[English] 日本語
Yorodumi
- PDB-1biq: RIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN MUTANT E238A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1biq
TitleRIBONUCLEOSIDE-DIPHOSPHATE REDUCTASE 1 BETA CHAIN MUTANT E238A
Components(PROTEIN R2 OF RIBONUCLEOTIDE ...) x 2
KeywordsOXIDOREDUCTASE / DNA REPLICATION / IRON
Function / homology
Function and homology information


ribonucleoside diphosphate metabolic process / 2'-deoxyribonucleotide biosynthetic process / nucleobase-containing small molecule interconversion / ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / iron ion binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Ribonucleotide reductase small subunit, acitve site / Ribonucleotide reductase small subunit signature. / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / : / : / HYDROXIDE ION / Ribonucleoside-diphosphate reductase 1 subunit beta
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER WITH INITIAL REFINEMENT / Resolution: 2.05 Å
AuthorsLogan, D.T. / Demare, F. / Persson, B.O. / Slaby, A. / Sjoberg, B.M. / Nordlund, P.
Citation
Journal: Biochemistry / Year: 1998
Title: Crystal structures of two self-hydroxylating ribonucleotide reductase protein R2 mutants: structural basis for the oxygen-insertion step of hydroxylation reactions catalyzed by diiron proteins.
Authors: Logan, D.T. / deMare, F. / Persson, B.O. / Slaby, A. / Sjoberg, B.M. / Nordlund, P.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Structure and Function of the Escherichia Coli Ribonucleotide Reductase Protein R2
Authors: Nordlund, P. / Eklund, H.
History
DepositionJun 18, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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_database_status.process_site / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_conn.ptnr2_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
Revision 1.4Aug 2, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE
B: PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,20525
Polymers86,7222
Non-polymers3,48423
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9020 Å2
ΔGint-482 kcal/mol
Surface area24080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.053, 83.780, 113.953
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.824671, 0.549974, 0.132088), (0.547596, 0.717853, 0.429914), (0.141621, 0.426868, -0.893155)
Vector: 20.886, -25.728, 76.66)

-
Components

-
PROTEIN R2 OF RIBONUCLEOTIDE ... , 2 types, 2 molecules AB

#1: Protein PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE / RNR R2


Mass: 43368.828 Da / Num. of mol.: 1 / Fragment: BETA CHAIN / Mutation: Y122F, E238A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MC1009 / Plasmid: PGP1-2/PTB2 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1009
References: UniProt: P69924, ribonucleoside-diphosphate reductase
#2: Protein PROTEIN R2 OF RIBONUCLEOTIDE REDUCTASE / RNR R2


Mass: 43352.828 Da / Num. of mol.: 1 / Fragment: BETA CHAIN / Mutation: Y122F, E238A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MC1009 / Plasmid: PGP1-2/PTB2 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1009
References: UniProt: P69924, ribonucleoside-diphosphate reductase

-
Non-polymers , 5 types, 348 molecules

#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#5: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: HO
#6: Chemical
ChemComp-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Hg
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.1 Å3/Da / Density % sol: 34 %
Description: THE CRYSTAL USED FOR DATA COLLECTION WAS IN THE APO FORM. IT WAS SOAKED WITH FE(II) IONS FOR 3 HOURS BEFORE BEING FLASH-COOLED. DURING THIS TIME THE SIDE CHAIN OF PHE 208 IN MONOMER 1 ...Description: THE CRYSTAL USED FOR DATA COLLECTION WAS IN THE APO FORM. IT WAS SOAKED WITH FE(II) IONS FOR 3 HOURS BEFORE BEING FLASH-COOLED. DURING THIS TIME THE SIDE CHAIN OF PHE 208 IN MONOMER 1 BECAME HYDROXYLATED AT THE EPSILON CARBON THROUGH INTERACTION OF OXYGEN WITH THE DIIRON SITE.
Crystal growpH: 6 / Details: pH 6.0
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 %PEG40001reservoir
30.2 M1reservoirNaCl
43 %dioxane1reservoir
50.05 MMES1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1996 / Details: BENT QUARTZ MIRROR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.05→27 Å / Num. obs: 161734 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 36.3 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 16.4

-
Processing

Software
NameVersionClassification
TNT/CCP4model building
TNT5Erefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4data scaling
TNTphasing
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER WITH INITIAL REFINEMENT
Starting model: DIFERROUS FORM OF R2 PROTEIN, PDB ENTRY 1XIK

1xik


Resolution: 2.05→25 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: R FREE THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT PROTGEO
RfactorNum. reflection% reflectionSelection details
Rfree0.26 1761 4 %RANDOM
Rwork0.191 ---
all0.192 43712 --
obs0.192 43712 98 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 220 Å2 / ksol: 0.785 e/Å3
Refinement stepCycle: LAST / Resolution: 2.05→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5573 0 23 325 5921
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01456982.2
X-RAY DIFFRACTIONt_angle_deg2.133581.2
X-RAY DIFFRACTIONt_dihedral_angle_d16.833580
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.00855
X-RAY DIFFRACTIONt_gen_planes0.01280410
X-RAY DIFFRACTIONt_it1.666569830
X-RAY DIFFRACTIONt_nbd0.0310460
Software
*PLUS
Name: TNT / Version: 5E / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.266
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_dihedral_angle_deg16.80

+
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