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- PDB-3gbv: Crystal structure of a putative LacI transcriptional regulator fr... -

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Basic information

Entry
Database: PDB / ID: 3gbv
TitleCrystal structure of a putative LacI transcriptional regulator from Bacteroides fragilis
ComponentsPutative LacI-family transcriptional regulator
KeywordsTRANSCRIPTION REGULATOR / NYSGXRC / PSI-II / 11231j / transcriptional regulator / Structural Genomics / Protein Structure Initiative / New York Structural GenomiX Research Consortium / DNA-binding / Transcription / Transcription regulation / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
LacI-type HTH domain signature. / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Periplasmic binding protein / Periplasmic binding protein domain / Lambda repressor-like, DNA-binding domain superfamily / Response regulator / Periplasmic binding protein-like I ...LacI-type HTH domain signature. / LacI-type HTH domain / Bacterial regulatory proteins, lacI family / LacI-type HTH domain profile. / helix_turn _helix lactose operon repressor / Periplasmic binding protein / Periplasmic binding protein 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
LacI-family transcriptional regulator / LacI-family transcriptional regulator
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsSyed Ibrahim, B. / Kumaran, D. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative LacI transcriptional regulator from Bacteroides fragilis
Authors: Syed Ibrahim, B. / Kumaran, D. / Burley, S.K. / Swaminathan, S.
History
DepositionFeb 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative LacI-family transcriptional regulator
B: Putative LacI-family transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,3479
Polymers70,9522
Non-polymers3957
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1880 Å2
ΔGint-11.4 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.976, 240.568, 119.214
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 Putative LacI-family transcriptional regulator


Mass: 35475.773 Da / Num. of mol.: 2 / Fragment: UNP residues 64-352
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: NCTC 9343 / Gene: BF2720 / Plasmid: (BC)pSGX2(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)RIL / References: UniProt: Q5LBV2, UniProt: A0A381D6S6*PLUS
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.36 Å3/Da / Density % sol: 47.82 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.4 M Sodium malonate, 30% 1,6-Hexanediol, 20% Xylitol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 29, 2009 / Details: Mirrors
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 32226 / Num. obs: 32226 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 14.6
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.455 / % possible all: 81.2

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.2→23.58 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 111121.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / 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
Rfree0.24 1480 5 %RANDOM
Rwork0.21 ---
obs0.21 29559 90.2 %-
all-32226 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.4301 Å2 / ksol: 0.390143 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-7.73 Å20 Å20 Å2
2---11.78 Å20 Å2
3---4.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.2→23.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4693 0 25 198 4916
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.451.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.832
X-RAY DIFFRACTIONc_scangle_it3.262.5
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.251 180 5.1 %
Rwork0.226 3364 -
obs--66.3 %

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