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- PDB-3nuf: Crystal structure of a PRD-containing transcription regulator (LS... -

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Basic information

Entry
Database: PDB / ID: 3nuf
TitleCrystal structure of a PRD-containing transcription regulator (LSEI_2718) from Lactobacillus casei ATCC 334 at 1.38 A resolution
ComponentsPRD-containing transcription regulator
KeywordsTranscription regulator / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-BIOLOGY / TRANSCRIPTION
Function / homology
Function and homology information


regulation of DNA-templated transcription
Similarity search - Function
PRD domain / PTS-regulatory domain, PRD / PRD domain protein, EF0829/AHA3910 / PRD domain / PRD domain superfamily / PRD domain profile. / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / PRD domain-containing protein
Similarity search - Component
Biological speciesLactobacillus casei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.38 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a PRD-containing transcription regulator (LSEI_2718) from Lactobacillus casei ATCC 334 at 1.38 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 20, 2011Group: Structure summary
Revision 1.3Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software
Revision 1.4Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Nov 6, 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_ref_seq_dif / 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_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: PRD-containing transcription regulator
B: PRD-containing transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,13112
Polymers26,3012
Non-polymers83110
Water5,693316
1
A: PRD-containing transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5677
Polymers13,1501
Non-polymers4166
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: PRD-containing transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,5655
Polymers13,1501
Non-polymers4144
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)67.160, 67.160, 99.733
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. ANALYSIS OF THE CRYSTAL PACKING SUGGESTS BOTH THE MONOMER AND THE DIMER IN THE CRYSTAL MIGHT BE STABLE.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein PRD-containing transcription regulator


Mass: 13150.302 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus casei (bacteria) / Strain: ATCC 334 / Gene: LSEI_2718 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q034D9

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Non-polymers , 5 types, 326 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 316 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 2.14 Å3/Da / Density % sol: 42.47 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 1.6000M ammonium sulfate, 4.0000% polyethylene glycol 400, 0.1M HEPES pH 7.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97954,0.97939
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 5, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979541
30.979391
ReflectionResolution: 1.38→28.759 Å / Num. obs: 47575 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.639 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 13.65
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.38-1.430.8771.7320708733196
1.43-1.490.6212.3349449368199.5
1.49-1.550.4283.4296977930199.7
1.55-1.640.3084.7372359903199.8
1.64-1.740.2236.3328298683199.9
1.74-1.870.159330878712199.9
1.87-2.060.08714.3346729090199.9
2.06-2.360.04923.3347689079199.9
2.36-2.970.03729.8343088949199.9
2.97-28.7590.02841344749021199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0110refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.38→28.759 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / Occupancy max: 1 / Occupancy min: 0.25 / SU B: 1.815 / SU ML: 0.037 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.061
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. SULFATE (SO4) IONS, AND PEG-400 FRAGMENTS (PG4 AND PEG) ARE MODELED FROM CRYSTALLIZATION CONDITIONS. 6. ETHYLENE GLYCOL (EDO) MOLECULES ARE MODELED FROM CRYO CONDITIONS. 7. THERE IS A 5.4 SIGMA PEAK IN THE FOFC ELECTRON DENSITY MAP NEAR CARBONYL OXYGEN OF VALINE 106, WHICH COULD BE A WATER OR AMMONIUM ION, THIS REMAINS UNMODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.192 2409 5.1 %RANDOM
Rwork0.171 ---
obs0.172 47498 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 64.26 Å2 / Biso mean: 20.531 Å2 / Biso min: 3.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20 Å2
2--0.31 Å20 Å2
3----0.62 Å2
Refinement stepCycle: LAST / Resolution: 1.38→28.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1748 0 53 316 2117
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222039
X-RAY DIFFRACTIONr_bond_other_d0.0010.021304
X-RAY DIFFRACTIONr_angle_refined_deg1.5671.9762772
X-RAY DIFFRACTIONr_angle_other_deg0.94333262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5755271
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32227.15988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.19515357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.886152
X-RAY DIFFRACTIONr_chiral_restr0.0950.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022323
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02343
X-RAY DIFFRACTIONr_mcbond_it1.55531294
X-RAY DIFFRACTIONr_mcbond_other0.4093505
X-RAY DIFFRACTIONr_mcangle_it2.67352107
X-RAY DIFFRACTIONr_scbond_it4.5118745
X-RAY DIFFRACTIONr_scangle_it7.0911665
LS refinement shellResolution: 1.38→1.415 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 175 -
Rwork0.282 3236 -
all-3411 -
obs--98.5 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.32110.1552-0.12550.2019-0.13480.3123-0.0012-0.01890.04960.0037-0.00030.03020.0460.11280.00150.0070.01870.00180.04760.0040.006814.45229.64316.0466
20.4164-0.0581-0.04670.18240.17560.2163-0.0306-0.0049-0.0583-0.0032-0.0024-0.0004-0.0483-0.02530.0330.020.0139-0.0080.018-0.0040.015419.38256.121417.5185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 118
2X-RAY DIFFRACTION2B7 - 118

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