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- PDB-4rk1: Crystal structure of LacI family transcriptional regulator from E... -

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Basic information

Entry
Database: PDB / ID: 4rk1
TitleCrystal structure of LacI family transcriptional regulator from Enterococcus faecium, Target EFI-512930, with bound ribose
ComponentsRibose transcriptional regulator
KeywordsTRANSCRIPTION REGULATOR / sugar binding / transcription regulation / Enzyme Function Initiative / EFI / structural genomics / transcriptional factor / D-glucose
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / LacI-type HTH domain signature. / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain ...Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / LacI-type HTH domain signature. / Periplasmic binding protein-like domain / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
alpha-D-ribofuranose / Ribose transcriptional regulator
Similarity search - Component
Biological speciesEnterococcus faecium DO (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsPatskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. ...Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Attonito, J.D. / Scott Glenn, A. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C. / Enzyme Function Initiative (EFI)
CitationJournal: To be Published
Title: Crystal Structure of LacI Transcriptional Regulator Rbsr from Enterococcus faecium, Target EFI-512930
Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. ...Authors: Patskovsky, Y. / Toro, R. / Bhosle, R. / Al Obaidi, N. / Chamala, S. / Scott Glenn, A. / Attonito, J.D. / Chowdhury, S. / Lafleur, J. / Siedel, R.D. / Hillerich, B. / Love, J. / Whalen, K.L. / Gerlt, J.A. / Almo, S.C.
History
DepositionOct 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Structure summary
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribose transcriptional regulator
B: Ribose transcriptional regulator
C: Ribose transcriptional regulator
D: Ribose transcriptional regulator
E: Ribose transcriptional regulator
F: Ribose transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,78233
Polymers190,1376
Non-polymers1,64527
Water21,1681175
1
A: Ribose transcriptional regulator
B: Ribose transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,96312
Polymers63,3792
Non-polymers58410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5100 Å2
ΔGint-98 kcal/mol
Surface area21170 Å2
MethodPISA
2
C: Ribose transcriptional regulator
D: Ribose transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,99813
Polymers63,3792
Non-polymers61911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-113 kcal/mol
Surface area21280 Å2
MethodPISA
3
E: Ribose transcriptional regulator
F: Ribose transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8218
Polymers63,3792
Non-polymers4426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-55 kcal/mol
Surface area21390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.371, 95.243, 123.602
Angle α, β, γ (deg.)90.00, 119.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A0 - 339
2116B0 - 339
3116C0 - 339
4116D0 - 339
5116E0 - 339
6116F0 - 339

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.491594, -0.005871, 0.870805), (0.014838, -0.999889, 0.001635), (0.870698, 0.013725, 0.491626)-162.81776, 133.85126, 94.30191
3given(0.999972, -0.005293, -0.005384), (-0.00536, -0.999908, -0.01247), (-0.005317, 0.012499, -0.999908)62.93181, 134.96434, 321.48819
4given(-0.495997, 0.019294, -0.86811), (0.020231, 0.999739, 0.010661), (0.868089, -0.012275, -0.496257)85.39262, 0.36896, 308.95572
5given(-0.500127, 0.017268, 0.86578), (-0.007185, 0.999684, -0.02409), (-0.865922, -0.018269, -0.499845)-225.43201, 5.33398, 230.76881
6given(-0.510403, -0.026837, -0.859517), (0.011071, -0.999635, 0.024638), (-0.859864, 0.00306, 0.510514)148.17445, 128.87421, 12.15934

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Components

#1: Protein
Ribose transcriptional regulator / LacI family transcriptional regulator


Mass: 31689.443 Da / Num. of mol.: 6 / Fragment: UNP residues 61-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecium DO (bacteria) / Gene: rbsR, HMPREF0351_10453 / Plasmid: pET / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I3TZ89
#2: Sugar
ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C5H10O5
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1175 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.01 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 1 M sodium acetate:HCl, pH 4.6, 1.5 M ammonium chloride, 10 mM D-glucose, ...Details: protein in 10 mM Bis-Tris, 500 mM sodium chloride, 10% glycerol, 5 mM DTT, TEV protease (1:100 ratio), reservoir: 1 M sodium acetate:HCl, pH 4.6, 1.5 M ammonium chloride, 10 mM D-glucose, cryoprotectant = reservoir + 30% w/v glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 5, 2014 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 197594 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 16.9
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.93 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.93 / % possible all: 95.7

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Processing

Software
NameVersionClassification
SHELXmodel building
ARP/wARPmodel building
REFMAC5.8.0073refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.814 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19234 5684 2.9 %RANDOM
Rwork0.15922 ---
obs0.16012 190152 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.347 Å2
Baniso -1Baniso -2Baniso -3
1--1.34 Å2-0 Å20.03 Å2
2--2.63 Å20 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12715 0 81 1175 13971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01913229
X-RAY DIFFRACTIONr_bond_other_d0.0010.0212740
X-RAY DIFFRACTIONr_angle_refined_deg1.221.98617932
X-RAY DIFFRACTIONr_angle_other_deg0.747329426
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96351643
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25124.693618
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.763152251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8841573
X-RAY DIFFRACTIONr_chiral_restr0.0710.22032
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02114818
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022923
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_it7.8036.4346494
X-RAY DIFFRACTIONr_mcbond_other7.8016.4336493
X-RAY DIFFRACTIONr_mcangle_it8.6219.518109
X-RAY DIFFRACTIONr_mcangle_other8.6219.5128110
X-RAY DIFFRACTIONr_scbond_it13.2098.1076735
X-RAY DIFFRACTIONr_scbond_other13.2088.1076735
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.26811.4229806
X-RAY DIFFRACTIONr_long_range_B_refined15.08320.64315702
X-RAY DIFFRACTIONr_long_range_B_other15.08420.64115701
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3996 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.362
2BLOOSE POSITIONAL0.342
3CLOOSE POSITIONAL0.342
4DLOOSE POSITIONAL0.352
5ELOOSE POSITIONAL0.532
6FLOOSE POSITIONAL0.452
1ALOOSE THERMAL3.9510
2BLOOSE THERMAL3.7310
3CLOOSE THERMAL3.9710
4DLOOSE THERMAL3.9110
5ELOOSE THERMAL4.2810
6FLOOSE THERMAL4.3510
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 369 -
Rwork0.284 14001 -
obs--99.83 %

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