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- PDB-9xpd: Crystal Structure of Redesigned HasAsm Variant (51-mutation) with Heme -

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Basic information

Entry
Database: PDB / ID: 9xpd
TitleCrystal Structure of Redesigned HasAsm Variant (51-mutation) with Heme
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 / CITRIC ACID / PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Hemophore HasA
Function and homology information
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 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 16, 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)19,5297
Polymers18,5131
Non-polymers1,0166
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1070 Å2
ΔGint-18 kcal/mol
Surface area7890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)30.357, 140.528, 80.708
Angle α, β, γ (deg.)90, 90, 90
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 18513.000 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

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Non-polymers , 6 types, 98 molecules

#2: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.33 Å3/Da / Density % sol: 47.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1M imidazole-HCl, 1M sodium citrate tribasic

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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: 1.22→35 Å / Num. obs: 51927 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 11.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.145 / Rpim(I) all: 0.043 / Rrim(I) all: 0.152 / Χ2: 1 / Net I/σ(I): 12.3
Reflection shellResolution: 1.22→1.24 Å / Redundancy: 13.3 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 2484 / CC1/2: 0.659 / Rpim(I) all: 0.876 / Χ2: 1.16 / % possible all: 99.4

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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: 1.22→35 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.341 / SU ML: 0.026 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.038
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1775 2633 5.073 %
Rwork0.1549 49267 -
all0.156 --
obs-51900 99.783 %
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: 17.589 Å2
Baniso -1Baniso -2Baniso -3
1--0.267 Å20 Å2-0 Å2
2---0.04 Å20 Å2
3---0.307 Å2
Refinement stepCycle: LAST / Resolution: 1.22→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 69 92 1443
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121413
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161200
X-RAY DIFFRACTIONr_angle_refined_deg1.9351.831946
X-RAY DIFFRACTIONr_angle_other_deg0.6871.6962755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0045181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.131512
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.65752
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.29610186
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.5161062
X-RAY DIFFRACTIONr_chiral_restr0.1070.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02343
X-RAY DIFFRACTIONr_nbd_refined0.2260.2272
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21068
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2704
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2747
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.030.21
X-RAY DIFFRACTIONr_metal_ion_refined0.2690.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2940.215
X-RAY DIFFRACTIONr_nbd_other0.220.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1450.219
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1040.21
X-RAY DIFFRACTIONr_mcbond_it4.611.563703
X-RAY DIFFRACTIONr_mcbond_other4.5781.562703
X-RAY DIFFRACTIONr_mcangle_it6.5692.81882
X-RAY DIFFRACTIONr_mcangle_other6.5782.814883
X-RAY DIFFRACTIONr_scbond_it7.3911.865710
X-RAY DIFFRACTIONr_scbond_other7.4271.878692
X-RAY DIFFRACTIONr_scangle_it10.3693.2841061
X-RAY DIFFRACTIONr_scangle_other10.3653.2831062
X-RAY DIFFRACTIONr_lrange_it12.24616.6531612
X-RAY DIFFRACTIONr_lrange_other12.05516.3931599
X-RAY DIFFRACTIONr_rigid_bond_restr4.19832613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.22-1.2520.2761770.2913555X-RAY DIFFRACTION99.2553
1.252-1.2860.2721780.2623519X-RAY DIFFRACTION99.4084
1.286-1.3230.2561700.2263428X-RAY DIFFRACTION99.5573
1.323-1.3640.2371740.1893290X-RAY DIFFRACTION99.7696
1.364-1.4080.1991790.1493210X-RAY DIFFRACTION99.7645
1.408-1.4580.1921760.1313118X-RAY DIFFRACTION99.8787
1.458-1.5130.1491560.1173010X-RAY DIFFRACTION100
1.513-1.5740.1561690.1182880X-RAY DIFFRACTION99.9344
1.574-1.6440.1721500.1342784X-RAY DIFFRACTION100
1.644-1.7240.1591370.1332680X-RAY DIFFRACTION99.9291
1.724-1.8170.2021340.1482549X-RAY DIFFRACTION99.9627
1.817-1.9270.1691340.1472407X-RAY DIFFRACTION99.8428
1.927-2.060.161320.1372269X-RAY DIFFRACTION99.7922
2.06-2.2240.1491140.1412115X-RAY DIFFRACTION99.9552
2.224-2.4360.1811020.1461967X-RAY DIFFRACTION99.9034
2.436-2.7210.163870.161805X-RAY DIFFRACTION99.9472
2.721-3.1390.187920.1671591X-RAY DIFFRACTION100
3.139-3.8370.153780.1511363X-RAY DIFFRACTION99.9306
3.837-5.3940.186610.1481074X-RAY DIFFRACTION100
5.394-350.177330.188653X-RAY DIFFRACTION99.4203

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