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- PDB-3egc: Crystal structure of a putative ribose operon repressor from Burk... -

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Basic information

Entry
Database: PDB / ID: 3egc
TitleCrystal structure of a putative ribose operon repressor from Burkholderia thailandensis
Componentsputative ribose operon repressor
Keywordsstructural genomics / unknown function / DNA-binding / Transcription / Transcription regulation / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I / Rossmann fold ...Periplasmic binding protein/LacI sugar binding domain / Periplasmic binding proteins and sugar binding domain of LacI family / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / 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
Ribose operon repressor, putative
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.35 Å
AuthorsBonanno, J.B. / Patskovsky, Y. / Gilmore, M. / Bain, K.T. / Hu, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative ribose operon repressor from Burkholderia thailandensis
Authors: Bonanno, J.B. / Patskovsky, Y. / Gilmore, M. / Bain, K.T. / Hu, S. / Romero, R. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionSep 10, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _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: putative ribose operon repressor
B: putative ribose operon repressor
C: putative ribose operon repressor
D: putative ribose operon repressor
E: putative ribose operon repressor
F: putative ribose operon repressor


Theoretical massNumber of molelcules
Total (without water)191,2766
Polymers191,2766
Non-polymers00
Water4,486249
1
A: putative ribose operon repressor
B: putative ribose operon repressor


Theoretical massNumber of molelcules
Total (without water)63,7592
Polymers63,7592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-10 kcal/mol
Surface area21080 Å2
MethodPISA
2
C: putative ribose operon repressor
D: putative ribose operon repressor


Theoretical massNumber of molelcules
Total (without water)63,7592
Polymers63,7592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-11 kcal/mol
Surface area21160 Å2
MethodPISA
3
E: putative ribose operon repressor
F: putative ribose operon repressor


Theoretical massNumber of molelcules
Total (without water)63,7592
Polymers63,7592
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-10 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.712, 288.651, 63.355
Angle α, β, γ (deg.)90.000, 113.590, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Refine code: 2 / Auth seq-ID: 1 - 1000 / Label seq-ID: 1 - 1000

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
putative ribose operon repressor


Mass: 31879.350 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / Gene: BTH_I0812 / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2T0D1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.64 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5.6
Details: 100mM tri-sodium citrate pH 5.6, 10% PEG MME 5K, 100mM magnesium acetate, Vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 25, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2.35→46.474 Å / Num. all: 69024 / Num. obs: 67644 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 20.6
Reflection shellResolution: 2.35→2.48 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 8.9 / Num. measured all: 73821 / Num. unique all: 10021 / Rsym value: 0.165 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
SCALA3.2.19data scaling
REFMACrefinement
PDB_EXTRACT3.006data extraction
MAR345CCDdata collection
DENZOdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.845 / Cor.coef. Fo:Fc free: 0.808 / WRfactor Rfree: 0.298 / WRfactor Rwork: 0.256 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.671 / SU B: 10.569 / SU ML: 0.271 / SU R Cruickshank DPI: 0.561 / SU Rfree: 0.315 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.561 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.299 3374 5 %RANDOM
Rwork0.257 ---
obs0.259 67534 98.05 %-
all-68877 --
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 max: 64.43 Å2 / Biso mean: 36.322 Å2 / Biso min: 16.02 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.22 Å2
2---0.21 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12046 0 0 249 12295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02212249
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.96316570
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30151554
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.38922.061553
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.989152071
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.16915156
X-RAY DIFFRACTIONr_chiral_restr0.1290.21899
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0219272
X-RAY DIFFRACTIONr_mcbond_it0.6871.57755
X-RAY DIFFRACTIONr_mcangle_it1.232212446
X-RAY DIFFRACTIONr_scbond_it2.29534494
X-RAY DIFFRACTIONr_scangle_it3.5114.54123
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A1043TIGHT POSITIONAL0.080.05
B1043TIGHT POSITIONAL0.080.05
C1043TIGHT POSITIONAL0.080.05
D1043TIGHT POSITIONAL0.070.05
E1043TIGHT POSITIONAL0.090.05
F1043TIGHT POSITIONAL0.090.05
A956MEDIUM POSITIONAL0.120.5
B956MEDIUM POSITIONAL0.10.5
C956MEDIUM POSITIONAL0.10.5
D956MEDIUM POSITIONAL0.090.5
E956MEDIUM POSITIONAL0.10.5
F956MEDIUM POSITIONAL0.10.5
A1043TIGHT THERMAL0.270.5
B1043TIGHT THERMAL0.260.5
C1043TIGHT THERMAL0.250.5
D1043TIGHT THERMAL0.260.5
E1043TIGHT THERMAL0.340.5
F1043TIGHT THERMAL0.350.5
A956MEDIUM THERMAL0.292
B956MEDIUM THERMAL0.272
C956MEDIUM THERMAL0.262
D956MEDIUM THERMAL0.262
E956MEDIUM THERMAL0.292
F956MEDIUM THERMAL0.42
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 260 -
Rwork0.234 4788 -
all-5048 -
obs-4788 99.9 %

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