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- PDB-7vf7: Crystal Structure of HasAp with Co-octaethylporphyrin -

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Basic information

Entry
Database: PDB / ID: 7vf7
TitleCrystal Structure of HasAp with Co-octaethylporphyrin
ComponentsHeme acquisition protein HasAp
KeywordsMETAL TRANSPORT / Heme acquisition protein
Function / homologyHaem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / metal ion binding / Co-octaethylporphyrin / DI(HYDROXYETHYL)ETHER / Heme acquisition protein HasAp
Function and homology information
Biological speciesPseudomonas aeruginosa str. PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsTakiguchi, A. / Sakakibara, E. / Sugimoto, H. / Shoji, O. / Shinokubo, H.
Funding support Japan, 7items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP17H01190 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP19KK0138 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)17H05896 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)18H02396 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)JP18H02084 Japan
Japan Society for the Promotion of Science (JSPS)JP20J11437 Japan
Japan Society for the Promotion of Science (JSPS)JP21J15614 Japan
CitationJournal: To Be Published
Title: Crystal Structure of HasAp with Co-octaethylporphyrin
Authors: Takiguchi, A. / Sakakibara, E. / Sugimoto, H. / Shoji, O. / Shinokubo, H.
History
DepositionSep 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6788
Polymers56,7053
Non-polymers1,9735
Water8,953497
1
A: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6914
Polymers18,9021
Non-polymers7903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4932
Polymers18,9021
Non-polymers5921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Heme acquisition protein HasAp
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4932
Polymers18,9021
Non-polymers5921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.280, 76.120, 168.620
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: 18901.535 Da / Num. of mol.: 3 / 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-6KI / Co-octaethylporphyrin


Mass: 591.695 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C36H44CoN4 / 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: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% PEG 8000, 100mM sodium acetate/acetic acid (pH 4.5), 200mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 9, 2021
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→45.26 Å / Num. obs: 131672 / % possible obs: 100 % / Redundancy: 28.721 % / Biso Wilson estimate: 26.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.111 / Rrim(I) all: 0.113 / Χ2: 0.813 / Net I/σ(I): 15.59 / Num. measured all: 3781691 / Scaling rejects: 747
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
1.35-1.3927.3224.5341.25262618961396120.5044.618100
1.39-1.4227.9083.3081.62261555937293720.6273.368100
1.42-1.4629.2922.5072.2267938914891470.752.55100
1.46-1.5128.9881.7483.06257009886788660.8511.778100
1.51-1.5628.4151.3034.03244848861786170.9091.326100
1.56-1.6127.8460.9785.16231989833183310.9460.996100
1.61-1.6728.1940.7216.86226571803680360.9660.734100
1.67-1.7429.8120.5419.1231429776477630.9820.551100
1.74-1.8229.5610.38611.92220820747074700.990.393100
1.82-1.9129.1210.27415.51207486712671250.9950.278100
1.91-2.0128.1840.1919.9192131681768170.9970.194100
2.01-2.1328.6880.14624.61184092641664170.9980.149100
2.13-2.2830.4670.12128.91184660606160610.9980.123100
2.28-2.4629.970.10631.69170438568756870.9990.108100
2.46-2.728.480.09434.47148977523152310.9980.095100
2.7-3.0228.1580.08338.3133498474147410.9990.085100
3.02-3.4929.7510.07243.88125848423042300.9990.073100
3.49-4.2729.3890.06446.88106623362836280.9990.065100
4.27-6.0427.1030.06145.9576864283628360.9990.062100
6.04-45.2627.4760.0646.2146297169216850.9980.06199.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRR rigid body: 0.594
Highest resolutionLowest resolution
Rotation45.22 Å1.9 Å

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ELL

3ell


Resolution: 1.35→45.26 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.976 / SU B: 1.819 / SU ML: 0.032 / SU R Cruickshank DPI: 0.0478 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.048 / ESU R Free: 0.045 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1621 6525 5 %RANDOM
Rwork0.1375 ---
obs0.1388 125044 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: 78.03 Å2 / Biso mean: 23.63 Å2 / Biso min: 10.19 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.38 Å2-0 Å2
3----0.59 Å2
Refinement stepCycle: final / Resolution: 1.35→45.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3984 0 218 497 4699
Biso mean--20.83 37.79 -
Num. residues----549
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134779
X-RAY DIFFRACTIONr_bond_other_d0.0050.0184146
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.6986641
X-RAY DIFFRACTIONr_angle_other_deg1.5011.6529599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3665644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.08924.526190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.04715619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.905158
X-RAY DIFFRACTIONr_chiral_restr0.0730.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026438
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021047
X-RAY DIFFRACTIONr_rigid_bond_restr2.07738925
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 511 -
Rwork0.301 9098 -
all-9609 -
obs--99.97 %

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