[English] 日本語
Yorodumi
- PDB-5f7r: ROK repressor Lmo0178 from Listeria monocytogenes bound to inducer -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5f7r
TitleROK repressor Lmo0178 from Listeria monocytogenes bound to inducer
ComponentsLmo0178 protein
KeywordsTRANSCRIPTION / Repressor / open reading frame / kinase / Structural Genomics / PSI-Biology / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


N-acylmannosamine kinase activity / N-acetylneuraminate catabolic process / metal ion binding
Similarity search - Function
ROK family / ROK family / Winged helix-turn-helix DNA-binding / ATPase, nucleotide binding domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / Lmo0178 protein
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLight, S.H. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Nat Microbiol / Year: 2016
Title: Structure to function of an alpha-glucan metabolic pathway that promotes Listeria monocytogenes pathogenesis.
Authors: Light, S.H. / Cahoon, L.A. / Halavaty, A.S. / Freitag, N.E. / Anderson, W.F.
History
DepositionDec 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: Lmo0178 protein
A: Lmo0178 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2419
Polymers90,1892
Non-polymers1,0527
Water4,756264
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6250 Å2
ΔGint-20 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.200, 95.064, 117.144
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein / Sugars , 2 types, 4 molecules EA

#1: Protein Lmo0178 protein / Rok repressor


Mass: 45094.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo0178 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q8YAF1
#2: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a6-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE

-
Non-polymers , 5 types, 269 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 264 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 1.77 Å3/Da / Density % sol: 30.34 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop
Details: 9.0 mg/mL protein in 0.5 M sodium chloride, 0.01 M Tris-HCl, pH 8.3 against Classics II D6 (Qiagen, 0.1 M Bis-Tris, pH 5.5, 25% w/v PEG3350)

-
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: Apr 27, 2015
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 55352 / % possible obs: 99.9 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 24.1
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.567 / Mean I/σ(I) obs: 2.7 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in-house structure

Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.098 / SU ML: 0.083 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20029 2664 4.8 %RANDOM
Rwork0.16659 ---
obs0.1682 52630 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.369 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4731 0 61 264 5056
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194999
X-RAY DIFFRACTIONr_bond_other_d0.0010.024749
X-RAY DIFFRACTIONr_angle_refined_deg1.2531.9656772
X-RAY DIFFRACTIONr_angle_other_deg0.76310957
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4865631
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5225.133226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91315855
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4651517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2759
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025712
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021141
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_it1.071.7982500
X-RAY DIFFRACTIONr_mcbond_other1.0691.7972499
X-RAY DIFFRACTIONr_mcangle_it1.7542.6843139
X-RAY DIFFRACTIONr_mcangle_other1.7542.6853140
X-RAY DIFFRACTIONr_scbond_it1.4542.0522499
X-RAY DIFFRACTIONr_scbond_other1.4422.052495
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.3782.9853628
X-RAY DIFFRACTIONr_long_range_B_refined5.26315.2015788
X-RAY DIFFRACTIONr_long_range_B_other5.26315.2065789
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 204 -
Rwork0.226 3811 -
obs--99.36 %
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)
14.4234-4.11561.03346.6942-1.71181.8519-0.03050.04440.026-0.2476-0.0729-0.43930.14840.35170.10340.08950.0530.06750.1040.00350.096449.05579.768787.989
22.7661-1.34970.56745.5647-1.22263.6336-0.09140.2935-0.2395-0.36040.06250.01660.20950.1040.02890.15280.0160.04940.0705-0.04170.072444.116775.978280.9788
30.9823-0.6855-0.42342.33940.58321.601-0.0771-0.0272-0.1470.0292-0.01490.10240.17770.07570.0920.05060.00940.03990.0358-0.00230.066535.546286.96695.9077
410.08760.3158-1.38325.4125-3.82162.85170.1580.45610.8211-0.3213-0.1797-0.1910.1130.04990.02170.49180.04420.08470.17260.09050.255439.5486113.457585.5271
57.11852.0383-0.20756.1114-1.85536.19130.170.12570.2171-0.3082-0.1713-0.6121-0.30210.3890.00120.1216-0.07260.08280.1060.02960.191147.8025109.179388.4956
60.9684-0.6151-0.54231.590.68271.9486-0.0579-0.24060.04730.03340.1541-0.20350.06980.3952-0.09630.01090.01120.00890.1437-0.01550.07944.104195.1455104.4693
72.8440.4488-0.77361.68540.61043.3156-0.131-0.5427-0.13680.21740.01140.1310.31520.25310.11950.09780.08980.05550.18160.07220.040221.519497.0404133.6458
811.47014.7233-11.3615.1721-2.982412.3591-0.55910.2963-0.85070.2588-0.1629-0.02851.1032-0.36070.7220.590.0484-0.20360.1575-0.10410.642516.500982.4105115.5036
91.1277-0.5547-0.15982.267-0.50811.9583-0.1035-0.1533-0.04830.00020.10260.0351-0.0350.11450.0010.04390.02280.01550.05340.00350.020424.8185104.0566113.0964
101.0784-0.66-0.23292.1772-0.21351.1527-0.09790.0063-0.09430.03660.14370.2558-0.132-0.28-0.04570.03780.03960.00560.11050.02170.064212.7384106.4081109.1219
111.7802-0.4263-1.69831.17770.64745.4584-0.17370.2333-0.33740.0632-0.07640.25320.3475-0.67770.250.0278-0.03980.04130.0935-0.0140.141215.926592.429110.0505
1210.4769-7.3274.553710.4066-8.42357.17890.545-0.3906-0.3222-0.6398-0.03160.56670.48280.1108-0.51340.23160.04380.01730.07920.08110.206822.070880.2246132.2078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A83 - 113
2X-RAY DIFFRACTION2A114 - 147
3X-RAY DIFFRACTION3A148 - 270
4X-RAY DIFFRACTION4A271 - 287
5X-RAY DIFFRACTION5A288 - 312
6X-RAY DIFFRACTION6A313 - 391
7X-RAY DIFFRACTION7E83 - 201
8X-RAY DIFFRACTION8E202 - 213
9X-RAY DIFFRACTION9E214 - 279
10X-RAY DIFFRACTION10E280 - 348
11X-RAY DIFFRACTION11E349 - 386
12X-RAY DIFFRACTION12E387 - 391

+
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