[English] 日本語
Yorodumi
- PDB-4h4n: 1.1 Angstrom Crystal Structure of Hypothetical Protein BA_2335 fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4h4n
Title1.1 Angstrom Crystal Structure of Hypothetical Protein BA_2335 from Bacillus anthracis
Componentshypothetical protein BA_2335
KeywordsUNKNOWN FUNCTION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / hypothetical protein
Function / homologyImmunoglobulin-like - #3750 / : / BA_2335-like / Immunoglobulin-like / Sandwich / Mainly Beta / BETA-MERCAPTOETHANOL / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.1 Å
AuthorsMinasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.1 Angstrom Crystal Structure of Hypothetical Protein BA_2335 from Bacillus anthracis.
Authors: Minasov, G. / Wawrzak, Z. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionSep 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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: hypothetical protein BA_2335
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9066
Polymers7,6261
Non-polymers2815
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.673, 40.248, 52.014
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein hypothetical protein BA_2335


Mass: 7625.771 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Ames / Gene: BAS2177, BA_2335, GBAA_2335 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81QT2, UniProt: A0A6L7H4C2*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.81 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 3.5mg/mL, 0.5M Sodium chloride, 0.01M Tris-HCl pH 8.3; Screen: Classics II (G4), 0.2M Lithium sulfate, 0.1M HEPES pH 7.5, 25% (w/v) PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 6, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.1→30 Å / Num. all: 23318 / Num. obs: 23318 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 10 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 26.3
Reflection shellResolution: 1.1→1.12 Å / Redundancy: 3 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.04 / Num. unique all: 1084 / % possible all: 93

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.1→26.01 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.953 / SU B: 0.634 / SU ML: 0.014
Isotropic thermal model: Thermal Factors Anisotropically Refined
Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18225 1195 5.1 %RANDOM
Rwork0.14581 ---
all0.14747 22013 --
obs0.14747 22013 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.142 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å2-0 Å2
2---0.04 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.1→26.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms499 0 12 87 598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022580
X-RAY DIFFRACTIONr_bond_other_d0.0020.02411
X-RAY DIFFRACTIONr_angle_refined_deg1.331.998794
X-RAY DIFFRACTIONr_angle_other_deg0.7631020
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.878573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.49524.28621
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.09315103
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.847152
X-RAY DIFFRACTIONr_chiral_restr0.0840.287
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021637
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02109
X-RAY DIFFRACTIONr_mcbond_it1.3661.5352
X-RAY DIFFRACTIONr_mcbond_other0.471.5129
X-RAY DIFFRACTIONr_mcangle_it2.2922595
X-RAY DIFFRACTIONr_scbond_it2.6053228
X-RAY DIFFRACTIONr_scangle_it3.8874.5199
X-RAY DIFFRACTIONr_rigid_bond_restr0.5831991
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 93 -
Rwork0.23 1517 -
obs-1517 94.65 %

+
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