[English] 日本語
Yorodumi
- PDB-2ql3: Crystal structure of the C-terminal domain of a probable LysR fam... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ql3
TitleCrystal structure of the C-terminal domain of a probable LysR family transcriptional regulator from Rhodococcus sp. RHA1
ComponentsProbable transcriptional regulator, LysR family protein
KeywordsTRANSCRIPTION / APC7314 / LysR family / transcriptional regulator / Rhodococcus sp. RHA1 / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Probable transcriptional regulator, LysR family protein
Similarity search - Component
Biological speciesRhodococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsTan, K. / Skarina, T. / Kagen, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the C-terminal domain of a probable LysR family transcriptional regulator from Rhodococcus sp. RHA1.
Authors: Tan, K. / Skarina, T. / Kagen, O. / Savchenko, A. / Edwards, A. / Joachimiak, A.
History
DepositionJul 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Remark 300 BIOMOLECULE: 1, 2, 3, 4, 5, 6 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH ... BIOMOLECULE: 1, 2, 3, 4, 5, 6 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 12 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS EXPERIMENTALLY UNKNOWN AT THE TIME OF DEPOSITION, AND THAT THE BIOLOGICAL UNIT ASSEMBLY SHOWN IN REMARK 350 IS PREDICTED BY THE ANALYSIS OF PROTEIN INTERFACES BASED ON THIS CRYSTAL STRUCTURE.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Probable transcriptional regulator, LysR family protein
B: Probable transcriptional regulator, LysR family protein
C: Probable transcriptional regulator, LysR family protein
D: Probable transcriptional regulator, LysR family protein
E: Probable transcriptional regulator, LysR family protein
F: Probable transcriptional regulator, LysR family protein
G: Probable transcriptional regulator, LysR family protein
H: Probable transcriptional regulator, LysR family protein
I: Probable transcriptional regulator, LysR family protein
J: Probable transcriptional regulator, LysR family protein
K: Probable transcriptional regulator, LysR family protein
L: Probable transcriptional regulator, LysR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)282,46888
Polymers275,25012
Non-polymers7,21876
Water24,3021349
1
A: Probable transcriptional regulator, LysR family protein
B: Probable transcriptional regulator, LysR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,92013
Polymers45,8752
Non-polymers1,04511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4840 Å2
ΔGint-83 kcal/mol
Surface area17780 Å2
MethodPISA
2
C: Probable transcriptional regulator, LysR family protein
D: Probable transcriptional regulator, LysR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,92013
Polymers45,8752
Non-polymers1,04511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-84 kcal/mol
Surface area18050 Å2
MethodPISA
3
E: Probable transcriptional regulator, LysR family protein
F: Probable transcriptional regulator, LysR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,49019
Polymers45,8752
Non-polymers1,61517
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-103 kcal/mol
Surface area18210 Å2
MethodPISA
4
G: Probable transcriptional regulator, LysR family protein
H: Probable transcriptional regulator, LysR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,5409
Polymers45,8752
Non-polymers6657
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-53 kcal/mol
Surface area18310 Å2
MethodPISA
5
I: Probable transcriptional regulator, LysR family protein
J: Probable transcriptional regulator, LysR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,20516
Polymers45,8752
Non-polymers1,33014
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-92 kcal/mol
Surface area18460 Å2
MethodPISA
6
K: Probable transcriptional regulator, LysR family protein
L: Probable transcriptional regulator, LysR family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,39518
Polymers45,8752
Non-polymers1,52016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4900 Å2
ΔGint-79 kcal/mol
Surface area18240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.277, 114.277, 175.359
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsExperimentally unknown. From molecular packing, it seems the molecule forms dimer. There are 6 dimers in asymmetric unit, A-B, C-D, E-F, G-H, I-J, K-L.

-
Components

#1: Protein
Probable transcriptional regulator, LysR family protein


Mass: 22937.527 Da / Num. of mol.: 12 / Fragment: Residues 99-303
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodococcus sp. (bacteria) / Strain: RHA1 / Gene: RHA1_ro01847 / Plasmid: p15Tv Lic / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q0SFM8
#2: Chemical...
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 76 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1349 / 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: 2.4 Å3/Da / Density % sol: 48.74 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.2
Details: 1M Sodium-potassium phosphate, pH 8.2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 5, 2007 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.05→36.6 Å / Num. all: 159207 / Num. obs: 159207 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 30.5 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 16.7
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 1.7 / Num. unique all: 13206 / % possible all: 98.4

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→36.6 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.93 / SU B: 9.371 / SU ML: 0.135 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.202 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23853 7989 5 %RANDOM
Rwork0.17504 ---
all0.17823 151134 --
obs0.17823 151134 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.308 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.05→36.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18888 0 380 1349 20617
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02219785
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9851.99327190
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.31752482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98422.224805
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.767152900
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.67315193
X-RAY DIFFRACTIONr_chiral_restr0.1620.23101
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215041
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.29117
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3150.213074
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.21320
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2030.2172
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1870.252
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2691.512737
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.65220166
X-RAY DIFFRACTIONr_scbond_it3.00737956
X-RAY DIFFRACTIONr_scangle_it4.5194.57008
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.105 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 590 -
Rwork0.212 11025 -
obs--97.87 %
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)
10.9991-0.35210.39180.7252-0.47050.50960.01370.02950.065-0.0368-0.0833-0.0857-0.00480.01060.0696-0.03940.04090.0206-0.03960.0281-0.0348-17.9985-53.980750.2673
21.28-0.2941-0.24110.72780.14120.5598-0.0265-0.0636-0.16470.0708-0.00360.03880.0702-0.08880.0301-0.06280.0144-0.0097-0.02110.0565-0.0423-26.5897-72.513561.9226
30.4434-0.17410.051.3508-0.27111.7017-0.1087-0.0189-0.06030.11260.1342-0.1110.05650.1303-0.0256-0.08080.0856-0.0145-0.0448-0.0435-0.0210.522-83.428735.4596
40.8253-0.5609-0.24311.30980.40720.7786-0.0080.0693-0.142-0.06040.02150.18050.0209-0.1175-0.0134-0.06040.0008-0.0316-0.04470.007-0.0283-17.7915-80.253521.1291
51.1242-0.48610.55320.745-0.21240.5677-0.03150.04190.14820.0396-0.0129-0.0562-0.04810.03190.0444-0.0536-0.0150.0153-0.02730.0087-0.0555.3362-72.757784.2165
61.0887-0.4689-0.23720.51750.19070.7607-0.0512-0.0307-0.08460.02390.02490.0910.0931-0.02850.0263-0.061-0.00910.011-0.02490.0258-0.032242.9317-88.672396.5709
71.3712-0.5406-0.43990.74210.05111.34860.0169-0.0071-0.17170.0518-0.01910.15930.3104-0.1990.0022-0.0288-0.0895-0.0257-0.0427-0.003-0.054831.3786-103.642667.8766
80.5331-0.10640.03660.16650.04791.29170.0531-0.01760.0212-0.0208-0.0670.0226-0.1047-0.07680.0139-0.00890.0211-0.001-0.0339-0.0139-0.064738.8167-86.512754.0538
90.6429-0.3719-0.13290.58260.17690.5827-0.01780.0089-0.00630.00610.0194-0.0026-0.003-0.0426-0.0016-0.0484-0.00580.0004-0.02810.0063-0.0423-19.1759-122.460293.6762
102.09350.08850.00170.0739-0.03920.54330.03910.18120.2976-0.02360.00460.0233-0.17130.0576-0.0437-0.0262-0.01830.0458-0.05520.0313-0.0039-8.046-105.411382.2852
111.03360.3905-0.22530.6647-0.11350.95420.02420.1018-0.09560.02780.0195-0.06020.03840.1173-0.0437-0.06150.011-0.0023-0.0058-0.038-0.063815.823-123.4909108.153
121.10320.17640.43740.36030.10560.4723-0.0469-0.01840.08560.04360.02690.042-0.0606-0.01050.0199-0.0173-0.01640.0158-0.0414-0.0143-0.05183.575-109.8799122.8418
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA99 - 3033 - 207
2X-RAY DIFFRACTION2BB99 - 3033 - 207
3X-RAY DIFFRACTION3CC99 - 3033 - 207
4X-RAY DIFFRACTION4DD99 - 3033 - 207
5X-RAY DIFFRACTION5EE99 - 3033 - 207
6X-RAY DIFFRACTION6FF99 - 3033 - 207
7X-RAY DIFFRACTION7GG99 - 3033 - 207
8X-RAY DIFFRACTION8HH99 - 3033 - 207
9X-RAY DIFFRACTION9II99 - 3033 - 207
10X-RAY DIFFRACTION10JJ99 - 3033 - 207
11X-RAY DIFFRACTION11KK99 - 3033 - 207
12X-RAY DIFFRACTION12LL99 - 3033 - 207

+
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