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- PDB-4pzj: 1.60 Angstrom resolution crystal structure of a transcriptional r... -

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Basic information

Entry
Database: PDB / ID: 4pzj
Title1.60 Angstrom resolution crystal structure of a transcriptional regulator of the LysR family from Eggerthella lenta DSM 2243
ComponentsTranscriptional regulator, LysR family
KeywordsTRANSCRIPTION / STRUCTURAL GENOMICS / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, LysR family
Similarity search - Component
Biological speciesEggerthella lenta (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsHalavaty, A.S. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Endres, M. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 1.60 Angstrom resolution crystal structure of a transcriptional regulator of the LysR family from Eggerthella lenta DSM 2243
Authors: Halavaty, A.S. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Endres, M. / Shuvalova, L. / Joachimiak, A. / Anderson, W.F.
History
DepositionMar 31, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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

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Assembly

Deposited unit
A: Transcriptional regulator, LysR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,2152
Polymers8,1791
Non-polymers351
Water1,15364
1
A: Transcriptional regulator, LysR family
hetero molecules

A: Transcriptional regulator, LysR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4294
Polymers16,3582
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area1570 Å2
ΔGint-33 kcal/mol
Surface area8160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.623, 31.623, 132.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-224-

HOH

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Components

#1: Protein Transcriptional regulator, LysR family


Mass: 8179.068 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Eggerthella lenta (bacteria) / Strain: DSM 2243 / Gene: Elen_0221 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: C8WJY2
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE FOLLOWING FULL-LENGTH PROTEIN WAS CRYSTALLIZED, HOWEVER ONLY 70 RESIDUES WERE OBSERVED IN THE ...THE FOLLOWING FULL-LENGTH PROTEIN WAS CRYSTALLIZED, HOWEVER ONLY 70 RESIDUES WERE OBSERVED IN THE CRYSTAL. SEQRES REPRESENTS THE OBSERVED RESIDUES ONLY. MHHHHHHSSGVDLWSHPQFEKGTENLYFQSNAMLDFRVETFLTV(CME)RTMNYTRAAEEL NITQPAVSQHIAHLERDYGVPLFAYRNKKLQLTDAGALLRDALSTMAHDERLLRDRMRSSA TGARVELSLGMTLTAGEYLVAAPLADYLRRHPELHVAVRSGGTSELLALLNAGEIDCAFVE GFFDKNAYAWDVFRTERLVCVCAADHEFAARPVRVEDLFDERLIVREPGSGTRAVLEHALA AQNLTVDGFAQASVVESLDVIKILVEHDLGISFLYEAAVARELAAGTLRVIDLEGLAILHD IAFIRLKNSVFEREFQNLFADL

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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: 2.02 Å3/Da / Density % sol: 39.19 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein at 1.3 mg/mL in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME. crystallization: The Classics II Suite (A12 (#12): 100 mM Tris pH 8.5, 3 M NaCl), VAPOR DIFFUSION, SITTING DROP, ...Details: protein at 1.3 mg/mL in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME. crystallization: The Classics II Suite (A12 (#12): 100 mM Tris pH 8.5, 3 M NaCl), VAPOR DIFFUSION, SITTING DROP, temperature 295K. Cryo condition: 25% (final) sucrose.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97875 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 20, 2014 / Details: Mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97875 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 9452 / Num. obs: 9452 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 12.2 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 51.2
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 7.7 % / Rmerge(I) obs: 0.496 / Mean I/σ(I) obs: 3.42 / Num. unique all: 377 / Rsym value: 0.496 / % possible all: 85.7

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.6→28.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.221 / SU ML: 0.076 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.094 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21322 452 4.8 %RANDOM
Rwork0.18955 ---
obs0.19072 8945 98.2 %-
all-8945 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.482 Å2
Baniso -1Baniso -2Baniso -3
1-2.19 Å20 Å20 Å2
2--2.19 Å2-0 Å2
3----4.39 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms565 0 1 64 630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.019594
X-RAY DIFFRACTIONr_bond_other_d0.0010.02578
X-RAY DIFFRACTIONr_angle_refined_deg2.1411.993805
X-RAY DIFFRACTIONr_angle_other_deg0.86331322
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.439573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.56322.85728
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.5211594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.259156
X-RAY DIFFRACTIONr_chiral_restr0.0980.294
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02668
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02142
LS refinement shellResolution: 1.602→1.643 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 31 -
Rwork0.307 583 -
obs-583 90.29 %

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