[English] 日本語
Yorodumi
- PDB-3djp: Bovine Seminal Ribonuclease- Uridine 3' phosphate complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3djp
TitleBovine Seminal Ribonuclease- Uridine 3' phosphate complex
ComponentsSeminal ribonuclease
KeywordsHYDROLASE / Ribonuclease / Allosteric enzyme / Endonuclease / Nuclease / Secreted
Function / homology
Function and homology information


pancreatic ribonuclease / ribonuclease A activity / RNA nuclease activity / nucleic acid binding / lyase activity / defense response to Gram-positive bacterium / extracellular region / identical protein binding
Similarity search - Function
P-30 Protein / Ribonuclease A-like domain / Pancreatic ribonuclease / Ribonuclease A, active site / Ribonuclease A-domain / Ribonuclease A-like domain superfamily / Pancreatic ribonuclease / Pancreatic ribonuclease family signature. / Pancreatic ribonuclease / Roll / Alpha Beta
Similarity search - Domain/homology
URACIL ARABINOSE-3'-PHOSPHATE / Seminal ribonuclease
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsDossi, K. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G.
CitationJournal: Eur.J.Med.Chem. / Year: 2009
Title: Mapping the ribonucleolytic active site of bovine seminal ribonuclease. The binding of pyrimidinyl phosphonucleotide inhibitors
Authors: Dossi, K. / Tsirkone, V.G. / Hayes, J.M. / Matousek, J. / Pouckova, P. / Soucek, J. / Zadinova, M. / Zographos, S.E. / Leonidas, D.D.
History
DepositionJun 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Seminal ribonuclease
B: Seminal ribonuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9144
Polymers27,2652
Non-polymers6482
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-26.7 kcal/mol
Surface area12740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.192, 59.218, 82.663
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Seminal ribonuclease / Seminal RNase / S-RNase / Ribonuclease BS-1


Mass: 13632.640 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00669, EC: 3.1.27.5
#2: Chemical ChemComp-UA3 / URACIL ARABINOSE-3'-PHOSPHATE / 1-(3-O-PHOSPHONO-BETA-L-ARABINOFURANOSYL)PYRIMIDINE-2,4(1H,3H)-DIONE


Mass: 324.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H13N2O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% PEG4000, 0.1M sodium acetate, 0.1M Tris/HCl, pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8088 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 14, 2007
RadiationMonochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8088 Å / Relative weight: 1
ReflectionResolution: 1.6→27.7 Å / Num. all: 31948 / Num. obs: 31892 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 19.786 Å2 / Rsym value: 0.041 / Net I/σ(I): 19
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.3 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 8774 / Rsym value: 0.389 / % possible all: 96.6

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1R5D

1r5d


Resolution: 1.6→27.7 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 1615 5.1 %RANDOM
Rwork0.18833 ---
obs0.19032 30276 99.57 %-
all-31948 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refine analyzeLuzzati coordinate error obs: 0.235 Å
Refinement stepCycle: LAST / Resolution: 1.6→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 42 291 2215
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221966
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9722652
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3555246
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.36324.86574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.23915362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.878158
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021420
X-RAY DIFFRACTIONr_nbd_refined0.1940.2953
X-RAY DIFFRACTIONr_nbtor_refined0.2940.21356
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2240
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2270.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.241
LS refinement shellResolution: 1.598→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 116 -
Rwork0.243 2089 -
obs--94.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.46260.2-0.04643.6389-0.89834.35080.0541-0.12420.13720.0541-0.07880.00320.05940.17730.02470.03060.00450.0030.0538-0.0110.0389.512820.664618.4015
24.19491.3262-0.61311.3718-0.45981.26720.0734-0.2138-0.01390.0467-0.06050.147-0.0779-0.0702-0.01290.0510.0245-0.02740.0249-0.02240.055726.325529.9695.8279
33.4908-5.6855-6.141513.360911.416214.1360.2102-0.0109-0.0124-0.95710.1924-0.3382-1.06150.4402-0.40250.0994-0.06490.0341-0.0076-0.0033-0.017142.68642.83211.5084
43.54531.37650.33622.04460.69181.26670.09510.27940.0516-0.2049-0.00240.048-0.12520.0844-0.09280.1150.0232-0.0350.01850.0210.029235.449737.0811-0.9122
55.25142.71350.02952.97952.41519.48830.0931-0.91661.26060.0166-0.52611.164-0.8828-1.190.4331-0.06670.07720.02290.0672-0.22750.292315.279936.90811.1569
64.3163-1.2092.31341.7504-0.76962.3205-0.02120.11490.0408-0.12850.00440.0274-0.11570.07610.01680.072-0.0096-0.0350.01480.01860.028336.726635.94891.698
74.82291.9742-0.2112.5670.11631.542-0.0182-0.1112-0.22230.0301-0.05220.0235-0.0638-0.06040.07040.04820.0094-0.01120.03090.0290.082630.751326.73276.6778
83.23723.45510.50924.8094-0.92453.6668-0.1663-0.08210.0095-0.31910.0554-0.22440.16790.1390.11080.03610.02250.06650.01780.00750.035718.696219.21127.7921
92.0150.1948-0.3932.1059-1.13772.254-0.0126-0.2376-0.078-0.0828-0.0084-0.0420.1810.02040.0210.06470.0179-0.00840.0681-0.00490.0287.20215.252715.8632
100.99620.71370.00122.9026-2.71033.6881-0.0428-0.10860.0095-0.26140.24050.16770.2944-0.3816-0.19770.0808-0.0381-0.03110.0644-0.00010.01360.017110.089115.6357
116.4270.84142.73532.8912-0.68496.6112-0.04370.057-0.5601-0.4327-0.2787-0.70460.73940.87380.32240.10770.14160.15940.02740.08740.107321.8610.47138.0304
120.8173-0.2990.05962.002-0.06364.49270.01130.01540.0196-0.05460.1266-0.02560.3326-0.0509-0.13790.0591-0.017-0.00120.0541-0.00940.01392.167612.549616.5417
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 181 - 18
2X-RAY DIFFRACTION2AA19 - 5819 - 58
3X-RAY DIFFRACTION3AA59 - 6859 - 68
4X-RAY DIFFRACTION4AA69 - 8569 - 85
5X-RAY DIFFRACTION5AA86 - 9986 - 99
6X-RAY DIFFRACTION6AA100 - 124100 - 124
7X-RAY DIFFRACTION7BB1 - 231 - 23
8X-RAY DIFFRACTION8BB24 - 3124 - 31
9X-RAY DIFFRACTION9BB32 - 6532 - 65
10X-RAY DIFFRACTION10BB66 - 8266 - 82
11X-RAY DIFFRACTION11BB83 - 10083 - 100
12X-RAY DIFFRACTION12BB101 - 124101 - 124

+
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