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- PDB-9w5y: Structure of heme transport protein Shr-NEAT2 from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 9w5y
TitleStructure of heme transport protein Shr-NEAT2 from Streptococcus pyogenes in complex with heme.
ComponentsStreptococcal hemoprotein receptor
KeywordsMETAL TRANSPORT / Heme binding Shr Streptococcus pyogenes Iron acquisition Antimicrobial strategy Heme transfer
Function / homology
Function and homology information


peptidoglycan-based cell wall / metal ion binding / plasma membrane
Similarity search - Function
Heme-binding protein Shr-like, Hb-interacting domain / Heme-binding protein Shr-like, Hb-interacting domain / : / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat ...Heme-binding protein Shr-like, Hb-interacting domain / Heme-binding protein Shr-like, Hb-interacting domain / : / NEAT domain / Iron Transport-associated domain / NEAT domain profile. / NEAr Transporter domain / NEAT domain superfamily / Leucine-rich repeat, SDS22-like subfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain.
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Streptococcal hemoprotein receptor
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsSenoo, A. / Caaveiro, J.M.M.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)24K18262 Japan
Japan Agency for Medical Research and Development (AMED)JP23ama121031 Japan
CitationJournal: J.Biol.Chem. / Year: 2026
Title: Structural basis for heme binding by the Shr protein from Streptococcus pyogenes.
Authors: Seki, K. / Senoo, A. / Nagatoishi, S. / Yanaka, S. / Nakakido, M. / Tsumoto, K. / Caaveiro, J.M.M.
History
DepositionAug 2, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Streptococcal hemoprotein receptor
B: Streptococcal hemoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,72511
Polymers35,8202
Non-polymers1,9059
Water1629
1
A: Streptococcal hemoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9116
Polymers17,9101
Non-polymers1,0015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-18 kcal/mol
Surface area9150 Å2
MethodPISA
2
B: Streptococcal hemoprotein receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8155
Polymers17,9101
Non-polymers9054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.684, 99.047, 123.762
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Streptococcal hemoprotein receptor / Heme-acquisition protein Shr / Heme-binding protein Shr / Hemoprotein binding receptor


Mass: 17909.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: shr, SPy_1798 / Production host: Escherichia coli (E. coli) / Strain (production host): BL23 / Variant (production host): DE3 / References: UniProt: Q99YA0
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.9 Å3/Da / Density % sol: 57.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 200 mM Lithium sulfate 100 mM TRIS-HCl 30% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 12, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.66→41.47 Å / Num. obs: 12321 / % possible obs: 100 % / Redundancy: 12.6 % / CC1/2: 1 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.019 / Net I/σ(I): 23.3
Reflection shellResolution: 2.66→2.79 Å / Redundancy: 13.6 % / Rmerge(I) obs: 1.01 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1621 / CC1/2: 0.898 / Rpim(I) all: 0.279 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
PDB_EXTRACTdata extraction
XDS20220820data reduction
Aimless0.8.2data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.66→41.47 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.921 / SU B: 32.964 / SU ML: 0.317 / Cross valid method: THROUGHOUT / ESU R: 0.796 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26165 636 5.2 %RANDOM
Rwork0.21466 ---
obs0.21711 11646 99.65 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 87.122 Å2
Baniso -1Baniso -2Baniso -3
1--2.5 Å20 Å2-0 Å2
2---4.51 Å20 Å2
3---7.02 Å2
Refinement stepCycle: 1 / Resolution: 2.66→41.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 121 9 2568
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122608
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162554
X-RAY DIFFRACTIONr_angle_refined_deg1.2161.913544
X-RAY DIFFRACTIONr_angle_other_deg0.4241.7685862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9385308
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.853536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.30210472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0520.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02572
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7416.4791238
X-RAY DIFFRACTIONr_mcbond_other2.7386.4791238
X-RAY DIFFRACTIONr_mcangle_it4.09611.6371544
X-RAY DIFFRACTIONr_mcangle_other4.09511.6361545
X-RAY DIFFRACTIONr_scbond_it3.6736.9771370
X-RAY DIFFRACTIONr_scbond_other3.3316.861341
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.12912.6011959
X-RAY DIFFRACTIONr_long_range_B_refined7.52260.822770
X-RAY DIFFRACTIONr_long_range_B_other7.52160.822771
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.66→2.729 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 49 -
Rwork0.353 850 -
obs--100 %
Refinement TLS params.

S32: 0.0517 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.08390.1257-1.38044.25340.35663.01210.0310.1850.4714-0.29210.0128-0.2028-0.0645-0.04380.05590.0314-0.00640.04640.01710.1155-17.9691-7.3726-30.5538
23.82460.2874-0.44943.1556-0.88413.24290.028-0.5093-0.21820.3233-0.090.05320.42180.06210.17840.0339-0.01920.1075-0.00080.0357-26.6933-23.7976-12.4917
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A975 - 1129
2X-RAY DIFFRACTION2B975 - 1129

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