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- PDB-4pz1: Crystal structure of a sHIP (UniProt Id: Q99XU0) mutant from Stre... -

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Basic information

Entry
Database: PDB / ID: 4pz1
TitleCrystal structure of a sHIP (UniProt Id: Q99XU0) mutant from Streptococcus pyogenes
ComponentssHIP
KeywordsUNKNOWN FUNCTION / helix-loop-helix
Function / homologyProtein of unknown function DUF4298 / Domain of unknown function (DUF4298) / identical protein binding / metal ion binding / DUF4298 domain-containing protein
Function and homology information
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsWisniewska, M. / Happonen, L. / Frick, I.-M. / Bjorck, L. / Streicher, W. / Malmstrom, J. / Wikstrom, M.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Functional and structural properties of a novel protein and virulence factor (Protein sHIP) in Streptococcus pyogenes.
Authors: Wisniewska, M. / Happonen, L. / Kahn, F. / Varjosalo, M. / Malmstrom, L. / Rosenberger, G. / Karlsson, C. / Cazzamali, G. / Pozdnyakova, I. / Frick, I.M. / Bjorck, L. / Streicher, W. / ...Authors: Wisniewska, M. / Happonen, L. / Kahn, F. / Varjosalo, M. / Malmstrom, L. / Rosenberger, G. / Karlsson, C. / Cazzamali, G. / Pozdnyakova, I. / Frick, I.M. / Bjorck, L. / Streicher, W. / Malmstrom, J. / Wikstrom, M.
History
DepositionMar 28, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: sHIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4624
Polymers11,3511
Non-polymers1113
Water1,40578
1
A: sHIP
hetero molecules

A: sHIP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9238
Polymers22,7012
Non-polymers2226
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_567x,-y+1,-z+21
Buried area6070 Å2
ΔGint-104 kcal/mol
Surface area11780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.370, 33.280, 89.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

#1: Protein sHIP


Mass: 11350.693 Da / Num. of mol.: 1 / Mutation: C65S, L84A, L88A, Y95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: M5005_Spy1730, SPy_2034 / Production host: Escherichia coli (E. coli) / References: UniProt: Q99XU0
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 1.93 Å3/Da / Density % sol: 36.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG 6000, 0.2 M calcium chloride, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03841 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Dec 12, 2013
RadiationMonochromator: Bent Si (111) crystal, horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03841 Å / Relative weight: 1
ReflectionResolution: 1.73→19.76 Å / Num. obs: 9571 / % possible obs: 98.8 % / Rmerge(I) obs: 0.064
Reflection shellResolution: 1.73→1.82 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4MER

4mer


Resolution: 1.73→19.76 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.935 / SU B: 2.071 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21065 461 4.8 %RANDOM
Rwork0.17794 ---
obs0.17957 9077 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.789 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0 Å2-0 Å2
2--0.3 Å2-0 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.73→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms792 0 3 78 873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.019811
X-RAY DIFFRACTIONr_bond_other_d0.0010.02743
X-RAY DIFFRACTIONr_angle_refined_deg1.2951.9551099
X-RAY DIFFRACTIONr_angle_other_deg0.79131717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.25596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.06825.90944
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6215140
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.774152
X-RAY DIFFRACTIONr_chiral_restr0.0740.2116
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02183
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 34 -
Rwork0.201 657 -
obs--97.74 %

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