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- PDB-7vm1: Crystal Structure of HasAp Capturing Iron Tetra(4-pyridyl)porphyrin -

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Basic information

Entry
Database: PDB / ID: 7vm1
TitleCrystal Structure of HasAp Capturing Iron Tetra(4-pyridyl)porphyrin
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 / Fe-Tetra(4-pyridyl)porphyrin / Heme acquisition protein HasAp
Function and homology information
Biological speciesPseudomonas aeruginosa str. PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsShisaka, Y. / Ueda, G. / 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
DepositionOct 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 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
D: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,57211
Polymers75,6064
Non-polymers2,9667
Water11,241624
1
A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5742
Polymers18,9021
Non-polymers6731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-2 kcal/mol
Surface area8210 Å2
MethodPISA
2
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5742
Polymers18,9021
Non-polymers6731
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-1 kcal/mol
Surface area8270 Å2
MethodPISA
3
C: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6663
Polymers18,9021
Non-polymers7652
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8050 Å2
MethodPISA
4
D: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7584
Polymers18,9021
Non-polymers8573
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.318, 43.981, 130.116
Angle α, β, γ (deg.)99.170, 93.900, 92.870
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Heme acquisition protein HasAp


Mass: 18901.535 Da / Num. of mol.: 4 / Fragment: UNP Residues 1-184
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-7OH / Fe-Tetra(4-pyridyl)porphyrin


Mass: 672.517 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C40H24FeN8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 624 / 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: 2.33 Å3/Da / Density % sol: 47.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100mM Tris-HCl (pH 8.5), 1260mM Ammonium sulfate, 200mM Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 8, 2020
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→43.37 Å / Num. obs: 44520 / % possible obs: 97.2 % / Redundancy: 2.596 % / Biso Wilson estimate: 24.745 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.086 / Rrim(I) all: 0.109 / Χ2: 0.896 / Net I/σ(I): 6.29 / Num. measured all: 115587 / Scaling rejects: 436
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
2-2.062.6650.3422.38555337932100.9270.42995
2.06-2.112.6610.3262.468549334732130.9280.41296
2.11-2.172.6290.2612.988150316131000.9510.32898.1
2.17-2.242.6170.2293.217947319430370.9580.28995.1
2.24-2.322.5270.1983.527515299729740.9690.2599.2
2.32-2.42.4270.1813.716885295928370.9750.22995.9
2.4-2.492.5230.1714.076794273826930.9760.21798.4
2.49-2.592.6420.1454.797160279127100.9830.18397.1
2.59-2.72.5120.135.096278255424990.9850.16597.8
2.7-2.842.5470.1066.086136248424090.9890.13497
2.84-2.992.7330.0927.076376236523330.9920.11598.6
2.99-3.172.7060.0778.245996227722160.9940.09897.3
3.17-3.392.6770.069.995592211220890.9950.07698.9
3.39-3.662.6210.05111.354922193318780.9960.06597.2
3.66-4.012.5510.04312.564475180617540.9980.05497.1
4.01-4.482.3960.03813.753774163515750.9970.04996.3
4.48-5.182.6020.03513.653624142913930.9980.04597.5
5.18-6.342.5030.04411.682953121511800.9970.05697.1
6.34-8.972.8030.03612.8625459199080.9980.04598.8
8.97-43.372.6580.02516.1113615195120.9990.03298.7

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Processing

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

3ell


Resolution: 2→43.37 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 6.405 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.288 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2604 2227 5 %RANDOM
Rwork0.2292 ---
obs0.2307 42292 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 58.42 Å2 / Biso mean: 17.047 Å2 / Biso min: 0.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.18 Å2-0.57 Å2-0.09 Å2
2--1.49 Å2-1.63 Å2
3----0.66 Å2
Refinement stepCycle: final / Resolution: 2→43.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 214 624 6142
Biso mean--15.42 27.53 -
Num. residues----731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135919
X-RAY DIFFRACTIONr_bond_other_d0.0030.0184959
X-RAY DIFFRACTIONr_angle_refined_deg1.5731.6868166
X-RAY DIFFRACTIONr_angle_other_deg1.6631.60311546
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.315792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.69324.625240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99615769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.853159
X-RAY DIFFRACTIONr_chiral_restr0.0690.2754
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027063
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021276
LS refinement shellResolution: 2.005→2.057 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 160 -
Rwork0.332 3048 -
all-3208 -
obs--95 %

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