[English] 日本語
Yorodumi
- PDB-3cp8: Crystal structure of GidA from Chlorobium tepidum -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3cp8
TitleCrystal structure of GidA from Chlorobium tepidum
ComponentstRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA
KeywordsOXIDOREDUCTASE / Rossmann fold / FAD-binding domain / dinucleotide-binding motif / glutathione reductase / oxido-reductase / tRNA-modification / Cytoplasm / Flavoprotein / tRNA processing
Function / homology
Function and homology information


tRNA wobble uridine modification / tRNA methylation / flavin adenine dinucleotide binding / cytosol
Similarity search - Function
GidA associated domain, C-terminal subdomain / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG/GidA / Elongation Factor Tu (Ef-tu); domain 3 - #260 / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal / tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain / : / : / tRNA modifying enzyme MnmG/GidA C-terminal helical bundle / tRNA modifying enzyme MnmG/GidA C-terminal helical domain ...GidA associated domain, C-terminal subdomain / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG/GidA / Elongation Factor Tu (Ef-tu); domain 3 - #260 / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG, C-terminal / tRNA uridine 5-carboxymethylaminomethyl modification enzyme, C-terminal subdomain / : / : / tRNA modifying enzyme MnmG/GidA C-terminal helical bundle / tRNA modifying enzyme MnmG/GidA C-terminal helical domain / Glucose inhibited division protein A family signature 1. / GidA associated domain 3 / MnmG-related, conserved site / Glucose inhibited division protein A family signature 2. / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG-related / MnmG, N-terminal domain / Glucose inhibited division protein A / Elongation Factor Tu (Ef-tu); domain 3 / FAD/NAD(P)-binding domain superfamily / DNA polymerase; domain 1 / Arc Repressor Mutant, subunit A / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / tRNA uridine 5-carboxymethylaminomethyl modification enzyme MnmG
Similarity search - Component
Biological speciesChlorobium tepidum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsMeyer, S. / Scrima, A. / Versees, W. / Wittinghofer, A.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of the conserved tRNA-modifying enzyme GidA: implications for its interaction with MnmE and substrate
Authors: Meyer, S. / Scrima, A. / Versees, W. / Wittinghofer, A.
History
DepositionMar 31, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 24, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA
B: tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA
C: tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA
D: tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)284,5718
Polymers281,4294
Non-polymers3,1424
Water00
1
A: tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA
B: tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,2864
Polymers140,7142
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA
D: tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,2864
Polymers140,7142
Non-polymers1,5712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)120.505, 71.836, 171.934
Angle α, β, γ (deg.)90.00, 91.82, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
12A
22B
32C
13A
23B
33C
43D
14A
24B
34C
44D

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETTHRTHRAA1 - 47821 - 498
211METMETTHRTHRBB1 - 47821 - 498
311METMETTHRTHRCC1 - 47821 - 498
411METMETTHRTHRDD1 - 47821 - 498
521PROPROASPASPAA536 - 560556 - 580
621PROPROASPASPBB536 - 560556 - 580
721PROPROASPASPCC536 - 560556 - 580
821PROPROASPASPDD536 - 560556 - 580
112LEULEULEULEUAA582 - 619602 - 639
212LEULEULEULEUBB582 - 619602 - 639
312LEULEULEULEUCC582 - 619602 - 639
113FADFADFADFADAE622
213FADFADFADFADBF622
313FADFADFADFADCG622
413FADFADFADFADDH622
114ALAALAASPASPAA479 - 535499 - 555
214ALAALAASPASPBB479 - 535499 - 555
314ALAALAASPASPCC479 - 535499 - 555
414ALAALAASPASPDD479 - 535499 - 555

NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein
tRNA uridine 5-carboxymethylaminomethyl modification enzyme gidA / Glucose-inhibited division protein A


Mass: 70357.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chlorobium tepidum (bacteria) / Gene: CT2283 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(De3) / References: UniProt: Q8KA85, Oxidoreductases
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.46 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 13-15% PEG 8000, 200mM ammonium sulfate, 100mM TRIS, 78mM HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97955 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 23, 2006 / Details: MIRRORS
RadiationMonochromator: SAGITALLY - HORIZONTALLY FOCUSED SI(111) MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97955 Å / Relative weight: 1
ReflectionResolution: 3.2→120.4 Å / Num. all: 49192 / Num. obs: 48825 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 106.34 Å2 / Rsym value: 0.084 / Net I/σ(I): 26.8
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.641 / % possible all: 98.8

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3CP2

3cp2


Resolution: 3.2→44.85 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.901 / SU B: 71.56 / SU ML: 0.553 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.574 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27809 2471 5.1 %RANDOM
Rwork0.25444 ---
obs0.25568 46351 99.27 %-
all-49192 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 126.569 Å2
Baniso -1Baniso -2Baniso -3
1--3.34 Å20 Å20.83 Å2
2--13.52 Å20 Å2
3----10.13 Å2
Refinement stepCycle: LAST / Resolution: 3.2→44.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18355 0 212 0 18567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.02218907
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1851.98825602
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92552377
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.7323.383804
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.693153304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.05715162
X-RAY DIFFRACTIONr_chiral_restr0.0780.22918
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214087
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2270.28631
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3040.212872
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2506
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2950.2123
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1981.512098
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.349219112
X-RAY DIFFRACTIONr_scbond_it1.98237673
X-RAY DIFFRACTIONr_scangle_it4.3924.56490
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3801tight positional0.030.05
12B3801tight positional0.030.05
13C3801tight positional0.020.05
14D3801tight positional0.020.05
21A289tight positional0.020.05
22B289tight positional0.020.05
23C289tight positional0.020.05
31A53tight positional0.020.05
32B53tight positional0.030.05
33C53tight positional0.030.05
34D53tight positional0.020.05
41A432tight positional0.030.05
42B432tight positional0.030.05
43C432tight positional0.020.05
44D432tight positional0.020.05
11A3801tight thermal0.040.5
12B3801tight thermal0.040.5
13C3801tight thermal0.030.5
14D3801tight thermal0.030.5
21A289tight thermal0.020.5
22B289tight thermal0.020.5
23C289tight thermal0.020.5
31A53tight thermal0.060.5
32B53tight thermal0.070.5
33C53tight thermal0.040.5
34D53tight thermal0.090.5
41A432tight thermal0.020.5
42B432tight thermal0.020.5
43C432tight thermal0.020.5
44D432tight thermal0.020.5
LS refinement shellResolution: 3.199→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.401 192 -
Rwork0.346 3309 -
obs--96.69 %

+
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