[English] 日本語
Yorodumi
- PDB-1pkv: The N-terminal domain of riboflavin synthase in complex with ribo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1pkv
TitleThe N-terminal domain of riboflavin synthase in complex with riboflavin
ComponentsRiboflavin synthase alpha chain
KeywordsTRANSFERASE / dimer / beta-barrel / greek key motif
Function / homology
Function and homology information


riboflavin synthase / riboflavin synthase activity / riboflavin biosynthetic process / cytosol
Similarity search - Function
Lumazine-binding protein / Lumazine-binding domain / Lumazine binding domain / Riboflavin synthase alpha chain lumazine-binding repeat profile. / Elongation Factor Tu (Ef-tu); domain 3 - #20 / ATP synthase subunit alpha, N-terminal domain-like superfamily / Elongation Factor Tu (Ef-tu); domain 3 / Riboflavin synthase-like beta-barrel / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RIBOFLAVIN / Riboflavin synthase / Riboflavin synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsMeining, W. / Eberhardt, S. / Bacher, A. / Ladenstein, R.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: The structure of the N-terminal domain of riboflavin synthase in complex with riboflavin at 2.6A resolution.
Authors: Meining, W. / Eberhardt, S. / Bacher, A. / Ladenstein, R.
#1: Journal: Eur.J.Biochem. / Year: 2001
Title: Domain structure of riboflavin synthase
Authors: Eberhardt, S. / Zingler, N. / Kemter, K. / Richter, G. / Cushman, M. / Bacher, A.
#2: Journal: J.Biol.Chem. / Year: 2001
Title: Riboflavin Synthase of Escherichia coli. Effect of single amino acid substitutions on reaction rate and ligand binding properties
Authors: Illarionov, B. / Kemter, K. / Eberhardt, S. / Richter, G. / Cushman, M. / Bacher, A.
History
DepositionJun 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 16, 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 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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: Riboflavin synthase alpha chain
B: Riboflavin synthase alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9054
Polymers21,1522
Non-polymers7532
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-9 kcal/mol
Surface area8540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.161, 104.383, 85.113
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B
291A
301B
311A
321B
331A
341B
351A
361B
12A
22B
13A
23B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PHEPHEILEILE1AA2 - 152 - 15
211PHEPHEILEILE1BB2 - 152 - 15
321ASPASPGLUGLU3AA16 - 1716 - 17
421ASPASPGLUGLU3BB16 - 1716 - 17
531PHEPHEPHEPHE1AA2121
631PHEPHEPHEPHE1BB2121
741ARGARGARGARG3AA2222
841ARGARGARGARG3BB2222
951THRTHRMETMET1AA23 - 3223 - 32
1051THRTHRMETMET1BB23 - 3223 - 32
1161THRTHRLEULEU1AA67 - 6867 - 68
1261THRTHRLEULEU1BB67 - 6867 - 68
1371ILEILELEULEU1AA70 - 7670 - 76
1471ILEILELEULEU1BB70 - 7670 - 76
1581LYSLYSASNASN6AA18 - 2018 - 20
1681LYSLYSASNASN6BB18 - 2018 - 20
1791METMETGLUGLU5AA64 - 6664 - 66
1891METMETGLUGLU5BB64 - 6664 - 66
19101ASNASNASNASN3AA55 - 5755 - 57
20101ASNASNASNASN3BB55 - 5755 - 57
21111HISHISLEULEU1AA58 - 6358 - 63
22111HISHISLEULEU1BB58 - 6358 - 63
23121ARGARGARGARG5AA6969
24121ARGARGARGARG5BB6969
25131LEULEUASPASP3AA33 - 3433 - 34
26131LEULEUASPASP3BB33 - 3433 - 34
27141GLYGLYLEULEU1AA35 - 3635 - 36
28141GLYGLYLEULEU1BB35 - 3635 - 36
29151GLUGLUGLUGLU3AA3737
30151GLUGLUGLUGLU3BB3737
31161THRTHRILEILE1AA38 - 5438 - 54
32161THRTHRILEILE1BB38 - 5438 - 54
33171LYSLYSLYSLYS3AA7777
34171LYSLYSLYSLYS3BB7777
35181VALVALALAALA1AA78 - 8778 - 87
36181VALVALALAALA1BB78 - 8778 - 87
112RBFRBFRBFRBF1AC100
212RBFRBFRBFRBF1BD101
113HOHHOHHOHHOH1AE101 - 116
213HOHHOHHOHHOH1BF103 - 116

NCS ensembles :
ID
1
2
3
Detailsthe asymmetric unit contains the dimer, which is also found in solution

-
Components

#1: Protein Riboflavin synthase alpha chain


Mass: 10575.960 Da / Num. of mol.: 2 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RIBE OR RIBC OR B1662 OR SF1690 / Cell line (production host): XL1-Blue cells / Production host: Escherichia coli (E. coli)
References: UniProt: P29015, UniProt: P0AFU8*PLUS, riboflavin synthase
#2: Chemical ChemComp-RBF / RIBOFLAVIN / RIBOFLAVINE / VITAMIN B2 / Riboflavin


Mass: 376.364 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H20N4O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.63 Å3/Da / Density % sol: 53.29 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 70 mM sodium potassium phosphate, pH 7.0, 100 mM sodium chloride, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8424 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8424 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 7171 / Num. obs: 7131 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.6→2.63 Å / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I8D

1i8d


Resolution: 2.6→19.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.906 / SU B: 8.765 / SU ML: 0.188 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.485 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Chains C and D in ncs group 2 correspond to the residues 100 and 101 in the coordinates; chain E in ncs group 3 corresponds to water molecules 1-17, 32, 34, 36, 37 and chain F in ncs group 3 ...Details: Chains C and D in ncs group 2 correspond to the residues 100 and 101 in the coordinates; chain E in ncs group 3 corresponds to water molecules 1-17, 32, 34, 36, 37 and chain F in ncs group 3 corresponds to water molecules 18-31, 33, 35 in the coordinates
RfactorNum. reflection% reflectionSelection details
Rfree0.23469 337 4.7 %RANDOM
Rwork0.17409 ---
all0.17699 7131 --
obs0.17699 6793 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.393 Å2
Baniso -1Baniso -2Baniso -3
1--1.58 Å20 Å20 Å2
2--2.17 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.6→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1330 0 54 37 1421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0211372
X-RAY DIFFRACTIONr_angle_refined_deg1.7981.9851869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0875170
X-RAY DIFFRACTIONr_chiral_restr0.1120.2225
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02997
X-RAY DIFFRACTIONr_nbd_refined0.2190.2544
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3180.244
X-RAY DIFFRACTIONr_mcbond_it1.0681.5848
X-RAY DIFFRACTIONr_mcangle_it2.15121373
X-RAY DIFFRACTIONr_scbond_it3.2163524
X-RAY DIFFRACTIONr_scangle_it5.2864.5496
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A551tight positional0.080.05
22B27tight positional0.040.05
33A7tight positional0.130.05
11A16medium positional0.210.5
11A63loose positional0.895
11A551tight thermal0.220.5
22B27tight thermal0.310.5
33A7tight thermal0.550.5
11A16medium thermal0.982
11A63loose thermal4.0410
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.318 31
Rwork0.242 475

+
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