[English] 日本語
Yorodumi
- PDB-2rjn: Crystal structure of an uncharacterized protein Q2BKU2 from Neptu... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2rjn
TitleCrystal structure of an uncharacterized protein Q2BKU2 from Neptuniibacter caesariensis
ComponentsResponse regulator receiver:Metal-dependent phosphohydrolase, HD subdomain
KeywordsHYDROLASE / STRUCTURAL GENOMICS / Oceanospirillum sp. MED92 / Neptuniibacter caesariensis / PSI-2 / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyResponse regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Response regulator receiver:Metal-dependent phosphohydrolase, HD subdomain / Response regulator receiver:Metal-dependent phosphohydrolase, HD subdomain
Function and homology information
Biological speciesNeptuniibacter caesariensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsMalashkevich, V.N. / Toro, R. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an uncharacterized protein Q2BKU2 from Neptuniibacter caesariensis.
Authors: Malashkevich, V.N. / Toro, R. / Meyer, A.J. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 15, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Response regulator receiver:Metal-dependent phosphohydrolase, HD subdomain


Theoretical massNumber of molelcules
Total (without water)17,6571
Polymers17,6571
Non-polymers00
Water1,15364
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.474, 52.973, 55.124
Angle α, β, γ (deg.)90.000, 124.960, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-188-

HOH

DetailsAuthors state that the biological unit is unknown.

-
Components

#1: Protein Response regulator receiver:Metal-dependent phosphohydrolase, HD subdomain


Mass: 17657.207 Da / Num. of mol.: 1 / Fragment: Residues 2-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neptuniibacter caesariensis (bacteria) / Strain: MED92 / Gene: MED92_01309 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Codon+RIL / References: UniProt: Q2BKU2, UniProt: A0A7U8C3V7*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 4 M Sodium formate, 0.01M Spermine tetrachloride, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2007 / Details: X29
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 14.6 / Number: 68890 / Rmerge(I) obs: 0.059 / Χ2: 2.37 / D res high: 2 Å / D res low: 50 Å / Num. obs: 19935 / % possible obs: 79.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.315098.910.0464.7743.8
3.424.3110010.0534.1043.8
2.993.4210010.072.8273.8
2.712.9999.410.0841.8013.7
2.522.7193.210.0961.3793.5
2.372.528110.1061.1713.3
2.252.3769.610.120.9763.2
2.152.2561.210.130.9313
2.072.1552.710.1540.82.9
22.0742.410.1880.6982.6
ReflectionResolution: 2→50 Å / Num. obs: 19935 / % possible obs: 79.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.059 / Χ2: 2.372 / Net I/σ(I): 14.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.072.60.18810610.698142.4
2.07-2.152.90.15413080.8152.7
2.15-2.2530.1315210.931161.2
2.25-2.373.20.1217370.976169.6
2.37-2.523.30.10620411.171181
2.52-2.713.50.09622851.379193.2
2.71-2.993.70.08425291.801199.4
2.99-3.423.80.0724912.8271100
3.42-4.313.80.05324814.1041100
4.31-503.80.04624814.774198.9

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3data extraction
CBASSdata collection
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→19.23 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.921 / SU B: 9.36 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.197 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Bijvoet differences were used in phasing. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.236 481 5 %RANDOM
Rwork0.185 ---
obs0.187 9628 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.612 Å2
Baniso -1Baniso -2Baniso -3
1--0.33 Å20 Å2-0.93 Å2
2---0.52 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1078 0 0 64 1142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0221093
X-RAY DIFFRACTIONr_angle_refined_deg1.8671.9911475
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9825134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.75524.90251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23515210
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.405158
X-RAY DIFFRACTIONr_chiral_restr0.130.2171
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02805
X-RAY DIFFRACTIONr_nbd_refined0.2260.2493
X-RAY DIFFRACTIONr_nbtor_refined0.3130.2741
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.263
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.29
X-RAY DIFFRACTIONr_mcbond_it1.7021.5689
X-RAY DIFFRACTIONr_mcangle_it4.835201089
X-RAY DIFFRACTIONr_scbond_it9.87720447
X-RAY DIFFRACTIONr_scangle_it5.6844.5386
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 22 -
Rwork0.194 432 -
all-454 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: -0.8908 Å / Origin y: 21.1673 Å / Origin z: 31.998 Å
111213212223313233
T-0.1617 Å2-0.0052 Å2-0.0095 Å2--0.0738 Å2-0.004 Å2---0.0947 Å2
L1.9996 °2-0.0959 °20.5858 °2-4.3592 °2-0.1243 °2--6.1434 °2
S0.0077 Å °0.0076 Å °0.0441 Å °-0.3241 Å °-0.0435 Å °0.3447 Å °0.0147 Å °-0.7191 Å °0.0358 Å °

+
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