[English] 日本語
Yorodumi
- PDB-8f8u: Bifunctional ligase/repressor BirA from Klebsiella pneumoniae (Do... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8f8u
TitleBifunctional ligase/repressor BirA from Klebsiella pneumoniae (Domain Swapped Dimer)
ComponentsBifunctional ligase/repressor BirA
KeywordsTRANSCRIPTION / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
Function / homology
Function and homology information


biotin-[biotin carboxyl-carrier protein] ligase / biotin-[acetyl-CoA-carboxylase] ligase activity / protein modification process / regulation of DNA-templated transcription / DNA binding / ATP binding
Similarity search - Function
Biotin operon repressor, helix-turn-helix domain / Bifunctional ligase/repressor BirA / Helix-turn-helix, type 11 / HTH domain / Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain ...Biotin operon repressor, helix-turn-helix domain / Bifunctional ligase/repressor BirA / Helix-turn-helix, type 11 / HTH domain / Biotin protein ligase, C-terminal / Biotin protein ligase C terminal domain / Biotin--acetyl-CoA-carboxylase ligase / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) catalytic domain profile. / Biotin/lipoate A/B protein ligase family / Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL), catalytic domain / Transcriptional repressor, C-terminal / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL) / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
IMIDAZOLE / Bifunctional ligase/repressor BirA
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae 1158 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorOD030394 United States
CitationJournal: To be published
Title: Bifunctional ligase/repressor BirA from Klebsiella pneumoniae (Domain Swapped Dimer)
Authors: Liu, L. / Battaile, K.P. / Lovell, S.
History
DepositionNov 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 30, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / diffrn / Item: _diffrn.ambient_temp

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Bifunctional ligase/repressor BirA
B: Bifunctional ligase/repressor BirA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,1444
Polymers73,0062
Non-polymers1382
Water362
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-18 kcal/mol
Surface area27700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.910, 155.740, 58.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Bifunctional ligase/repressor BirA / Biotin operon repressor / Biotin--[acetyl-CoA-carboxylase] ligase / Biotin--protein ligase / Biotin- ...Biotin operon repressor / Biotin--[acetyl-CoA-carboxylase] ligase / Biotin--protein ligase / Biotin-[acetyl-CoA carboxylase] synthetase


Mass: 36502.785 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae 1158 (bacteria)
Gene: birA, B4U61_27335, B5L96_27980, BL124_00027250, BN49_4485, DDJ63_29720, DRB11_28835, EAO17_15035, FXN67_30565, G7Z27_25945, GJJ08_025595, GNE24_27625, GNG14_18750, HV479_27705, NCTC11679_05451, ...Gene: birA, B4U61_27335, B5L96_27980, BL124_00027250, BN49_4485, DDJ63_29720, DRB11_28835, EAO17_15035, FXN67_30565, G7Z27_25945, GJJ08_025595, GNE24_27625, GNG14_18750, HV479_27705, NCTC11679_05451, NCTC204_01612, NCTC3279_04746, NCTC5047_03297, NCTC5052_03568, NCTC8849_00281, NCTC9140_00986, NCTC9637_06311, NCTC9645_02159, NCTC9661_00981, SAMEA3499874_05300, SAMEA3499901_05308, SAMEA3500057_05333, SAMEA3512100_05201, SAMEA3538828_05246, SAMEA3649758_05372, SAMEA3720909_05478, SAMEA3727643_05796, SAMEA3727679_05497, SAMEA4364603_05401
Plasmid: Klpnc.17896.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0W7ZMT5, biotin-[biotin carboxyl-carrier protein] ligase
#2: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.13 Å3/Da / Density % sol: 60.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus G3: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Imidazole/MES, pH 6.5, 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic, 20 mM Potassium sodium tartrate ...Details: Morpheus G3: 20%(v/v) Glycerol, 10% w/v PEG 4000, 100 mM Imidazole/MES, pH 6.5, 20 mM Sodium formate, 20 mM Ammonium acetate, 20 mM Sodium citrate tribasic, 20 mM Potassium sodium tartrate and 20 mM Sodium oxamate, KlpnC.17896.a.B1.PW39036 at 30 mg/mL. Tray: Clover-Liu-S-045 / B1 , Puck: CPS5110_06, Cryo: 150% Morpheus G3. Protein crystals were dehydrated in this solution for 3 days before freezing.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.97949 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Oct 30, 2022
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.85→84.093 Å / Num. obs: 20235 / % possible obs: 94.2 % / Redundancy: 6.7 % / CC1/2: 1 / Rmerge(I) obs: 0.062 / Net I/σ(I): 17.1
Reflection shellResolution: 2.85→2.98 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.709 / Mean I/σ(I) obs: 1 / Num. unique obs: 1012 / CC1/2: 0.427 / % possible all: 49.3

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.85→29.74 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2552 1001 4.96 %
Rwork0.2147 --
obs0.2167 20186 91.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.85→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4541 0 10 2 4553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054629
X-RAY DIFFRACTIONf_angle_d0.7886282
X-RAY DIFFRACTIONf_dihedral_angle_d18.5331678
X-RAY DIFFRACTIONf_chiral_restr0.055731
X-RAY DIFFRACTIONf_plane_restr0.007806
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-30.4054640.35351238X-RAY DIFFRACTION42
3-3.190.37861470.33592839X-RAY DIFFRACTION97
3.19-3.430.34791450.28282986X-RAY DIFFRACTION100
3.43-3.780.30661610.24432954X-RAY DIFFRACTION100
3.78-4.320.26751680.21712988X-RAY DIFFRACTION100
4.32-5.440.24751460.18463038X-RAY DIFFRACTION100
5.44-29.740.20351700.1933142X-RAY DIFFRACTION99
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)
16.09352.15983.06153.77012.23092.97980.1524-0.5297-0.67410.1728-0.33520.75340.1499-0.67160.15790.69190.0320.13270.94250.02790.71547.679716.319533.5975
23.3052-0.18761.36557.7109-1.82023.80340.33430.19160.09670.0684-0.20370.1666-0.25710.0823-0.12440.47270.0560.06480.55020.03420.222738.884127.260249.3296
34.5164-0.70342.28384.2145-0.13662.2343-0.0075-0.0454-0.01050.417-0.0823-0.77270.1460.30960.13750.6467-0.03570.01580.65240.03730.401149.090625.253254.0056
41.24881.5596-0.0363.75250.51080.1516-0.20790.20070.5607-0.14590.29290.1051-0.51560.1998-0.05211.07570.0358-0.05630.90160.07860.996129.683446.94734.5347
53.3386-0.3062-1.62393.34631.49793.7634-0.1890.2325-0.4492-0.1489-0.17680.0455-0.00730.3420.38660.48870.0208-0.00470.64010.12750.387530.80887.308715.2031
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 89 )
2X-RAY DIFFRACTION2chain 'A' and (resid 90 through 175 )
3X-RAY DIFFRACTION3chain 'A' and (resid 176 through 317 )
4X-RAY DIFFRACTION4chain 'B' and (resid 3 through 89 )
5X-RAY DIFFRACTION5chain 'B' and (resid 90 through 317 )

+
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