[English] 日本語
Yorodumi
- PDB-3vc2: Crystal structure of geranyl diphosphate C-methyltransferase from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3vc2
TitleCrystal structure of geranyl diphosphate C-methyltransferase from Streptomyces coelicolor A3(2) in complex with Mg2+, geranyl diphosphate, and S-adenosyl-L-homocysteine
ComponentsGeranyl diphosphate 2-C-methyltransferase
KeywordsTRANSFERASE / Rossmann fold / methyltransferase fold / SAM-dependent methyltransferase / C-methyltransferase / terpenoid biosynthesis / 2-methylisoborneol biosynthesis
Function / homology
Function and homology information


geranyl diphosphate 2-C-methyltransferase / C-methyltransferase activity / terpene metabolic process / S-adenosylmethionine-dependent methyltransferase activity / S-adenosyl-L-methionine binding / methylation / magnesium ion binding
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
GERANYL DIPHOSPHATE / S-ADENOSYL-L-HOMOCYSTEINE / Geranyl diphosphate 2-C-methyltransferase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.046 Å
AuthorsKoksal, M. / Christianson, D.W.
CitationJournal: Biochemistry / Year: 2012
Title: Structure of Geranyl Diphosphate C-Methyltransferase from Streptomyces coelicolor and Implications for the Mechanism of Isoprenoid Modification.
Authors: Koksal, M. / Chou, W.K. / Cane, D.E. / Christianson, D.W.
History
DepositionJan 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Geranyl diphosphate 2-C-methyltransferase
B: Geranyl diphosphate 2-C-methyltransferase
C: Geranyl diphosphate 2-C-methyltransferase
D: Geranyl diphosphate 2-C-methyltransferase
E: Geranyl diphosphate 2-C-methyltransferase
F: Geranyl diphosphate 2-C-methyltransferase
G: Geranyl diphosphate 2-C-methyltransferase
H: Geranyl diphosphate 2-C-methyltransferase
I: Geranyl diphosphate 2-C-methyltransferase
J: Geranyl diphosphate 2-C-methyltransferase
K: Geranyl diphosphate 2-C-methyltransferase
L: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)426,54433
Polymers420,48112
Non-polymers6,06321
Water20,9871165
1
A: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7634
Polymers35,0401
Non-polymers7233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4252
Polymers35,0401
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4252
Polymers35,0401
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7634
Polymers35,0401
Non-polymers7233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5213
Polymers35,0401
Non-polymers4802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4252
Polymers35,0401
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4252
Polymers35,0401
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7634
Polymers35,0401
Non-polymers7233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
9
I: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4252
Polymers35,0401
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
10
J: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7634
Polymers35,0401
Non-polymers7233
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
11
K: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4252
Polymers35,0401
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
12
L: Geranyl diphosphate 2-C-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,4252
Polymers35,0401
Non-polymers3841
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)98.128, 103.252, 204.132
Angle α, β, γ (deg.)90.00, 99.05, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Geranyl diphosphate 2-C-methyltransferase / GPP methyltransferase


Mass: 35040.090 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: orf4, SCBAC12C8.02, SCO7701 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9F1Y5, Transferases; Transferring one-carbon groups; Methyltransferases

-
Non-polymers , 5 types, 1186 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical
ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H20O7P2
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1165 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.36 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 100 mM Bis-Tris (pH 6.5), 25% polyethylene glycol 3350, 200 mM (NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 3, 2011
Details: Cryogenically cooled double crystal monochrometer with horizontal focusing sagittal bend second mono crystal with 4:1 magnification ratio and vertically focusing mirror
RadiationMonochromator: Double silicon(111) crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.046→50 Å / Num. all: 263284 / Num. obs: 246191 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 10.2
Reflection shellResolution: 2.046→2.12 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.1 / Num. unique all: 24533 / Rsym value: 0.574 / % possible all: 97.3

-
Processing

Software
NameVersionClassification
CBASSdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3VC1

3vc1


Resolution: 2.046→48.891 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0.05 / Phase error: 23.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1857 81 %random
Rwork0.1814 ---
all0.1817 246191 --
obs0.1817 228997 90.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.236 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.6823 Å2-0 Å24.2667 Å2
2---4.08 Å20 Å2
3----5.6023 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.046→48.891 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26197 0 397 1165 27759
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00727358
X-RAY DIFFRACTIONf_angle_d1.04437144
X-RAY DIFFRACTIONf_dihedral_angle_d15.9089868
X-RAY DIFFRACTIONf_chiral_restr0.0753897
X-RAY DIFFRACTIONf_plane_restr0.0044886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0461-2.10140.3061140.247315223X-RAY DIFFRACTION79
2.1014-2.16330.28321380.226516155X-RAY DIFFRACTION84
2.1633-2.23310.27141290.215316357X-RAY DIFFRACTION85
2.2331-2.31290.27731420.205716461X-RAY DIFFRACTION86
2.3129-2.40550.27721300.196816804X-RAY DIFFRACTION87
2.4055-2.5150.28011450.197116976X-RAY DIFFRACTION88
2.515-2.64760.23241270.187117178X-RAY DIFFRACTION89
2.6476-2.81340.20231550.191517609X-RAY DIFFRACTION91
2.8134-3.03060.23951450.190418031X-RAY DIFFRACTION93
3.0306-3.33560.22611580.187418514X-RAY DIFFRACTION96
3.3356-3.81810.19351510.16519007X-RAY DIFFRACTION98
3.8181-4.80970.17051620.140919247X-RAY DIFFRACTION99
4.8097-48.90540.20321610.165119578X-RAY DIFFRACTION99

+
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