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- PDB-3go4: Crystal structure of a duf574 family protein (sav_2177) from stre... -

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Basic information

Entry
Database: PDB / ID: 3go4
TitleCrystal structure of a duf574 family protein (sav_2177) from streptomyces avermitilis ma-4680 at 1.80 A resolution
ComponentsProtein of unknown function DUF574
KeywordsUNKNOWN FUNCTION / Rossmann-fold protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyS-adenosyl-L-methionine dependent methyltransferase, SAV2177 type / S-adenosyl methyltransferase / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / S-ADENOSYL-L-HOMOCYSTEINE / Methyltransferase
Function and homology information
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Rossmann-fold protein of unknown function (DUF574) (NP_823353.1) from Streptomyces avermitilis MA-4680 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 18, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: pdbx_struct_special_symmetry / software / struct_conn
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
Revision 1.4Feb 1, 2023Group: 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 1.5Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein of unknown function DUF574
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2434
Polymers30,7001
Non-polymers5433
Water3,621201
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.637, 49.439, 77.811
Angle α, β, γ (deg.)90.000, 123.800, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-290-

HOH

21A-318-

HOH

31A-450-

HOH

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Components

#1: Protein Protein of unknown function DUF574


Mass: 30700.152 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces avermitilis (bacteria) / Strain: MA-4680 / Gene: NP_823353.1, SAV2177, SAV_2177 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q82L35
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 2.46 Å3/Da / Density % sol: 50.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: NANODROP, 0.2M Sodium chloride, 2.0M Ammonium sulfate, 0.1M Sodium cacodylate pH 6.5, Additive: 0.001 M S-adenosyl-L-homocysteine, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 22, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91837 Å / Relative weight: 1
ReflectionResolution: 1.8→27.482 Å / Num. obs: 26949 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.486 Å2 / Rmerge(I) obs: 0.099
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.8-1.860.4781.682134709192.4
1.86-1.940.388297525537194.2
1.94-2.030.2742.792265235194.9
2.03-2.130.2073.485554876195
2.13-2.270.1674.295385405195.1
2.27-2.440.137590425121195.9
2.44-2.690.11693455323196.2
2.69-3.070.0827.691145163196.2
3.07-3.870.05811.193345298196.5
3.87-27.4820.04813.793475309196.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GIW

3giw


Resolution: 1.8→27.482 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.903 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 3.277 / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.138 / ESU R Free: 0.139 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. S-ADENOSYL HOMOCYSTEINE (SAH) USED IN CO-CRYSTALLIZATION HAS BEEN MODELED IN THE PUTATIVE ACTIVE SITE. 4. SULFATE (SO4) AND 1,2-ETHANEDIOL (EDO) FROM THE CRYSTALLIZATION AND CRYOPROTECTION CONDITION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. RESIDUE D259 IS A RAMACHANDRAN OUTLIER IN A REGION OF POOR ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1345 5 %RANDOM
Rwork0.2 ---
obs0.202 26949 96.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 44.03 Å2 / Biso mean: 17.22 Å2 / Biso min: 5.33 Å2
Baniso -1Baniso -2Baniso -3
1-3.12 Å20 Å20.59 Å2
2---1.93 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 35 201 2259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222148
X-RAY DIFFRACTIONr_bond_other_d0.0010.021442
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9862940
X-RAY DIFFRACTIONr_angle_other_deg0.95333509
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6195275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96923.3100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.33415338
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6811521
X-RAY DIFFRACTIONr_chiral_restr0.0970.2330
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212419
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02429
X-RAY DIFFRACTIONr_mcbond_it1.1621337
X-RAY DIFFRACTIONr_mcbond_other0.312529
X-RAY DIFFRACTIONr_mcangle_it1.78332162
X-RAY DIFFRACTIONr_scbond_it1.262811
X-RAY DIFFRACTIONr_scangle_it1.9453771
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 99 -
Rwork0.29 1844 -
all-1943 -
obs--94.5 %

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