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- PDB-2qne: Crystal structure of putative methyltransferase (ZP_00558420.1) f... -

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Basic information

Entry
Database: PDB / ID: 2qne
TitleCrystal structure of putative methyltransferase (ZP_00558420.1) from Desulfitobacterium hafniense Y51 at 2.30 A resolution
ComponentsPutative methyltransferase
KeywordsTRANSFERASE / ZP_00558420.1 / putative methyltransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Uncharacterized protein / UNKNOWN FUNCTION
Function / homology
Function and homology information


methanogenesis / Transferases; Transferring one-carbon groups; Methyltransferases / methyltransferase activity / one-carbon metabolic process / methylation
Similarity search - Function
Trimethylamine methyltransferase-like / Trimethylamine methyltransferase / MttB-like superfamily / Trimethylamine methyltransferase (MTTB) / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Glycine betaine methyltransferase
Similarity search - Component
Biological speciesDesulfitobacterium hafniense (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative methyltransferase (ZP_00558420.1) from Desulfitobacterium hafniense Y51 at 2.30 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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 1.4Jan 25, 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
Remark 300 BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ... BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999 SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative methyltransferase
B: Putative methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,76012
Polymers111,1402
Non-polymers62110
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.863, 123.863, 122.844
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-510-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: GLY / End label comp-ID: GLY / Refine code: 4 / Auth seq-ID: 0 - 474 / Label seq-ID: 19 - 493

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
DetailsSIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative methyltransferase /


Mass: 55569.844 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Desulfitobacterium hafniense (bacteria)
Strain: Y51 / Gene: ZP_00558420.1, DSY3156 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q24SP7
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.4549.75TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. A 2.30 ANGSTROM MAD DATA COLLECTED FROM ONE CRYSTAL WAS USED TO PHASE AND TRACE AN INITIAL MODEL. THE MODEL WAS THEN REFINED USING THE AMPLITUDES FROM A SECOND CRYSTAL THAT DIFFRACTED TO THE SAME RESOLUTION BUT BETTER QUALITY DATA.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop7.5NANODROP, 1.4M Na3Citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop7.5NANODROP, 1.4M Na3Citrate, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-110.99184
SYNCHROTRONSSRL BL11-120.918370, 0.979440, 0.979035
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDFeb 9, 2007Flat mirror (vertical focusing)
MARMOSAIC 325 mm CCD2CCDFeb 9, 2007Flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Single crystal Si(111) bent (horizontal focusing)SINGLE WAVELENGTHMx-ray1
2Single crystal Si(111) bent (horizontal focusing)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.991841
20.918371
30.979441
40.9790351
ReflectionResolution: 2.3→29.748 Å / Num. obs: 48701 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.08 / Rsym value: 0.08 / Net I/σ(I): 6.9
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.3-2.365.50.6021.31860033840.60298.7
2.36-2.425.50.4921.61916934750.492100
2.42-2.495.50.4061.91871834090.406100
2.49-2.575.50.3272.31810632890.327100
2.57-2.665.50.2752.71757231870.275100
2.66-2.755.50.2263.21699531000.226100
2.75-2.855.70.193.81692229920.19100
2.85-2.9710.90.2582.73135028880.258100
2.97-3.1110.1993.53054227640.199100
3.1-3.2511.10.1544.52936226570.154100
3.25-3.43110.1225.52771425140.122100
3.43-3.64110.1036.32644824080.103100
3.64-3.8910.90.0887.32463422530.088100
3.89-4.2110.0728.72292520900.072100
4.2-4.6110.05910.42149619580.059100
4.6-5.1410.90.05511.51943317820.055100
5.14-5.9410.80.06110.41686715560.061100
5.94-7.2710.70.05611.41442213480.056100
7.27-10.2910.20.03616.61077710610.036100
10.29-29.7488.80.0321.251815860.0396.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.748 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.952 / SU B: 13.011 / SU ML: 0.154 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.248 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN RIDING POSITIONS. 2. ATOM RECORD CONTAINS 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. THE ELECTRON DENSITIES FOR MANY REGIONS OF B CHAIN ARE VERY POOR AND MODELED BASED ON CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 2499 5.1 %RANDOM
Rwork0.158 ---
obs0.161 48668 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.715 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20.67 Å20 Å2
2--1.34 Å20 Å2
3----2 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7174 0 40 145 7359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227397
X-RAY DIFFRACTIONr_bond_other_d0.0020.024949
X-RAY DIFFRACTIONr_angle_refined_deg1.5721.9699996
X-RAY DIFFRACTIONr_angle_other_deg0.985312117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2265959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.01124.79309
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.966151231
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.921531
X-RAY DIFFRACTIONr_chiral_restr0.0950.21109
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021443
X-RAY DIFFRACTIONr_nbd_refined0.2110.21687
X-RAY DIFFRACTIONr_nbd_other0.1910.25249
X-RAY DIFFRACTIONr_nbtor_refined0.1790.23616
X-RAY DIFFRACTIONr_nbtor_other0.090.23799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2253
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3550.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1540.215
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.24
X-RAY DIFFRACTIONr_mcbond_it1.74934881
X-RAY DIFFRACTIONr_mcbond_other0.57231954
X-RAY DIFFRACTIONr_mcangle_it2.59257564
X-RAY DIFFRACTIONr_scbond_it4.94382856
X-RAY DIFFRACTIONr_scangle_it6.439112432
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 5858 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.310.5
MEDIUM THERMAL1.022
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 194 -
Rwork0.203 3355 -
obs-3549 99.5 %
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)
10.7462-0.193-0.2392.22361.30581.4550.02850.191-0.06070.0334-0.2040.23310.0271-0.27250.1755-0.2344-0.00720.0352-0.1398-0.1375-0.23528.972326.742439.7753
20.9479-0.2409-0.18812.63561.19081.74280.22330.3090.4799-1.11210.1554-0.9064-0.99080.321-0.37870.4188-0.10370.4061-0.01050.01180.135948.372854.313228.5515
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA0 - 47519 - 494
2X-RAY DIFFRACTION2BB0 - 47419 - 493

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