[English] 日本語
Yorodumi
- PDB-3d2l: Crystal structure of SAM-dependent methyltransferase (ZP_00538691... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3d2l
TitleCrystal structure of SAM-dependent methyltransferase (ZP_00538691.1) from EXIGUOBACTERIUM SP. 255-15 at 1.90 A resolution
ComponentsSAM-dependent methyltransferase
KeywordsTRANSFERASE / ZP_00538691.1 / SAM-dependent methyltransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Methyltransferase domain
Function / homology
Function and homology information


methyltransferase activity / methylation / metal ion binding
Similarity search - Function
S-adenosyl-L-methionine-dependent methyltransferases / Methyltransferase domain 25 / Methyltransferase domain / N-terminal domain of TfIIb / Single Sheet / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Methyltransferase type 12 / :
Similarity search - Component
Biological speciesExiguobacterium sibiricum 255-15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of SAM-dependent methyltransferase (ZP_00538691.1) from EXIGUOBACTERIUM SP. 255-15 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 8, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _pdbx_entry_details.has_protein_modification / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SAM-dependent methyltransferase
B: SAM-dependent methyltransferase
C: SAM-dependent methyltransferase
D: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,68310
Polymers112,5374
Non-polymers1466
Water9,296516
1
A: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1592
Polymers28,1341
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1833
Polymers28,1341
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1592
Polymers28,1341
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SAM-dependent methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1833
Polymers28,1341
Non-polymers492
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.830, 70.920, 77.190
Angle α, β, γ (deg.)116.570, 104.630, 102.320
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLN / Beg label comp-ID: GLN / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 5 / Auth seq-ID: 5 - 242 / Label seq-ID: 6 - 243

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsAUTHORS STATE THAT SIZE-EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

-
Components

#1: Protein
SAM-dependent methyltransferase


Mass: 28134.326 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Exiguobacterium sibiricum 255-15 (bacteria)
Gene: ZP_00538691.1, ExigDRAFT_1659 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q41FK2, UniProt: B1YKR8*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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 FOLLOWED BY THE TARGET SEQUENCE.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2000M MgCl2, 20.0000% PEG-8000, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 23, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→29.374 Å / Num. obs: 84662 / % possible obs: 92.2 % / Observed criterion σ(I): -3 / Redundancy: 7.86 % / Biso Wilson estimate: 30.367 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 14.73
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.9-1.970.6492.284626211976163.7
1.97-2.050.47936529616533189.4
2.05-2.140.3424.26587316733195.1
2.14-2.250.2246.16751217066195.6
2.25-2.390.1667.96932417478196
2.39-2.580.12510.17253918234196.5
2.58-2.840.07914.97011217690196.6
2.84-3.250.04822.47011117676197.2
3.25-4.080.03132.36921017605197.3
4.08-29.370.02438.46914217817196

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.004data extraction
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.374 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.943 / SU B: 7.801 / SU ML: 0.115 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.154 / ESU R Free: 0.145
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE 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 THE 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.MAGNESIUM WAS MODELED BASED ON CRYSTALLIZATION CONDITIONS AND COORDINATION GEOMETRY.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 4235 5 %RANDOM
Rwork0.187 ---
obs0.189 84658 93.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.362 Å2
Baniso -1Baniso -2Baniso -3
1-2.03 Å20.45 Å21.72 Å2
2---1.37 Å2-0.17 Å2
3---0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.374 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7631 0 6 516 8153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227937
X-RAY DIFFRACTIONr_bond_other_d0.0010.025174
X-RAY DIFFRACTIONr_angle_refined_deg1.5871.94610850
X-RAY DIFFRACTIONr_angle_other_deg0.933312620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7435987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66824.444396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.583151256
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3911539
X-RAY DIFFRACTIONr_chiral_restr0.0950.21194
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028975
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021660
X-RAY DIFFRACTIONr_nbd_refined0.2140.21516
X-RAY DIFFRACTIONr_nbd_other0.1950.25310
X-RAY DIFFRACTIONr_nbtor_refined0.1820.23823
X-RAY DIFFRACTIONr_nbtor_other0.0890.24041
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1540.2495
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1480.22
X-RAY DIFFRACTIONr_metal_ion_refined0.1030.29
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.2106
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1440.235
X-RAY DIFFRACTIONr_mcbond_it1.84135157
X-RAY DIFFRACTIONr_mcbond_other0.64731934
X-RAY DIFFRACTIONr_mcangle_it2.54657825
X-RAY DIFFRACTIONr_scbond_it4.68183466
X-RAY DIFFRACTIONr_scangle_it6.083113007
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1383MEDIUM POSITIONAL0.190.5
2B1383MEDIUM POSITIONAL0.20.5
3C1383MEDIUM POSITIONAL0.280.5
4D1383MEDIUM POSITIONAL0.260.5
1A1641LOOSE POSITIONAL0.45
2B1641LOOSE POSITIONAL0.425
3C1641LOOSE POSITIONAL0.585
4D1641LOOSE POSITIONAL0.565
1A1383MEDIUM THERMAL1.062
2B1383MEDIUM THERMAL0.862
3C1383MEDIUM THERMAL0.972
4D1383MEDIUM THERMAL1.072
1A1641LOOSE THERMAL2.3710
2B1641LOOSE THERMAL2.4710
3C1641LOOSE THERMAL2.7110
4D1641LOOSE THERMAL2.7310
LS refinement shellResolution: 1.899→1.948 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.355 208 -
Rwork0.269 3974 -
all-4182 -
obs--62.42 %
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)
11.1366-0.6255-0.35161.3042-0.13111.23460.0017-0.01130.03-0.0383-0.041-0.0217-0.15610.03360.0393-0.1184-0.0301-0.0182-0.09180.0011-0.053971.699930.444544.7822
23.4076-2.1164-2.53012.89671.55562.40180.0440.0553-0.1875-0.2751-0.2016-0.0033-0.0817-0.21810.1575-0.02990.0455-0.0203-0.06550.0045-0.088674.66627.108124.0353
30.9579-0.0776-0.2673.8696-0.60551.793-0.07220.0887-0.0885-0.08740.0193-0.108-0.0337-0.05730.0528-0.13420.03410.0175-0.1073-0.006-0.0493.8145-5.622353.8987
41.06091.3944-1.09713.6199-2.52972.6069-0.06630.0076-0.15610.3622-0.108-0.095-0.21750.0660.17440.03430.05930.0186-0.0970.0113-0.03111.5932-9.750774.5823
51.25270.2342-1.15231.9407-0.42833.4288-0.33360.0825-0.1611-0.05860.2108-0.11110.377-0.10330.12270.027-0.04980.04110.0629-0.1096-0.056616.723138.972978.903
62.06350.6353-2.26231.3121-2.28264.7336-0.26370.150.013-0.14690.2831-0.03860.5534-0.6739-0.01940.2534-0.138-0.05960.0701-0.0438-0.031815.386854.308164.4474
71.96620.7835-0.74242.1957-0.61511.1164-0.03930.04880.11220.06730.04430.08170.1151-0.0697-0.0051-0.14260.00830.0086-0.08760.0094-0.087938.75419.279749.943
80.96321.2790.07365.81621.462.20520.02010.0295-0.15770.2759-0.0539-0.38030.169-0.09920.0338-0.00480.016-0.0067-0.06010.0362-0.030741.6894-0.23758.037
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA5 - 1386 - 139
2X-RAY DIFFRACTION1AA201 - 242202 - 243
3X-RAY DIFFRACTION2AA139 - 200140 - 201
4X-RAY DIFFRACTION3BB5 - 1386 - 139
5X-RAY DIFFRACTION3BB201 - 242202 - 243
6X-RAY DIFFRACTION4BB139 - 200140 - 201
7X-RAY DIFFRACTION5CC1 - 1382 - 139
8X-RAY DIFFRACTION5CC201 - 242202 - 243
9X-RAY DIFFRACTION6CC139 - 200140 - 201
10X-RAY DIFFRACTION7DD5 - 1386 - 139
11X-RAY DIFFRACTION7DD201 - 242202 - 243
12X-RAY DIFFRACTION8DD139 - 200140 - 201

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more