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- PDB-9xok: Crystal Structure of Redesigned HasAsm Variant (51-mutation) with... -

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Basic information

Entry
Database: PDB / ID: 9xok
TitleCrystal Structure of Redesigned HasAsm Variant (51-mutation) with Iron Tetraphenylporphyrin
ComponentsHemophore HasA
KeywordsTRANSPORT PROTEIN / Heme transport protein
Function / homologyHaem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / extracellular region / metal ion binding / Chem-MQP / Hemophore HasA
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKim, S. / Sugimoto, H. / Shoji, O.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP24K22051 Japan
Japan Society for the Promotion of Science (JSPS)JP25H00910 Japan
Japan Society for the Promotion of Science (JSPS)JP24KJ1279 Japan
CitationJournal: Chem Lett. / Year: 2026
Title: Computational redesign of the heme acquisition protein HasA for enhanced thermostability while retaining its ability to bind synthetic metalloporphyrins
Authors: Kim, S. / Urushibata, A. / Yamauchi, N. / Sugimoto, H. / Nakano, S. / Shoji, O.
History
DepositionNov 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemophore HasA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0325
Polymers18,0831
Non-polymers9494
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area390 Å2
ΔGint-2 kcal/mol
Surface area7720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.282, 142.558, 81.231
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Hemophore HasA / Heme acquisition system protein A


Mass: 18083.465 Da / Num. of mol.: 1
Mutation: F11L, G12D, G13N, Y14L, S15T, I16L, H17Q, D18E, Y19F, L20F, G21N, Q22E, S25A, T26S, S58T, A61K, N62D, Q63G, Q88T, S93A, D96N, D102S, T103S, S104T, Q109T, V110E, D112Q, V113F, S114R, F115L, ...Mutation: F11L, G12D, G13N, Y14L, S15T, I16L, H17Q, D18E, Y19F, L20F, G21N, Q22E, S25A, T26S, S58T, A61K, N62D, Q63G, Q88T, S93A, D96N, D102S, T103S, S104T, Q109T, V110E, D112Q, V113F, S114R, F115L, N119G, L120W, S121T, L123E, Q124I, A125S, Q126E, T144S, G145T, A146P, E148L, T149Q, G153N, I154Q, D156Q, D157Q, V162T, D167M, Q168E, V169I, A170R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Gene: hasA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q54450
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium cacodylate-HCl, 2M ammonium sulfate, 0.2M NaCl

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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 X 6M / Detector: PIXEL / Date: Oct 15, 2025
RadiationMonochromator: Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→40.6 Å / Num. obs: 16787 / % possible obs: 99.7 % / Redundancy: 13.6 % / Biso Wilson estimate: 33.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.035 / Rrim(I) all: 0.096 / Χ2: 1 / Net I/σ(I): 16.2
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 12.8 % / Rmerge(I) obs: 2.496 / Mean I/σ(I) obs: 1 / Num. unique obs: 951 / CC1/2: 0.694 / Rpim(I) all: 0.715 / Rrim(I) all: 2.598 / Χ2: 0.97 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.100)refinement
XDSv Jun 30, 2024data reduction
Aimless0.8.2data scaling
MOLREP11.9.02phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→40.6 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.914 / SU B: 6.655 / SU ML: 0.189 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.177
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3301 807 4.811 %
Rwork0.2564 15966 -
all0.26 --
obs-16773 99.549 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 40.922 Å2
Baniso -1Baniso -2Baniso -3
1-0.238 Å20 Å2-0 Å2
2---3.274 Å20 Å2
3---3.036 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1226 0 66 62 1354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0121336
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161091
X-RAY DIFFRACTIONr_angle_refined_deg1.6141.7931838
X-RAY DIFFRACTIONr_angle_other_deg0.5331.6752503
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7935172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.235512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.87210153
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.1981053
X-RAY DIFFRACTIONr_chiral_restr0.0740.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02340
X-RAY DIFFRACTIONr_nbd_refined0.240.2326
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2060.21172
X-RAY DIFFRACTIONr_nbtor_refined0.1930.2707
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.2678
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.264
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0550.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1940.213
X-RAY DIFFRACTIONr_nbd_other0.1710.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.23
X-RAY DIFFRACTIONr_mcbond_it3.6224.218688
X-RAY DIFFRACTIONr_mcbond_other3.6174.217688
X-RAY DIFFRACTIONr_mcangle_it5.1287.555860
X-RAY DIFFRACTIONr_mcangle_other5.1257.558861
X-RAY DIFFRACTIONr_scbond_it3.5294.222648
X-RAY DIFFRACTIONr_scbond_other3.5274.225649
X-RAY DIFFRACTIONr_scangle_it5.3717.681978
X-RAY DIFFRACTIONr_scangle_other5.3687.682979
X-RAY DIFFRACTIONr_lrange_it7.60439.8661586
X-RAY DIFFRACTIONr_lrange_other7.6139.6921583
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.559460.4031147X-RAY DIFFRACTION98.7583
1.847-1.8970.394570.3711136X-RAY DIFFRACTION99.2512
1.897-1.9520.423550.3491075X-RAY DIFFRACTION99.1228
1.952-2.0120.401630.3351072X-RAY DIFFRACTION99.387
2.012-2.0780.403640.3421012X-RAY DIFFRACTION99.1705
2.078-2.1510.327550.3351005X-RAY DIFFRACTION99.1581
2.151-2.2310.371510.302964X-RAY DIFFRACTION99.8033
2.231-2.3220.379410.302947X-RAY DIFFRACTION99.4965
2.322-2.4250.404410.281893X-RAY DIFFRACTION99.6798
2.425-2.5430.425430.259890X-RAY DIFFRACTION99.8929
2.543-2.680.335400.305806X-RAY DIFFRACTION100
2.68-2.8420.463330.318785X-RAY DIFFRACTION99.8779
2.842-3.0370.387450.308758X-RAY DIFFRACTION99.8756
3.037-3.2790.359440.272673X-RAY DIFFRACTION100
3.279-3.5890.285340.246629X-RAY DIFFRACTION100
3.589-4.0090.34220.222601X-RAY DIFFRACTION100
4.009-4.6220.151240.171518X-RAY DIFFRACTION100
4.622-5.6430.227230.18460X-RAY DIFFRACTION100
5.643-7.9040.379160.214366X-RAY DIFFRACTION99.7389
7.904-40.60.231100.18229X-RAY DIFFRACTION99.5833

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