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- PDB-2rgy: Crystal structure of transcriptional regulator of LacI family fro... -

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Basic information

Entry
Database: PDB / ID: 2rgy
TitleCrystal structure of transcriptional regulator of LacI family from Burkhoderia phymatum
ComponentsTranscriptional regulator, LacI family
KeywordsTRANSCRIPTION REGULATOR / 11011j / NYSGXRC / Transctiptional regulator / LacI family / sugar binding protein / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


alanine racemase / alanine racemase activity / regulation of DNA-templated transcription / DNA binding
Similarity search - Function
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 / 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
: / Transcriptional regulator, LacI family
Similarity search - Component
Biological speciesBurkholderia phymatum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsAgarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structural analysis of transcription regulator of LacI family from Burkholderia phymatum.
Authors: Agarwal, R. / Burley, S.K. / Swaminathan, S.
History
DepositionOct 5, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcriptional regulator, LacI family


Theoretical massNumber of molelcules
Total (without water)32,1671
Polymers32,1671
Non-polymers00
Water3,135174
1
A: Transcriptional regulator, LacI family

A: Transcriptional regulator, LacI family


Theoretical massNumber of molelcules
Total (without water)64,3352
Polymers64,3352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.543, 118.777, 85.439
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Transcriptional regulator, LacI family


Mass: 32167.475 Da / Num. of mol.: 1 / Fragment: Residues 81-359
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia phymatum (bacteria) / Strain: STM815 / Gene: BphyDRAFT_4885 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: A0FW12, UniProt: B2JNW3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.33 Å3/Da / Density % sol: 47.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Magnesium chloride, 0.1M Bis-tris, 25% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 2, 2007 / Details: mirrors
RadiationMonochromator: Si-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 19243 / Num. obs: 19243 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.7
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.319 / Mean I/σ(I) obs: 2 / Num. unique all: 1892 / % possible all: 99.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHELXEmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→42.72 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 100792.86 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: Residues listed as missing in Remark 465 are due to lack of electron density. Residues with missing atoms listed in Remark 470 are due to lack of electron density for side chains and modeled as alanines.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 552 3 %RANDOM
Rwork0.21 ---
obs0.21 18661 97.7 %-
all-19243 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.8927 Å2 / ksol: 0.349963 e/Å3
Displacement parametersBiso mean: 25 Å2
Baniso -1Baniso -2Baniso -3
1-1.26 Å20 Å20 Å2
2---2.64 Å20 Å2
3---1.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.05→42.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 0 174 2296
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.276 98 3.3 %
Rwork0.231 2855 -
obs--94.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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