[English] 日本語
Yorodumi
- PDB-3c3p: Crystal structure of a methyltransferase (NP_951602.1) from Geoba... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3c3p
TitleCrystal structure of a methyltransferase (NP_951602.1) from Geobacter sulfurreducens at 1.90 A resolution
ComponentsMethyltransferase
KeywordsTRANSFERASE / NP_951602.1 / O-Methyltransferase / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


O-methyltransferase activity / methylation
Similarity search - Function
Class I-like SAM-dependent O-methyltransferase / O-methyltransferase / SAM-dependent O-methyltransferase class I-type profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / SAM-dependent methyltransferase, putative
Similarity search - Component
Biological speciesGeobacter sulfurreducens PCA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a methyltransferase (NP_951602.1) from Geobacter sulfurreducens at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 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 / 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 30, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Methyltransferase
B: Methyltransferase
C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,34638
Polymers70,8313
Non-polymers2,51635
Water3,513195
1
A: Methyltransferase
B: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,82323
Polymers47,2202
Non-polymers1,60321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
MethodPISA
2
C: Methyltransferase
hetero molecules

C: Methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,04630
Polymers47,2202
Non-polymers1,82628
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.880, 76.044, 85.173
Angle α, β, γ (deg.)90.000, 118.270, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING ANALYSIS AND SIZE EXCLUSION CHROMATOGRAPHY SUPPORT THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

-
Components

#1: Protein Methyltransferase


Mass: 23610.211 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacter sulfurreducens PCA (bacteria)
Species: Geobacter sulfurreducens / Strain: PCA / DSM 12127 / Gene: NP_951602.1, GSU0544 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q74FR2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
13.1661.06TWO CRYSTALS WERE USED FOR THE SOLUTION OF THIS STRUCTURE. A 2.4 ANGSTROM MAD DATA SET 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 AN ENHANCED RESOLUTION OF 1.9 ANGSTROM. THE 2.4 ANGSTROM MAD PHASES FROM THE FIRST CRYSTAL WERE USED AS PHASE RESTRAINTS DURING THE REFINEMENT.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop10.3NANODROP, 0.2M Sodium chloride, 18.0% PEG 8000, 0.1M CAPS pH 10.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K
2772vapor diffusion, sitting drop10.5NANODROP, 0.2M Sodium chloride, 20.0% PEG 8000, 0.1M CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL11-111
SYNCHROTRONAPS 23-ID-D20.97939, 0.97953, 0.91840
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDNov 20, 2007Flat mirror (vertical focusing)
MARMOSAIC 300 mm CCD2CCDOct 25, 2007Adjustable focusing mirrors in K-B geometry
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) Double crystalSINGLE WAVELENGTHMx-ray1
2Si(111) Double crystalMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979391
30.979531
40.91841
ReflectionResolution: 1.9→28.318 Å / Num. obs: 69499 / % possible obs: 99.9 % / Redundancy: 3.8 % / Biso Wilson estimate: 35.05 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.953.80.5071.31933751260.507100
1.95-23.80.381.91896650270.38100
2-2.063.80.2992.51820548110.299100
2.06-2.123.80.2422.41795747380.242100
2.12-2.193.80.1933.91732645690.193100
2.19-2.273.80.1651.21671544060.165100
2.27-2.363.80.1156.31634642970.115100
2.36-2.453.80.10271561441040.102100
2.45-2.563.80.0947.31508939660.094100
2.56-2.693.80.0887.41424537380.088100
2.69-2.833.80.0768.51383336320.076100
2.83-33.80.0659.61300734070.065100
3-3.213.80.055111214831830.055100
3.21-3.473.80.04812.61147530000.048100
3.47-3.83.80.04114.31047327410.041100
3.8-4.253.80.03716.2951624950.037100
4.25-4.913.80.03915.2834421990.039100
4.91-6.013.80.04114.5713818790.041100
6.01-8.53.70.03716.3545114610.03799.8
8.5-28.3183.30.0322.423677200.0388.2

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALAdata scaling
PDB_EXTRACT3data extraction
MAR345CCDdata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.9→28.318 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.602 / SU ML: 0.085 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.127 / ESU R Free: 0.123
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. 1,2-ETHANEDIOL, CHLORIDE AND PEG MOLECULES FROM THE CRYSTALLIZATION CONDITIONS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. AMINO ACID LEU178 IN CHAIN A IS A RAMACHANDRAN OUTLIER AND IS IN A REGION OF WEAK ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 3515 5.1 %RANDOM
Rwork0.199 ---
obs0.201 69497 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.203 Å2
Baniso -1Baniso -2Baniso -3
1--0.41 Å20 Å20.24 Å2
2---0.3 Å20 Å2
3---0.93 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4466 0 161 195 4822
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0224870
X-RAY DIFFRACTIONr_bond_other_d0.0020.023444
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.9846580
X-RAY DIFFRACTIONr_angle_other_deg1.49638328
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.4575640
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.78722.682220
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.80315804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4851558
X-RAY DIFFRACTIONr_chiral_restr0.0950.2760
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215399
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02997
X-RAY DIFFRACTIONr_mcbond_it1.09722994
X-RAY DIFFRACTIONr_mcbond_other0.25221219
X-RAY DIFFRACTIONr_mcangle_it1.80534848
X-RAY DIFFRACTIONr_scbond_it1.27321876
X-RAY DIFFRACTIONr_scangle_it1.91831703
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 265 -
Rwork0.244 4833 -
all-5098 -
obs--100 %
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)
11.51080.07020.15831.89270.2481.7132-0.0794-0.3578-0.04680.40470.04340.01780.0085-0.1110.0359-0.00680.04510.0027-0.00890.0369-0.07229.1917-50.108122.4467
20.99010.0983-0.39161.73490.01080.8868-0.09870.0802-0.1113-0.28560.0644-0.11340.0310.00750.0343-0.04240.00770.0205-0.0943-0.0019-0.016434.4266-54.7691-2.3408
32.4333-0.044-0.07851.5251-0.28150.93450.07240.46980.1903-0.2476-0.0281-0.0218-0.01220.06-0.0443-0.0796-0.00030.00050.01020.0443-0.10393.9004-26.4859-12.5566
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 2083 - 209
2X-RAY DIFFRACTION2BB3 - 2084 - 209
3X-RAY DIFFRACTION3CC2 - 2083 - 209

+
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