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- PDB-3ege: Crystal structure of Putative methyltransferase from antibiotic b... -

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Basic information

Entry
Database: PDB / ID: 3ege
TitleCrystal structure of Putative methyltransferase from antibiotic biosynthesis pathway (YP_324569.1) from ANABAENA VARIABILIS ATCC 29413 at 2.40 A resolution
ComponentsPutative methyltransferase from antibiotic biosynthesis pathway
KeywordsTRANSFERASE / YP_324569.1 / Putative methyltransferase from antibiotic biosynthesis pathway / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Methyltransferase domain
Function / homology
Function and homology information


S-adenosylmethionine-dependent methyltransferase activity / methylation
Similarity search - Function
: / Methyltransferase type 11 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MerR-family transcriptional regulator
Similarity search - Component
Biological speciesAnabaena variabilis ATCC 29413 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Putative methyltransferase from antibiotic biosynthesis pathway (YP_324569.1) from ANABAENA VARIABILIS ATCC 29413 at 2.40 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 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 16, 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: Putative methyltransferase from antibiotic biosynthesis pathway
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9462
Polymers29,8841
Non-polymers621
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)76.609, 76.609, 134.815
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-353-

HOH

DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative methyltransferase from antibiotic biosynthesis pathway / Putative MerR-family transcriptional regulator


Mass: 29883.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria)
Gene: YP_324569.1, Ava_4070 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M5R2
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 124 / 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: 3.82 Å3/Da / Density % sol: 67.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 31.0% ethylene glycol, 0.1M phosphate-citrate pH 4.2, 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: 0.97915 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 11, 2008 / 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: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→29.761 Å / Num. obs: 18494 / % possible obs: 99.8 % / Redundancy: 8.7 % / Biso Wilson estimate: 48.467 Å2 / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 6.022
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.465.60.7141.1750713350.71498.7
2.46-2.536.80.6471.1862412660.64799.9
2.53-2.68.60.5651.41110912870.565100
2.6-2.689.20.4871.61145812400.487100
2.68-2.779.30.38921114412030.389100
2.77-2.879.30.3332.31093611790.333100
2.87-2.989.30.2592.91039511200.259100
2.98-3.19.20.18741012710950.187100
3.1-3.249.20.1574.6963510430.157100
3.24-3.399.20.122690959880.122100
3.39-3.589.20.0957.688499670.095100
3.58-3.799.20.077984369190.077100
3.79-4.069.10.06610.277608540.066100
4.06-4.3890.06410.171117860.064100
4.38-4.890.0649.867287500.064100
4.8-5.378.90.0689.560236800.068100
5.37-6.28.80.0699.452796020.069100
6.2-7.598.60.0768.345255250.076100
7.59-10.738.30.0451334494140.045100
10.73-29.767.40.0441217882410.04495.2

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→29.761 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.948 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 10.455 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.217 / ESU R Free: 0.172
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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. EDO MOLECULE FROM THE CRYSTALLIZATION SOLUTION IS MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 946 5.1 %RANDOM
Rwork0.182 ---
obs0.184 18460 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 130.54 Å2 / Biso mean: 70.806 Å2 / Biso min: 47.24 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å2-0.51 Å20 Å2
2---1.02 Å20 Å2
3---1.53 Å2
Refinement stepCycle: LAST / Resolution: 2.4→29.761 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1990 0 4 124 2118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222047
X-RAY DIFFRACTIONr_bond_other_d0.0040.021371
X-RAY DIFFRACTIONr_angle_refined_deg1.6891.9532786
X-RAY DIFFRACTIONr_angle_other_deg1.42233329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3945248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.88523.762101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.03415339
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7141515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022274
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02432
X-RAY DIFFRACTIONr_nbd_refined0.170.2364
X-RAY DIFFRACTIONr_nbd_other0.1520.21419
X-RAY DIFFRACTIONr_nbtor_refined0.1530.2965
X-RAY DIFFRACTIONr_nbtor_other0.0740.2987
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2108
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1730.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2090.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.29
X-RAY DIFFRACTIONr_mcbond_it1.44321420
X-RAY DIFFRACTIONr_mcbond_other0.1792498
X-RAY DIFFRACTIONr_mcangle_it2.25541993
X-RAY DIFFRACTIONr_scbond_it3.6536912
X-RAY DIFFRACTIONr_scangle_it4.9358792
LS refinement shellResolution: 2.4→2.463 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 72 -
Rwork0.235 1269 -
all-1341 -
obs--98.31 %
Refinement TLS params.Method: refined / Origin x: 46.682 Å / Origin y: 29.363 Å / Origin z: 0.336 Å
111213212223313233
T-0.0409 Å2-0.1336 Å20.0336 Å2--0.2232 Å20.0227 Å2---0.2262 Å2
L0.7346 °20.1545 °20.3869 °2-2.3912 °21.9521 °2--2.1391 °2
S-0.1113 Å °-0.0292 Å °-0.0441 Å °-0.4589 Å °0.0388 Å °0.0352 Å °-0.2284 Å °-0.1576 Å °0.0725 Å °

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