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- PDB-3loc: Crystal structure of putative transcriptional regulator ycdc -

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Basic information

Entry
Database: PDB / ID: 3loc
TitleCrystal structure of putative transcriptional regulator ycdc
ComponentsHTH-type transcriptional regulator rutR
KeywordsTRANSCRIPTION / HELIX-TURN-HELIX / PUTATIVE TRANSCRIPTIONAL REGULATOR / DIMER / URACIL / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / NYSGXRC / DNA-binding / Repressor / Transcription regulation
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription
Similarity search - Function
Transcription regulator YcdC, C-terminal / Transcription regulator, pyrimidine utilisation, RutR / YcdC-like protein, C-terminal region / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like ...Transcription regulator YcdC, C-terminal / Transcription regulator, pyrimidine utilisation, RutR / YcdC-like protein, C-terminal region / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
URACIL / HTH-type transcriptional regulator RutR
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsPatskovsky, Y.V. / Knapik, A.A. / Mennella, V. / Burley, S.K. / Minor, W. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of Hypothetical Transcriptional Regulator Ycdc from Escherichia Coli
Authors: Patskovsky, Y.V. / Mennella, V. / Almo, S.C.
History
DepositionFeb 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
SupersessionJun 16, 2010ID: 1PB6
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 10, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / database_2
Item: _audit_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator rutR
B: HTH-type transcriptional regulator rutR
C: HTH-type transcriptional regulator rutR
D: HTH-type transcriptional regulator rutR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,2538
Polymers95,8044
Non-polymers4484
Water1,24369
1
A: HTH-type transcriptional regulator rutR
B: HTH-type transcriptional regulator rutR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1264
Polymers47,9022
Non-polymers2242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4950 Å2
ΔGint-36 kcal/mol
Surface area17100 Å2
MethodPISA
2
C: HTH-type transcriptional regulator rutR
D: HTH-type transcriptional regulator rutR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1264
Polymers47,9022
Non-polymers2242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-33 kcal/mol
Surface area17220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.020, 139.610, 156.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

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Components

#1: Protein
HTH-type transcriptional regulator rutR / Rut operon repressor


Mass: 23951.070 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b1013, JW0998, rutR, ycdC / Plasmid: T7 TOPO-CT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0ACU2
#2: Chemical
ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 3.15 Å3/Da / Density % sol: 60.6 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7
Details: SODIUM CHLORIDE, SODIUM FORMATE, GLYCEROL, PH 7, VAPOR DIFFUSION, TEMPERATURE 290K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12001
22001
Diffraction source
SourceSiteBeamlineIDWavelengthWavelength (Å)
SYNCHROTRONAPS 19-BM10.963670.96367
SYNCHROTRONNSLS X9A20.972, 0.9786, 0.9789
Detector
TypeIDDetectorDateDetails
SBC-31CCDMar 11, 2003MIRRORS
MARRESEARCH2IMAGE PLATEMar 13, 2003MIRRORS
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1MIRRORSSINGLE WAVELENGTHMx-ray1
2MIRRORSMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.963671
20.9721
30.97861
40.97891
ReflectionResolution: 2.5→50 Å / Num. all: 40218 / Num. obs: 40218 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.48 % / Rmerge(I) obs: 0.064 / Rsym value: 0.093 / Net I/σ(I): 8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.43 / % possible all: 99.3

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Processing

Software
NameVersionClassification
SBC-CollectCollectdata collection
SOLVEphasing
RESOLVEmodel building
HKL-3000phasing
REFMAC5.5.0109refinement
Cootmodel building
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→49.35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / SU B: 19.52 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.377 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22905 1931 5 %RANDOM
Rwork0.19537 ---
all0.19704 36793 --
obs0.19704 36793 96.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.88 Å20 Å20 Å2
2---2.28 Å20 Å2
3---1.41 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6235 0 32 69 6336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0226435
X-RAY DIFFRACTIONr_bond_other_d0.0010.024345
X-RAY DIFFRACTIONr_angle_refined_deg1.4471.9768735
X-RAY DIFFRACTIONr_angle_other_deg2.243310601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2675805
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83823.502257
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.644151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1981538
X-RAY DIFFRACTIONr_chiral_restr0.0840.21006
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217101
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021333
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_it0.4851.54032
X-RAY DIFFRACTIONr_mcbond_other0.081.51608
X-RAY DIFFRACTIONr_mcangle_it0.94426468
X-RAY DIFFRACTIONr_scbond_it2.12332403
X-RAY DIFFRACTIONr_scangle_it3.1324.52267
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 2471 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.730.5
Bmedium positional0.630.5
Cmedium positional0.520.5
Dmedium positional0.660.5
Amedium thermal0.592
Bmedium thermal0.552
Cmedium thermal0.62
Dmedium thermal0.552
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 127 -
Rwork0.348 2379 -
obs--85.65 %
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)
115.45810.77515.51932.29461.21079.3056-0.2538-0.85910.2326-0.06320.034-0.0982-0.2647-0.12610.21980.02180.02290.00010.68590.04680.0442-5.56437.526-1.292
24.08330.54952.35272.2270.37984.454-0.51490.37280.408-0.36860.0527-0.1155-0.75461.01110.46220.2373-0.1861-0.05240.64190.17050.1403-11.93840.189-27.766
34.2944.7826-1.46129.0472-3.44981.30080.6097-0.51810.49390.6724-0.68380.3366-0.12860.34450.07410.4107-0.07320.11770.4310.04340.3165-26.4411.049-14.075
43.31940.07141.86592.346-0.09235.29520.06920.26-0.355-0.3361-0.1317-0.06880.31810.35950.06250.1690.00350.00830.45780.06080.1278-20.56826.541-33.272
512.3003-6.08342.00112.1669-2.27121.74120.1917-0.225-1.6486-0.0115-0.04670.5274-0.35670.0497-0.1450.1076-0.0305-0.00930.39250.12720.35238.12-31.5631.733
63.5890.9014-0.96753.4284-0.94892.06840.3433-0.21790.14110.3519-0.28880.1645-0.5595-0.0006-0.05450.2757-0.02050.03880.28790.0010.15364.53-7.105-6.253
74.26942.64341.92164.70612.6673.9642-0.0045-0.0439-0.1248-0.22710.0941-0.16810.1385-0.2344-0.08960.31480.0254-0.09130.4354-0.05220.1455-12.243-29.818-28.083
83.39690.8155-0.35843.0998-0.62612.2010.130.4560.28-0.38-0.03070.5845-0.3432-0.3283-0.09940.3020.1416-0.05680.40040.0340.2492-4.074-6.867-20.665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 70
2X-RAY DIFFRACTION2A71 - 211
3X-RAY DIFFRACTION3B11 - 76
4X-RAY DIFFRACTION4B77 - 211
5X-RAY DIFFRACTION5C12 - 76
6X-RAY DIFFRACTION6C77 - 211
7X-RAY DIFFRACTION7D10 - 76
8X-RAY DIFFRACTION8D77 - 211

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