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- PDB-1z0p: Crystal structure of the Protein of Unknown Function SPY1572 from... -

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Basic information

Entry
Database: PDB / ID: 1z0p
TitleCrystal structure of the Protein of Unknown Function SPY1572 from Streptococcus pyogenes
Componentshypothetical protein SPy1572
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Streptococcus pyogenes / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein of unknown function DUF1912 / SPy1572-like superfamily / Domain of unknown function (DUF1912) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha / Aldose 1-epimerase
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsZhang, R. / Lezondra, L. / Clancy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The 1.7A Crystal structure of the hypothetical protein SPy1572 from Streptococcus pyogenes
Authors: Zhang, R. / Lezondra, L. / Clancy, S. / Collart, F. / Joachimiak, A.
History
DepositionMar 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 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: hypothetical protein SPy1572


Theoretical massNumber of molelcules
Total (without water)9,9481
Polymers9,9481
Non-polymers00
Water1,18966
1
A: hypothetical protein SPy1572

A: hypothetical protein SPy1572


Theoretical massNumber of molelcules
Total (without water)19,8962
Polymers19,8962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area2580 Å2
ΔGint-24 kcal/mol
Surface area8960 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)67.583, 67.583, 28.592
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
DetailsThis protein existed as dimer.The second part of the biological assembly is generated by the axis: -x+y, -x, z

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Components

#1: Protein hypothetical protein SPy1572


Mass: 9947.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: M1 GAS / Gene: gi:13622656 / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99YR7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 1.885 Å3/Da / Density % sol: 32.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20% butanediol, 0.1M acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 4, 2004 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 16058 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 10.1 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 41.88
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 2.83 / Num. unique all: 828 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
SBC-Collectdata collection
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→25.69 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 481465.31 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 760 4.9 %RANDOM
Rwork0.22 ---
obs0.22 15405 95.6 %-
all-16114 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 81.5796 Å2 / ksol: 0.382325 e/Å3
Displacement parametersBiso mean: 32.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.25 Å20.61 Å20 Å2
2---0.25 Å20 Å2
3---0.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 1.7→25.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms611 0 0 66 677
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_dihedral_angle_d15.7
X-RAY DIFFRACTIONc_improper_angle_d0.63
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.367 116 5 %
Rwork0.338 2210 -
obs-2011 86.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
X-RAY DIFFRACTION3ION.PARAM

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