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- PDB-3hyn: Crystal structure of a putative signal transduction protein (eubr... -

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Basic information

Entry
Database: PDB / ID: 3hyn
TitleCrystal structure of a putative signal transduction protein (eubrec_0645) from eubacterium rectale atcc 33656 at 1.20 A resolution
ComponentsPutative signal transduction protein
KeywordsSIGNALING PROTEIN / Duf1863 family protein / nucleotide-binding protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyRossmann fold - #11200 / Thoeris protein ThsB, TIR-like domain / Thoeris protein ThsB, TIR-like domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Thoeris protein ThsB TIR-like domain-containing protein
Function and homology information
Biological speciesEubacterium rectale ATCC 33656 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative signal transduction protein (YP_002936568.1) from Eubacterium rectale at 1.20 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.3Jul 24, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: software / struct_conn / struct_ref_seq
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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

Downloads & links

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Assembly

Deposited unit
A: Putative signal transduction protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2032
Polymers22,0851
Non-polymers1181
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.797, 60.962, 76.701
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative signal transduction protein


Mass: 22084.646 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eubacterium rectale ATCC 33656 (bacteria)
Gene: YP_002936568.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: C4ZCS9*PLUS
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 1.84 Å3/Da / Density % sol: 33.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 40.0000% MPD, 0.1M Bicine pH 9.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 13, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97922 Å / Relative weight: 1
ReflectionResolution: 1.2→32.461 Å / Num. obs: 51559 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 8.178 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.2-1.240.3742.414177452995
1.24-1.290.3183181775194100
1.29-1.350.2683.7185085256100
1.35-1.420.2244.517865505799.9
1.42-1.510.1885.5185285220100
1.51-1.630.1477.418782528999.9
1.63-1.790.1219.217854505599.7
1.79-2.050.0921220302523299.6
2.05-2.580.07717.932414524099.8
2.58-32.4610.05623.636452548399

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0092refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→32.461 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.978 / Occupancy max: 1 / Occupancy min: 0.17 / SU B: 1.059 / SU ML: 0.021 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.034
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.85 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. (4R)-2-METHYLPENTANE-2,4-DIOL (MRD) MODELED IS PRESENT IN CRYSTALLIZATION SOLUTION. 4. CISPEPTIDE 28-29 ARE SUPPORTED BY DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.139 2621 5.1 %RANDOM
Rwork0.117 ---
obs0.118 51494 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 77.73 Å2 / Biso mean: 12.96 Å2 / Biso min: 3.76 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.2→32.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1499 0 8 301 1808
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221743
X-RAY DIFFRACTIONr_bond_other_d0.0010.021186
X-RAY DIFFRACTIONr_angle_refined_deg1.5331.9442391
X-RAY DIFFRACTIONr_angle_other_deg0.94932914
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445233
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49724.88990
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.49915308
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.899159
X-RAY DIFFRACTIONr_chiral_restr0.0930.2252
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022003
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02362
X-RAY DIFFRACTIONr_mcbond_it1.5961.51044
X-RAY DIFFRACTIONr_mcbond_other0.5251.5412
X-RAY DIFFRACTIONr_mcangle_it2.34721712
X-RAY DIFFRACTIONr_scbond_it3.2393699
X-RAY DIFFRACTIONr_scangle_it4.3714.5662
X-RAY DIFFRACTIONr_rigid_bond_restr1.37132929
LS refinement shellResolution: 1.2→1.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 190 -
Rwork0.201 3330 -
all-3520 -
obs--93.64 %

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