[English] 日本語
Yorodumi
- PDB-1b2x: BARNASE WILDTYPE STRUCTURE AT PH 7.5 FROM A CRYO_COOLED CRYSTAL A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1b2x
TitleBARNASE WILDTYPE STRUCTURE AT PH 7.5 FROM A CRYO_COOLED CRYSTAL AT 100K
ComponentsPROTEIN (BARNASE)
KeywordsHYDROLASE / MICROBIAL RIBONUCLEASE / ALPHA/BETA PROTEIN
Function / homology
Function and homology information


Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA endonuclease activity / RNA binding / extracellular region
Similarity search - Function
Barnase / Guanine-specific ribonuclease N1/T1/U2 / ribonuclease / Microbial ribonucleases / Ribonuclease/ribotoxin / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesBacillus amyloliquefaciens (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 1.8 Å
AuthorsHarrison, P. / Vaughan, C.K. / Buckle, A.M. / Fersht, A.R.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: A structural double-mutant cycle: estimating the strength of a buried salt bridge in barnase.
Authors: Vaughan, C.K. / Harryson, P. / Buckle, A.M. / Fersht, A.R.
#1: Journal: Nature / Year: 1982
Title: Molecular Structure of a New Family of Ribonucleases
Authors: Mauguen, Y. / Hartley, R.W. / Dodson, E.J. / Dodson, G.G. / Bricogne, G. / Chothia, C. / Jack, A.
History
DepositionDec 3, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Dec 9, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 9, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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.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.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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: PROTEIN (BARNASE)
B: PROTEIN (BARNASE)
C: PROTEIN (BARNASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2624
Polymers37,1963
Non-polymers651
Water6,846380
1
A: PROTEIN (BARNASE)


Theoretical massNumber of molelcules
Total (without water)12,3991
Polymers12,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTEIN (BARNASE)


Theoretical massNumber of molelcules
Total (without water)12,3991
Polymers12,3991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: PROTEIN (BARNASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,4642
Polymers12,3991
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.630, 57.630, 80.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.756734, 0.647669, 0.088756), (0.645866, -0.761703, 0.051627), (0.101043, 0.018256, -0.994714)0.9197, 73.283, 100.6052
2given(0.584995, 0.807333, 0.077419), (0.804959, -0.589624, 0.066215), (0.099106, 0.023584, -0.994797)-5.9188, 34.3541, 81.8944

-
Components

#1: Protein PROTEIN (BARNASE)


Mass: 12398.721 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus amyloliquefaciens (bacteria) / Cellular location: EXTRACELLULARGlossary of biology / Plasmid: PMT410 / Production host: Escherichia coli (E. coli) / References: UniProt: P00648, EC: 3.1.27.3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.09 Å3/Da / Density % sol: 41 %
Crystal growpH: 7.5
Details: DROP: 8-12 MG/ML PROTEIN 6 MM ZNSO4 0.6 M (NH4)2SO4 WELL: 2.58-2.73 M AMMONIUM PHOSPHATE BUFFER, PH 7.5 1-2 MM ZNSO4 0.15-0.30 M (NH4)2SO4 5-10 MM NH4OH
Components of the solutions
IDNameCrystal-IDSol-ID
1ZN SULFATE11
2NH4 SULFATE11
3ZN SULFATE12
4NH4 SULFATE12
5NH4OH12
6NH4 PHOSPHATE12
Crystal grow
*PLUS
Temperature: 288 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18-12 mg/mlprotein1drop
26 mM1dropZnSO4
30.1 Mammonium sulfate1drop
42.58-2.73 Mammonium phosphate1reservoir
51-2 mM1reservoirZn2SO4
60.15-0.30 Mammonium sulfate1reservoir
75-10 mM1reservoirNH4OH

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ELLIOTT GX-13 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: SUPER DOUBLE MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→10.8 Å / Num. obs: 27056 / % possible obs: 96.9 % / Redundancy: 1.9 % / Biso Wilson estimate: 14.37 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 12.62
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 6.01 / % possible all: 88
Reflection
*PLUS
Rmerge(I) obs: 0.062
Reflection shell
*PLUS
% possible obs: 88 % / Rmerge(I) obs: 0.187

-
Processing

Software
NameVersionClassification
iMOSFLMdata reduction
SCALAdata scaling
X-PLORmodel building
REFMACrefinement
CCP4(SCALA)data scaling
X-PLORphasing
RefinementMethod to determine structure: OTHER
Starting model: 1BNJ

1bnj


Resolution: 1.8→10.8 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.236 -5 %
Rwork0.173 --
obs-25666 96.9 %
Displacement parametersBiso mean: 16.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→10.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2604 0 1 380 2985
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.5722
X-RAY DIFFRACTIONp_mcangle_it2.1343
X-RAY DIFFRACTIONp_scbond_it1.7972
X-RAY DIFFRACTIONp_scangle_it2.5243
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1310.15
X-RAY DIFFRACTIONp_singtor_nbd0.1740.3
X-RAY DIFFRACTIONp_multtor_nbd0.250.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1530.3
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor14.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor18.220
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Rfactor obs: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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