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- PDB-3giw: CRYSTAL STRUCTURE OF a DUF574 family protein (SAV_2177) FROM STRE... -

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Basic information

Entry
Database: PDB / ID: 3giw
TitleCRYSTAL STRUCTURE OF a DUF574 family protein (SAV_2177) FROM STREPTOMYCES AVERMITILIS MA-4680 AT 1.45 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 / Unknown ligand / Methyltransferase
Function and homology information
Biological speciesStreptomyces avermitilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.45 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 1.45 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 6, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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: 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 1.5Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)30,8844
Polymers30,7001
Non-polymers1843
Water5,386299
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.716, 49.669, 45.132
Angle α, β, γ (deg.)90.000, 94.720, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-290-

HOH

21A-314-

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-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.36 Å3/Da / Density % sol: 47.88 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.0 M Na citrate, 0.1 M Sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97927
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 8, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979271
ReflectionResolution: 1.45→27.186 Å / Num. obs: 50240 / % possible obs: 94.8 % / Observed criterion σ(I): -3 / Redundancy: 4.063 % / Biso Wilson estimate: 15.987 Å2 / Rmerge(I) obs: 0.036 / Net I/σ(I): 13.4
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsDiffraction-ID% possible all
1.45-1.50.3332.517590185.9
1.5-1.560.2543.320604194.8
1.56-1.630.1844.520398195.2
1.63-1.720.1356.121723195.4
1.72-1.830.0928.621142195.8
1.83-1.970.06411.820506195.7
1.97-2.170.04317.120735195.7
2.17-2.480.03421.720356196.1
2.48-3.120.02825.720439196.4
3.12-27.1860.02331.120616196.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.45→27.186 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 1.909 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. AN UNIDENTIFIED LIGAND (UNL) WHICH LOOKS LIKE PHENYLALANINE OR A SIMILAR MOLECULE HAS BEEN MODELED IN THE PUTATIVE ACTIVE SITE. 5. GLYCEROL (GOL) FROM THE CRYOPROTECTANT HAS BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.176 2551 5.1 %RANDOM
Rwork0.156 ---
obs0.157 50239 98.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.51 Å2 / Biso mean: 18.557 Å2 / Biso min: 5.93 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å2-0.42 Å2
2---0.8 Å20 Å2
3---1.08 Å2
Refinement stepCycle: LAST / Resolution: 1.45→27.186 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2023 0 24 299 2346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222207
X-RAY DIFFRACTIONr_bond_other_d0.0040.021496
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.9713026
X-RAY DIFFRACTIONr_angle_other_deg1.00333641
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.865291
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.73523.019106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.9615358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1081523
X-RAY DIFFRACTIONr_chiral_restr0.0990.2335
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022520
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02451
X-RAY DIFFRACTIONr_nbd_refined0.2190.2469
X-RAY DIFFRACTIONr_nbd_other0.2030.21637
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21059
X-RAY DIFFRACTIONr_nbtor_other0.0810.21080
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2211
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1020.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1740.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2860.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.231
X-RAY DIFFRACTIONr_mcbond_it1.24921405
X-RAY DIFFRACTIONr_mcbond_other0.3072539
X-RAY DIFFRACTIONr_mcangle_it1.81532227
X-RAY DIFFRACTIONr_scbond_it1.7192898
X-RAY DIFFRACTIONr_scangle_it2.4983785
LS refinement shellResolution: 1.45→1.49 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 179 -
Rwork0.207 3214 -
all-3393 -
obs--91.46 %
Refinement TLS params.Method: refined / Origin x: 44.7045 Å / Origin y: 2.7946 Å / Origin z: 15.1233 Å
111213212223313233
T-0.0285 Å20.0001 Å20.0053 Å2--0.0225 Å2-0.0053 Å2---0.0485 Å2
L0.819 °20.1055 °20.1548 °2-1.2003 °2-0.0841 °2--0.2864 °2
S-0.0167 Å °-0.0213 Å °0.0474 Å °-0.0118 Å °-0.0006 Å °-0.0593 Å °-0.0115 Å °0.0085 Å °0.0173 Å °

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