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- PDB-2q7a: Crystal structure of the cell surface heme transfer protein Shp -

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Basic information

Entry
Database: PDB / ID: 2q7a
TitleCrystal structure of the cell surface heme transfer protein Shp
ComponentsCell surface heme-binding protein
Keywordsheme binding protein / beta sandwich
Function / homology
Function and homology information


heme binding / metal ion binding / membrane
Similarity search - Function
Cell surface protein Shp, haem-binding domain / Cell surface heme-binding protein Shp / Immunoglobulin-like - #1850 / NEAT domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Heme-binding protein
Similarity search - Component
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsAranda IV, R. / Worley, C.E. / Bitto, E. / Phillips Jr., G.N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Bis-methionyl coordination in the crystal structure of the heme-binding domain of the streptococcal cell surface protein Shp.
Authors: Aranda IV, R. / Worley, C.E. / Liu, M. / Bitto, E. / Cates, M.S. / Olson, J.S. / Lei, B. / Phillips Jr., G.N.
History
DepositionJun 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cell surface heme-binding protein
B: Cell surface heme-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,53415
Polymers33,2392
Non-polymers3,29513
Water5,819323
1
A: Cell surface heme-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2217
Polymers16,6201
Non-polymers1,6016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Cell surface heme-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3138
Polymers16,6201
Non-polymers1,6937
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-93 kcal/mol
Surface area14320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.317, 82.317, 106.054
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Detailsthere are two biological units of Shp180 in the asymmetric unit.

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Components

#1: Protein Cell surface heme-binding protein


Mass: 16619.590 Da / Num. of mol.: 2 / Fragment: Shp180 / Mutation: C37S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Gene: shp / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q06A48
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.8M ammonium sulfate, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDCrystal-ID
11
21
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 23-ID-D10.9793
SYNCHROTRONAPS 21-ID-D21.6531
Detector
TypeIDDetectorDate
MARMOSAIC 300 mm CCD1CCDApr 16, 2007
MARMOSAIC 225 mm CCD2CCDMar 10, 2007
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromator and K-B pair of biomorph mirrorsSINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
21.65311
ReflectionResolution: 2.1→80 Å / Num. obs: 23738 / % possible obs: 99.6 % / Redundancy: 10.8 % / Rmerge(I) obs: 0.115 / Χ2: 1.035 / Net I/σ(I): 20.4
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.593 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1496 / Χ2: 0.934 / % possible all: 95.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→41.17 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.359 / SU ML: 0.116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.17 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1194 5 %RANDOM
Rwork0.163 ---
obs0.166 23696 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 29.782 Å2
Baniso -1Baniso -2Baniso -3
1-0.69 Å20.35 Å20 Å2
2--0.69 Å20 Å2
3----1.04 Å2
Refinement stepCycle: LAST / Resolution: 2.1→41.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2332 0 226 323 2881
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222633
X-RAY DIFFRACTIONr_angle_refined_deg1.1642.1683605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2845306
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.67525.091110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94715402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3561510
X-RAY DIFFRACTIONr_chiral_restr0.0810.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022002
X-RAY DIFFRACTIONr_nbd_refined0.1950.21173
X-RAY DIFFRACTIONr_nbtor_refined0.2930.21774
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1410.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.230
X-RAY DIFFRACTIONr_mcbond_it0.7181.51548
X-RAY DIFFRACTIONr_mcangle_it1.10222412
X-RAY DIFFRACTIONr_scbond_it1.53131272
X-RAY DIFFRACTIONr_scangle_it2.2844.51183
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 102 -
Rwork0.221 1554 -
obs-1656 95.28 %

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