[English] 日本語
Yorodumi
- PDB-7p4r: Ultra High Resolution X-ray Structure of Orthorhombic Bovine Panc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p4r
TitleUltra High Resolution X-ray Structure of Orthorhombic Bovine Pancreatic Ribonuclease at 100K
ComponentsRibonuclease pancreatic
KeywordsHYDROLASE / Nucleic acid / RNA / multiple conformations / water structure
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / defense response to Gram-positive bacterium / lyase activity / extracellular region
Similarity search - Function
Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease
Similarity search - Domain/homology
ETHANOL / Ribonuclease pancreatic
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.85 Å
AuthorsLisgarten, D.R. / Palmer, R.A. / Cooper, J.B. / Naylor, C.E. / Howlin, B.J. / Lisgarten, J.N. / Najmudin, S. / Lobley, C.M.C.
Citation
Journal: BMC Chem / Year: 2023
Title: Ultra-high resolution X-ray structure of orthorhombic bovine pancreatic Ribonuclease A at 100K.
Authors: Lisgarten, D.R. / Palmer, R.A. / Cooper, J.B. / Naylor, C.E. / Talbert, R.C. / Howlin, B.J. / Lisgarten, J.N. / Konc, J. / Najmudin, S. / Lobley, C.M.C.
#1: Journal: Acta Crystallogr A / Year: 1989
Title: Segmented anisotropic refinement of bovine ribonuclease A by the application of the rigid-body TLS model.
Authors: Howlin, B. / Moss, D.S. / Harris, G.W.
History
DepositionJul 12, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 2.0Aug 16, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id ..._atom_site.label_alt_id / _atom_site_anisotrop.pdbx_label_alt_id / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_validate_close_contact.label_alt_id_1
Revision 2.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Ribonuclease pancreatic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,88819
Polymers13,7081
Non-polymers1,17918
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-62 kcal/mol
Surface area7790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.998, 45.697, 51.890
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Ribonuclease pancreatic / RNase 1 / RNase A


Mass: 13708.326 Da / Num. of mol.: 1 / Mutation: None
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: RNASE1, RNS1 / Organ: Pancreas / Production host: Bos taurus (domestic cattle) / References: UniProt: P61823, pancreatic ribonuclease
#2: Chemical
ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.3 %
Description: The Ribonuclease A crystals were long needles of the order of 0.5 mm long by about 0.05 mm by 0.05 mm.
Crystal growTemperature: 277 K / Method: evaporation / pH: 7
Details: 100mg of powdered Ribonuclease A in 1ml of distilled water dissolved in 2ml of ice cold absolute ethanol.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.77 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.77 Å / Relative weight: 1
ReflectionResolution: 0.85→51.89 Å / Num. obs: 87934 / % possible obs: 95.2 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.049 / Rrim(I) all: 0.091 / Net I/σ(I): 13.2
Reflection shellResolution: 0.85→0.86 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.697 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2925 / Rpim(I) all: 0.55 / Rrim(I) all: 0.893 / % possible all: 65.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
XDSdata reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rn3

3rn3


Resolution: 0.85→34.294 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.122 / WRfactor Rwork: 0.106 / SU B: 0.399 / SU ML: 0.011 / Average fsc free: 0.9674 / Average fsc work: 0.9705 / Cross valid method: FREE R-VALUE / ESU R: 0.015 / ESU R Free: 0.016
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1291 4279 5.014 %
Rwork0.1123 81067 -
all0.113 --
obs-85346 92.225 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 7.596 Å2
Baniso -1Baniso -2Baniso -3
1-0.173 Å2-0 Å20 Å2
2--0.379 Å2-0 Å2
3----0.551 Å2
Refinement stepCycle: LAST / Resolution: 0.85→34.294 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms951 0 68 293 1312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0131229
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181185
X-RAY DIFFRACTIONr_angle_refined_deg2.4741.6661688
X-RAY DIFFRACTIONr_angle_other_deg1.681.6112766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5035178
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.72224.51662
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53715236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.337155
X-RAY DIFFRACTIONr_chiral_restr0.1270.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021429
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02277
X-RAY DIFFRACTIONr_nbd_refined0.2630.2276
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2220.21065
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2538
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.1070.2571
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3310.2274
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.3010.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3830.249
X-RAY DIFFRACTIONr_nbd_other0.3440.2152
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3520.2104
X-RAY DIFFRACTIONr_mcbond_it0.9260.405565
X-RAY DIFFRACTIONr_mcbond_other0.9220.405564
X-RAY DIFFRACTIONr_mcangle_it1.2550.619718
X-RAY DIFFRACTIONr_mcangle_other1.2540.619719
X-RAY DIFFRACTIONr_scbond_it1.5820.594664
X-RAY DIFFRACTIONr_scbond_other1.450.577637
X-RAY DIFFRACTIONr_scangle_it1.7260.816941
X-RAY DIFFRACTIONr_scangle_other1.3480.774900
X-RAY DIFFRACTIONr_lrange_it5.4229.8291585
X-RAY DIFFRACTIONr_lrange_other3.2516.6331427
X-RAY DIFFRACTIONr_rigid_bond_restr5.28432414
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
0.85-0.8720.2831920.27339500.27367690.8240.85861.19070.243
0.872-0.8960.2382680.23148660.23166230.9130.91177.51770.202
0.896-0.9220.1772640.18353770.18364140.9530.94887.94820.156
0.922-0.950.1752700.15654460.15762010.9550.96192.17870.129
0.95-0.9810.153000.13653610.13760610.9650.96993.40040.114
0.981-1.0160.1282860.11652490.11758670.9740.97894.34120.098
1.016-1.0540.1132500.09950980.156280.9820.98495.02490.083
1.054-1.0970.12820.08749780.08754760.9850.98896.05550.074
1.097-1.1460.0992440.0848190.08152140.9870.9997.1040.069
1.146-1.2020.0872560.07446520.07550290.990.99297.5940.065
1.202-1.2670.0932400.07844530.07947830.990.99198.11830.07
1.267-1.3430.0982320.08342130.08445200.9880.98998.34070.076
1.343-1.4360.1062130.08240030.08342710.9850.98998.71220.076
1.436-1.5510.1052110.08437240.08539690.9860.98999.14340.08
1.551-1.6980.1091870.0934610.09136760.9860.98899.23830.089
1.698-1.8980.1211570.09731650.09833410.9830.98699.43130.1
1.898-2.1910.1251690.10128080.10229850.9820.98599.7320.108
2.191-2.6810.1411150.11424070.11525250.9770.98399.88120.126
2.681-3.7790.138880.13119120.13120070.980.9899.65120.155
3.779-34.2940.207550.16211250.16411820.9690.97499.83080.232

+
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