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- PDB-3miz: Crystal structure of a putative transcriptional regulator protein... -

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Basic information

Entry
Database: PDB / ID: 3miz
TitleCrystal structure of a putative transcriptional regulator protein, Lacl family from Rhizobium etli
ComponentsPutative transcriptional regulator protein, LacI family
KeywordsTRANSCRIPTION REGULATOR / Lacl family / Protein Structure Initiative II (PSI II) / NYSGXRC / Structural Genomics / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


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
Putative transcriptional regulator protein, LacI family
Similarity search - Component
Biological speciesRhizobium etli (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsPalani, K. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative transcriptional regulator protein, Lacl family from Rhizobium etli
Authors: Palani, K. / Burley, S.K. / Swaminathan, S.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: 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_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: Putative transcriptional regulator protein, LacI family
B: Putative transcriptional regulator protein, LacI family


Theoretical massNumber of molelcules
Total (without water)68,1462
Polymers68,1462
Non-polymers00
Water3,369187
1
A: Putative transcriptional regulator protein, LacI family

A: Putative transcriptional regulator protein, LacI family


Theoretical massNumber of molelcules
Total (without water)68,1462
Polymers68,1462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3290 Å2
ΔGint-30 kcal/mol
Surface area22620 Å2
MethodPISA
2
B: Putative transcriptional regulator protein, LacI family

B: Putative transcriptional regulator protein, LacI family


Theoretical massNumber of molelcules
Total (without water)68,1462
Polymers68,1462
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area3330 Å2
ΔGint-33 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.508, 71.912, 212.375
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 transcriptional regulator protein, LacI family


Mass: 34073.078 Da / Num. of mol.: 2 / Fragment: sequence database residues 50-339
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli (bacteria) / Strain: CFN 42/ATCC 51251 / Gene: RHE_PE00360 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2K0Z9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 1.95 Å3/Da / Density % sol: 36.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Sodium formate, 20% Polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 27, 2010 / Details: Mirrors
RadiationMonochromator: Si(III) CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.91→45.22 Å / Num. all: 41886 / Num. obs: 41279 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 30.7 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 14 % / Rmerge(I) obs: 0.329 / Mean I/σ(I) obs: 2.4 / Num. unique all: 4051 / % possible all: 98.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
SHARPphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.91→45.22 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 110364.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 2067 5 %RANDOM
Rwork0.238 ---
obs0.238 41279 98.9 %-
all-41886 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.5836 Å2 / ksol: 0.373577 e/Å3
Displacement parametersBiso mean: 27.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.24 Å20 Å20 Å2
2--6.7 Å20 Å2
3----7.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.91→45.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4391 0 0 187 4578
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.83
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 1.91→2.03 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 318 4.8 %
Rwork0.249 6290 -
obs-4051 96.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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