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- PDB-6dkq: Crystal structure of the Shr Hemoglobin Interacting Domain 2 -

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Basic information

Entry
Database: PDB / ID: 6dkq
TitleCrystal structure of the Shr Hemoglobin Interacting Domain 2
ComponentsHeme-binding protein Shr
KeywordsTRANSPORT PROTEIN / Hemoglobin Interacting Domain / DUF-1533 / gram-positive pathogen
Function / homology
Function and homology information


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 ...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
Heme-binding protein Shr
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsMacdonald, R. / Cascio, D. / Collazo, M.J. / Clubb, R.T.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI52217 United States
Department of Energy (DOE, United States)DE-FC02-02ER63421 United States
National Science Foundation (NSF, United States)MCB-1716948 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM007185 United States
CitationJournal: J.Biol.Chem. / Year: 2018
Title: The Streptococcus pyogenes Shr protein captures human hemoglobin using two structurally unique binding domains.
Authors: Macdonald, R. / Cascio, D. / Collazo, M.J. / Phillips, M. / Clubb, R.T.
History
DepositionMay 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2018Provider: repository / Type: Initial release
Revision 1.1May 15, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation / Item: _citation.title
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heme-binding protein Shr
B: Heme-binding protein Shr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9845
Polymers24,6962
Non-polymers2883
Water2,036113
1
A: Heme-binding protein Shr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5403
Polymers12,3481
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Heme-binding protein Shr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4442
Polymers12,3481
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.470, 59.140, 102.710
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-binding protein Shr


Mass: 12347.937 Da / Num. of mol.: 2 / Fragment: residues 175-285
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: shr / Plasmid: pHis-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B0LFQ8
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
1238.4
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2951vapor diffusion, hanging drop4.550% PEG-400, 100mM sodium acetate, 0.2M lithium sulfate
2952vapor diffusion, hanging drop4.532.7% PEG-400, 100mM sodium acetate, 108mM lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→19.77 Å / Num. obs: 32509 / % possible obs: 99.7 % / Redundancy: 6.343 % / Biso Wilson estimate: 22.11 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.046 / Χ2: 1.058 / Net I/σ(I): 23.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.5-1.546.180.5723.1223420.9050.62598.4
1.54-1.585.9050.4274.2222740.9330.46999.8
1.58-1.636.4780.3345.6722690.9650.363100
1.63-1.686.6450.2627.3721630.9810.284100
1.68-1.736.5550.2119.0921460.9890.229100
1.73-1.796.4710.17810.8520570.9920.193100
1.79-1.866.1250.12814.6719620.9940.1499.7
1.86-1.946.3310.118.919130.9960.10999.8
1.94-2.026.7020.07624.4718500.9970.08399.9
2.02-2.126.6280.06429.6117670.9980.06999.9
2.12-2.236.4940.05432.2916710.9980.05999.9
2.23-2.376.0060.04833.9416000.9980.05399.9
2.37-2.536.4820.04437.4514950.9990.04899.6
2.53-2.746.7060.03941.7114080.9990.04399.8
2.74-36.4550.03546.2612990.9980.03899.9
3-3.356.0240.03248.5811760.9990.03599.5
3.35-3.875.9250.0351.5110480.9990.03399.5
3.87-4.746.2260.02954.339200.9990.03299.8
4.74-6.75.7440.02851.757220.9990.03199.3
6.7-19.775.7520.02853.054270.9990.031100

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.28 Å51.35 Å
Translation5.28 Å51.35 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHASER2.8.2phasing
BUSTER2.10.3refinement
PDB_EXTRACT3.24data extraction
XDSJun 1 2017data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.77 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.949 / SU R Cruickshank DPI: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.082 / SU Rfree Blow DPI: 0.08 / SU Rfree Cruickshank DPI: 0.079
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1625 5.01 %RANDOM
Rwork0.197 ---
obs0.198 32457 99.8 %-
Displacement parametersBiso max: 83.1 Å2 / Biso mean: 25.74 Å2 / Biso min: 12.15 Å2
Baniso -1Baniso -2Baniso -3
1--3.3821 Å20 Å20 Å2
2--1.592 Å20 Å2
3---1.7901 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.5→19.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1696 0 15 113 1824
Biso mean--54.15 29.91 -
Num. residues----221
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d626SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes51HARMONIC2
X-RAY DIFFRACTIONt_gen_planes243HARMONIC5
X-RAY DIFFRACTIONt_it1745HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion251SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2106SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1745HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2360HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion4.25
X-RAY DIFFRACTIONt_other_torsion16
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0 / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.2685 155 5.3 %
Rwork0.2388 2770 -
all0.2405 2925 -
obs--99.73 %
Refinement TLS params.

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 °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84810.25510.37580.61610.04292.4252-0.02970.10140.0643-0.0550.0275-0.0268-0.24420.05490.0022-0.0047-0.0024-0.0064-0.0473-0.0045-0.0488.590131.240512.9721
20.63010.07990.34240.98410.04212.0649-0.0306-0.04980.0163-0.00060.09350.02210.1205-0.1305-0.0629-0.0359-0.00980.0052-0.01910.0056-0.035819.339631.406136.2805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A174 - 285
2X-RAY DIFFRACTION2{ B|* }B174 - 283

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