[English] 日本語
Yorodumi
- PDB-4f8b: Crystal Structure of the Covalent Thioimide Intermediate of Unimo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f8b
TitleCrystal Structure of the Covalent Thioimide Intermediate of Unimodular Nitrile Reductase QueF
ComponentsNADPH-dependent 7-cyano-7-deazaguanine reductase
KeywordsOXIDOREDUCTASE / beta barrel / protein thioimide complex / pterin binding fold / tunnel fold / tRNA modification enzyme / 7-cyano-7-deazaguanine / NADPH
Function / homology
Function and homology information


preQ1 synthase / preQ1 synthase activity / queuosine biosynthetic process / metal ion binding / cytoplasm
Similarity search - Function
NADPH-dependent 7-cyano-7-deazaguanine reductase, QueF type 1 / NADPH-dependent 7-cyano-7-deazaguanine reductase QueF / QueF-like protein / GTP Cyclohydrolase I, domain 2 / GTP cyclohydrolase I, C-terminal domain/NADPH-dependent 7-cyano-7-deazaguanine reductase, N-terminal domain / GTP cyclohydrolase I, C-terminal/NADPH-dependent 7-cyano-7-deazaguanine reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-GD1 / PHOSPHATE ION / NADPH-dependent 7-cyano-7-deazaguanine reductase
Similarity search - Component
Biological speciesBacillus subtilis subsp. subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.502 Å
AuthorsStec, B. / Swairjo, M.A.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Structural basis of biological nitrile reduction.
Authors: Chikwana, V.M. / Stec, B. / Lee, B.W. / de Crecy-Lagard, V. / Iwata-Reuyl, D. / Swairjo, M.A.
History
DepositionMay 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Sep 19, 2012Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Sep 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_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.pdbx_leaving_atom_flag / _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_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: NADPH-dependent 7-cyano-7-deazaguanine reductase
B: NADPH-dependent 7-cyano-7-deazaguanine reductase
C: NADPH-dependent 7-cyano-7-deazaguanine reductase
D: NADPH-dependent 7-cyano-7-deazaguanine reductase
E: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,24015
Polymers96,9855
Non-polymers1,25510
Water2,972165
1
A: NADPH-dependent 7-cyano-7-deazaguanine reductase
B: NADPH-dependent 7-cyano-7-deazaguanine reductase
C: NADPH-dependent 7-cyano-7-deazaguanine reductase
D: NADPH-dependent 7-cyano-7-deazaguanine reductase
E: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules

A: NADPH-dependent 7-cyano-7-deazaguanine reductase
B: NADPH-dependent 7-cyano-7-deazaguanine reductase
C: NADPH-dependent 7-cyano-7-deazaguanine reductase
D: NADPH-dependent 7-cyano-7-deazaguanine reductase
E: NADPH-dependent 7-cyano-7-deazaguanine reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,48030
Polymers193,97010
Non-polymers2,51120
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area41190 Å2
ΔGint-187 kcal/mol
Surface area48840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.507, 93.507, 193.696
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

-
Protein , 1 types, 5 molecules ABCDE

#1: Protein
NADPH-dependent 7-cyano-7-deazaguanine reductase / QueF / 7-cyano-7-carbaguanine reductase / NADPH-dependent nitrile oxidoreductase / PreQ(0) reductase


Mass: 19396.955 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis subsp. subtilis (bacteria)
Strain: 168 / Gene: BSU13750, queF, ykvM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O31678, preQ1 synthase

-
Non-polymers , 5 types, 175 molecules

#2: Chemical
ChemComp-GD1 / 2-amino-5-[(Z)-iminomethyl]-3,7-dihydro-4H-pyrrolo[2,3-d]pyrimidin-4-one / 7-cyano-7-deazaguanine, bound form


Mass: 177.163 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H7N5O
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 16-20% PEG500 MME, 60 mM imidazole, 40 mM imidazolium chloride, pH 7.4, 30 mM calcium chloride or magnesium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

-
Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 1.000003 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 10, 2006 / Details: mirrors
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal, asymmetric cut 12.2 degrees
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000003 Å / Relative weight: 1
ReflectionResolution: 2.502→41.56 Å / Num. all: 34623 / Num. obs: 34623 / % possible obs: 98.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9.9 % / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 7.8
Reflection shellResolution: 2.502→2.57 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.1 / % possible all: 89.9

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASESphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BP1

3bp1


Resolution: 2.502→41.56 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.886 / SU B: 9.355 / SU ML: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.445 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27195 1720 5 %RANDOM
Rwork0.18918 ---
obs0.19334 32475 98.72 %-
all-33897 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.536 Å2
Baniso -1Baniso -2Baniso -3
1-1.93 Å20.96 Å20 Å2
2--1.93 Å20 Å2
3----2.89 Å2
Refinement stepCycle: LAST / Resolution: 2.502→41.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6013 0 85 165 6263
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0226292
X-RAY DIFFRACTIONr_angle_refined_deg2.0571.9778508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5335714
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.63924.08326
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.63151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1211529
X-RAY DIFFRACTIONr_chiral_restr0.1290.2837
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.024933
X-RAY DIFFRACTIONr_nbd_refined0.2510.22963
X-RAY DIFFRACTIONr_nbtor_refined0.3290.24190
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2309
X-RAY DIFFRACTIONr_metal_ion_refined0.2380.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2540.292
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.220
X-RAY DIFFRACTIONr_mcbond_it1.3391.53740
X-RAY DIFFRACTIONr_mcangle_it2.2125898
X-RAY DIFFRACTIONr_scbond_it2.92333031
X-RAY DIFFRACTIONr_scangle_it4.3484.52610
LS refinement shellResolution: 2.502→2.567 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 96 -
Rwork0.275 2153 -
obs--89.1 %

+
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://pdbjlvh1.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