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- PDB-1s7o: Crystal structure of putative DNA binding protein SP_1288 from St... -

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Basic information

Entry
Database: PDB / ID: 1s7o
TitleCrystal structure of putative DNA binding protein SP_1288 from Streptococcus pygenes
ComponentsHypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Putative DNA binding protein / Signal recognition particle / RNA polymerase Sigma Factor / X-Rat crystallography / UPF0122 / structure funded by NIH / PSI / Protein Structure Initiative / Berkeley Structural Genomics Center / BSGC
Function / homology
Function and homology information


Putative helix-turn-helix protein, YlxM/p13-like / : / Putative helix-turn-helix protein, YlxM / p13 like / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
UPF0122 protein SpyM3_0842 / UPF0122 protein SPy_1201/M5005_Spy0916
Similarity search - Component
Biological speciesStreptococcus pyogenes serotype M3 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsOganesyan, V. / Pufan, R. / DeGiovanni, A. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Structure of the putative DNA-binding protein SP_1288 from Streptococcus pyogenes.
Authors: Oganesyan, V. / Pufan, R. / DeGiovanni, A. / Yokota, H. / Kim, R. / Kim, S.H.
History
DepositionJan 29, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152
B: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152
C: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152


Theoretical massNumber of molelcules
Total (without water)40,8133
Polymers40,8133
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152
C: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152


Theoretical massNumber of molelcules
Total (without water)27,2092
Polymers27,2092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-20 kcal/mol
Surface area12560 Å2
MethodPISA, PQS
3
A: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152

A: Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152


Theoretical massNumber of molelcules
Total (without water)27,2092
Polymers27,2092
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)127.608, 69.685, 55.247
Angle α, β, γ (deg.)90.00, 103.04, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is probably dimer; molecules with chain identifiers B and C

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Components

#1: Protein Hypothetical UPF0122 protein SPy1201/SpyM3_0842/SPs1042/spyM18_1152


Mass: 13604.293 Da / Num. of mol.: 3 / Fragment: gi 15675166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M3 (bacteria)
Species: Streptococcus pyogenes / Strain: serotype M3 / Gene: SPY1201, SPYM3_0842, SPS1042, SPYM18_1152 / Plasmid: pB3.1325B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star / References: UniProt: P67253, UniProt: P0DG80*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.19 Å3/Da / Density % sol: 61.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.2
Details: Citric Acid, Ammonium Nitrate, pH 3.2, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 8, 2003 / Details: Mirrors
RadiationMonochromator: Double-crystal, Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.3→38 Å / Num. all: 40688 / Num. obs: 40607 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 39 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 19
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.336 / Mean I/σ(I) obs: 4 / Num. unique all: 4066 / Rsym value: 0.336 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5refinement
Blu-Icedata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.31→38.35 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.911 / SU B: 6.301 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.281 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23686 1053 5.1 %RANDOM
Rwork0.20651 ---
all0.2081 19476 --
obs0.2081 19476 98.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.264 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å2-0.4 Å2
2--2.2 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.31→38.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2691 0 0 103 2794
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222731
X-RAY DIFFRACTIONr_angle_refined_deg1.5581.9523688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6283315
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.00715498
X-RAY DIFFRACTIONr_chiral_restr0.10.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022082
X-RAY DIFFRACTIONr_nbd_refined0.2540.31237
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.5105
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3130.379
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3350.516
X-RAY DIFFRACTIONr_mcbond_it0.861.51587
X-RAY DIFFRACTIONr_mcangle_it1.74322568
X-RAY DIFFRACTIONr_scbond_it3.03831144
X-RAY DIFFRACTIONr_scangle_it5.0054.51120
LS refinement shellResolution: 2.308→2.368 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 61 -
Rwork0.224 1321 -
obs-1360 99.8 %
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)
14.82152.2332.83894.65594.39266.45620.1383-0.46680.06170.2855-0.08170.20010.1256-0.2581-0.05660.0392-0.01240.02720.09610.01770.0757.836544.360842.2744
23.8237-0.1634-1.34216.72281.06480.65690.0568-0.3721-0.17690.3477-0.18190.0312-0.03090.27260.12510.0384-0.002-0.04010.14520.02420.076558.57916.518832.2443
30.87521.03221.64582.21333.594911.9206-0.0462-0.19140.0581-0.0039-0.0748-0.0289-0.2271-0.21980.1210.08680.0366-0.00260.0721-0.00450.043385.822814.216749.8748
43.21520.43581.07231.8264-1.60962.8289-0.0081-0.17090.30610.2409-0.02480.2716-0.2017-0.06240.03290.06480.03620.03830.0583-0.03360.102279.067623.943223.5662
52.0745-1.9137-0.78755.97370.36342.21060.020.0949-0.1245-0.1908-0.06050.24920.1557-0.32310.04050.0571-0.0247-0.01210.10420.010.05578.8301-9.785431.6162
62.9860.87670.12323.1696-1.83941.3892-0.17110.3443-0.3006-0.14640.28680.21550.058-0.1017-0.11570.0596-0.0078-0.00940.0982-0.0340.076676.869615.873116.7497
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 747 - 74
2X-RAY DIFFRACTION2AA75 - 11175 - 111
3X-RAY DIFFRACTION3BB6 - 746 - 74
4X-RAY DIFFRACTION4BB75 - 11075 - 110
5X-RAY DIFFRACTION5CC5 - 745 - 74
6X-RAY DIFFRACTION6CC75 - 11175 - 111

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