[English] 日本語
Yorodumi
- PDB-4rfa: Crystal structure of cyclic nucleotide-binding domain containing ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4rfa
TitleCrystal structure of cyclic nucleotide-binding domain containing protein from Listeria monocytogenes EGD-e
ComponentsLmo0740 protein
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Crp
Function / homologyCyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Lmo0740 protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å
AuthorsFilippova, E.V. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of cyclic nucleotide-binding domain containing protein from Listeria monocytogenes EGD-e
Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 27, 2024Group: 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 / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lmo0740 protein


Theoretical massNumber of molelcules
Total (without water)26,7161
Polymers26,7161
Non-polymers00
Water81145
1
A: Lmo0740 protein

A: Lmo0740 protein


Theoretical massNumber of molelcules
Total (without water)53,4312
Polymers53,4312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3850 Å2
ΔGint-33 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.987, 91.987, 144.079
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

-
Components

#1: Protein Lmo0740 protein


Mass: 26715.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo0740 / Plasmid: pMCSG87 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q8Y902
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.0 M tri-Sodium Citrate, 0.1 M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
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: Jul 21, 2014 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. all: 18733 / Num. obs: 18733 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 21.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 34.9
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 4.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.8.0069refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.21→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.823 / SU ML: 0.132 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24253 920 4.9 %RANDOM
Rwork0.20607 ---
obs0.20792 17762 99.71 %-
all-17762 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.671 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.36 Å20 Å2
2--0.73 Å2-0 Å2
3----2.35 Å2
Refinement stepCycle: LAST / Resolution: 2.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 0 45 1781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021790
X-RAY DIFFRACTIONr_bond_other_d0.0010.021728
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9972425
X-RAY DIFFRACTIONr_angle_other_deg0.83233989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7335216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3892582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97315313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.645157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021978
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02385
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.224.438864
X-RAY DIFFRACTIONr_mcbond_other3.2214.434863
X-RAY DIFFRACTIONr_mcangle_it4.7046.6281080
X-RAY DIFFRACTIONr_mcangle_other4.7026.6341081
X-RAY DIFFRACTIONr_scbond_it3.9684.978924
X-RAY DIFFRACTIONr_scbond_other3.9684.969922
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0417.2891345
X-RAY DIFFRACTIONr_long_range_B_refined8.9836.7152050
X-RAY DIFFRACTIONr_long_range_B_other8.97136.6492044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.209→2.266 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 77 -
Rwork0.282 1245 -
obs--98.95 %
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)
16.4581-2.75550.45372.8568-1.67641.47950.0813-0.26710.0869-0.41010.04040.09510.2914-0.1601-0.12170.17220.0648-0.07650.30930.00860.046319.470735.3752-4.031
26.1047-0.11592.16172.3639-0.85831.71670.00520.1030.3594-0.4591-0.0964-0.0872-0.0349-0.07460.09120.16850.05260.03740.06090.0110.035835.616931.6781-1.4753
31.6206-1.11171.34182.7523-2.58273.96020.0847-0.28250.3048-0.4119-0.1380.0538-0.1812-0.40290.05330.28880.1623-0.05810.3803-0.07320.209825.378236.9171.5297
411.3825-3.62481.36622.45990.38921.1042-0.2277-0.01180.2060.12870.05980.0830.0134-0.16690.16790.1268-0.0072-0.02780.14650.01580.095630.102430.047712.4413
52.1873-1.02830.57265.513-0.95283.67650.0364-0.1855-0.4442-0.4220.22060.35310.441-0.1946-0.2570.1975-0.0116-0.08060.0310.03250.128139.18611.61764.4268
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 37
2X-RAY DIFFRACTION2A38 - 71
3X-RAY DIFFRACTION3A72 - 116
4X-RAY DIFFRACTION4A117 - 140
5X-RAY DIFFRACTION5A141 - 218

+
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