutation: L85A
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.: 3 / 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.26 Å3/Da / Density % sol: 45.55 % / Mosaicity: 0.13 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 100mM Tris-HCl (pH 8.5), 20% PEG 8000, 200mM MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Oct 10, 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: 1.85→45.16 Å / Num. obs: 41904 / % possible obs: 98.7 % / Redundancy: 3.5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.061 / Rrim(I) all: 0.116 / Net I/σ(I): 10.4 / Num. measured all: 147137 / Scaling rejects: 43
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
1.85-1.893.70.783947325840.6630.4740.9171.799.2
9.06-45.1630.03210993630.9970.0220.03932.294.2

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
REFMAC5.8.0257refinement
PDB_EXTRACT3.27data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELL

3ell


Resolution: 1.85→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.442 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.145 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 2155 5.2 %RANDOM
Rwork0.1666 ---
obs0.1685 39685 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.66 Å2 / Biso mean: 18.938 Å2 / Biso min: 11.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0 Å20.14 Å2
2--1.05 Å20 Å2
3----0.5 Å2
Refinement stepCycle: final / Resolution: 1.85→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3972 0 159 359 4490
Biso mean--16.88 28.71 -
Num. residues----549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134333
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173634
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.6865958
X-RAY DIFFRACTIONr_angle_other_deg1.4241.6038428
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4845560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.26824.246179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.28915552
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.828158
X-RAY DIFFRACTIONr_chiral_restr0.0630.2543
X-RAY DIFFRACTIONr_gen_planes_refined0.010.025132
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02957
LS refinement shellResolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 168 -
Rwork0.26 2889 -
all-3057 -
obs--99.12 %

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