[English] 日本語
Yorodumi
- PDB-7mmw: Crystal Structure of the Class Ie Ribonucleotide Reductase Beta S... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7mmw
TitleCrystal Structure of the Class Ie Ribonucleotide Reductase Beta Subunit from Aerococcus urinae (in alternate conformation)
ComponentsRibonucleoside-diphosphate reductase
KeywordsOXIDOREDUCTASE / ribonucleotide reductase / beta subunit / RNR / R2 / class Ie / metal-free / METAL BINDING PROTEIN
Function / homology
Function and homology information


ribonucleoside-diphosphate reductase complex / ribonucleoside-diphosphate reductase / ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor / deoxyribonucleotide biosynthetic process / membrane / metal ion binding
Similarity search - Function
Ribonucleoside-diphosphate reductase subunit beta / Ribonucleotide Reductase, subunit A / Ribonucleotide Reductase, subunit A / Ribonucleotide reductase small subunit / Ribonucleotide reductase small subunit family / Ribonucleotide reductase, small chain / Ribonucleotide reductase-like / Ferritin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ribonucleoside-diphosphate reductase
Similarity search - Component
Biological speciesAerococcus urinae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.55 Å
AuthorsPalowitch, G.M. / Boal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To be published
Title: Ribonucleotide Reductase
Authors: Palowitch, G.M. / Boal, A.K.
History
DepositionApr 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribonucleoside-diphosphate reductase
B: Ribonucleoside-diphosphate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,7224
Polymers78,6422
Non-polymers802
Water7,764431
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5460 Å2
ΔGint-57 kcal/mol
Surface area24930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.375, 52.876, 74.534
Angle α, β, γ (deg.)109.400, 106.410, 91.470
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Ribonucleoside-diphosphate reductase


Mass: 39320.973 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aerococcus urinae (strain ACS-120-V-Col10a) (bacteria)
Strain: ACS-120-V-Col10a / Gene: HMPREF9243_0731 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: F2I8X9, ribonucleoside-diphosphate reductase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 431 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.69 % / Mosaicity: 0.326 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 15% (w/v) PEG 3350, 0.2 M calcium chloride, 0.1 M HEPBS pH 8.5, 10 mM sodium dithionite

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 86931 / % possible obs: 96.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.021 / Rpim(I) all: 0.012 / Rrim(I) all: 0.024 / Χ2: 0.736 / Net I/σ(I): 21.2 / Num. measured all: 343382
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.583.90.10542650.9860.0620.1220.83594.8
1.58-1.6140.09443180.9890.0540.1080.82295.1
1.61-1.6440.08142650.9910.0470.0940.81695.2
1.64-1.6740.07142480.9920.0410.0820.78995.3
1.67-1.7140.06343280.9930.0360.0730.75695.6
1.71-1.7540.05543320.9930.0320.0640.75995.7
1.75-1.7940.04942610.9940.0280.0560.7496.1
1.79-1.8440.04343630.9950.0250.0490.73496.1
1.84-1.8940.03743870.9950.0220.0430.71596.5
1.89-1.9540.03443250.9950.020.040.77396.4
1.95-2.0240.02943350.9960.0160.0330.73397
2.02-2.140.02543900.9960.0150.0290.73397.1
2.1-2.240.02343620.9970.0130.0260.69397.2
2.2-2.323.90.02143770.9970.0120.0240.66197.4
2.32-2.4640.0243880.9970.0120.0230.65797.8
2.46-2.6540.02344390.9970.0130.0260.97898
2.65-2.9240.0244140.9970.0120.0230.89198.4
2.92-3.3440.01644290.9970.0090.0190.64798.6
3.34-4.213.60.01343350.9980.0080.0150.42595.9
4.21-503.80.01543700.9970.0090.0180.50897.2

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EBO

6ebo


Resolution: 1.55→33.82 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.263 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.083
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.198 4402 5.1 %RANDOM
Rwork0.1732 ---
obs0.1744 82529 96.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 38.15 Å2 / Biso mean: 12.004 Å2 / Biso min: 5.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0.04 Å20 Å2
2--0.01 Å2-0.11 Å2
3----0.03 Å2
Refinement stepCycle: final / Resolution: 1.55→33.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5119 0 2 431 5552
Biso mean--19.55 20.41 -
Num. residues----628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0135438
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174882
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.6387418
X-RAY DIFFRACTIONr_angle_other_deg1.3021.57111378
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3285670
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.81323.867300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.05315923
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.0191523
X-RAY DIFFRACTIONr_chiral_restr0.060.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026207
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021170
LS refinement shellResolution: 1.55→1.591 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 309 -
Rwork0.189 5902 -
all-6211 -
obs--93.33 %

+
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