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- PDB-3e97: Crystal structure of transcriptional regulator of Crp/Fnr family ... -

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Basic information

Entry
Database: PDB / ID: 3.0E+97
TitleCrystal structure of transcriptional regulator of Crp/Fnr family (YP_604437.1) from DEINOCOCCUS GEOTHERMALIS DSM 11300 at 1.86 A resolution
ComponentsTranscriptional regulator, Crp/Fnr family
Keywordstranscription regulator / YP_604437.1 / transcriptional regulator / Crp/Fnr family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / DNA-binding / Transcription / Transcription regulation / Cyclic nucleotide-binding domain
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain ...helix_turn_helix, cAMP Regulatory protein / Crp-type HTH domain profile. / Crp-like helix-turn-helix domain / Crp-type HTH domain / Cyclic nucleotide-binding domain signature 2. / Cyclic nucleotide-binding, conserved site / Cyclic nucleotide-monophosphate binding domain / Cyclic nucleotide-binding domain / cAMP/cGMP binding motif profile. / Cyclic nucleotide-binding domain / Cyclic nucleotide-binding domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Jelly Rolls / Winged helix-like DNA-binding domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, Crp/Fnr family
Similarity search - Component
Biological speciesDeinococcus geothermalis DSM 11300 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.86 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of transcriptional regulator of Crp/Fnr family (YP_604437.1) from DEINOCOCCUS GEOTHERMALIS DSM 11300 at 1.86 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 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 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _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: Transcriptional regulator, Crp/Fnr family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0253
Polymers25,9011
Non-polymers1242
Water3,387188
1
A: Transcriptional regulator, Crp/Fnr family
hetero molecules

A: Transcriptional regulator, Crp/Fnr family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0506
Polymers51,8022
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area4120 Å2
ΔGint-14 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.000, 68.000, 111.450
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsAUTHORS STATE THAT CRYSTAL PACKING ANALYSIS SUGGESTS A DIMER AS THE OLIGOMERIC FORM IN SOLUTION.

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Components

#1: Protein Transcriptional regulator, Crp/Fnr family


Mass: 25900.938 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus geothermalis DSM 11300 (bacteria)
Gene: YP_604437.1, Dgeo_0968 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1IZR6
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / Source method: isolated from a natural source / Formula: H2O
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: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 0.2000M KAcetate, 20.0000% PEG-3350, No Buffer pH 7.8, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97929
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 6, 2008 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979291
ReflectionResolution: 1.86→29.399 Å / Num. obs: 22704 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 11.45 % / Biso Wilson estimate: 26.147 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 17.84
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.86-1.930.6312.4316702437699.6
1.93-20.4173.614624383599.8
2-2.090.342518056414099.6
2.09-2.20.2677.522685421199.9
2.2-2.340.2189.726205430899.8
2.34-2.520.18412.931082418899.9
2.52-2.780.12917.8333004297100
2.78-3.180.07626.5321814163100
3.18-40.04341.8325044193100
4-29.3990.03450.532687422999.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.86→29.399 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 3.037 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.149 / ESU R Free: 0.14
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. 1,2-ETHANEDIOL FROM THE CRYOPROTECANT HAS BEEN MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1158 5.1 %RANDOM
Rwork0.208 ---
obs0.21 22645 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.58 Å2 / Biso mean: 30.37 Å2 / Biso min: 12.68 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2---0.77 Å20 Å2
3---1.55 Å2
Refinement stepCycle: LAST / Resolution: 1.86→29.399 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1762 0 8 188 1958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221803
X-RAY DIFFRACTIONr_bond_other_d0.0010.021218
X-RAY DIFFRACTIONr_angle_refined_deg1.4581.982465
X-RAY DIFFRACTIONr_angle_other_deg0.95332978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0675242
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.75423.12580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.49915315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.771520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2304
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022011
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02356
X-RAY DIFFRACTIONr_nbd_refined0.2140.2378
X-RAY DIFFRACTIONr_nbd_other0.2010.21295
X-RAY DIFFRACTIONr_nbtor_refined0.1670.2854
X-RAY DIFFRACTIONr_nbtor_other0.0830.2979
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2920.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.210
X-RAY DIFFRACTIONr_mcbond_it2.03431239
X-RAY DIFFRACTIONr_mcbond_other0.4583454
X-RAY DIFFRACTIONr_mcangle_it2.9651856
X-RAY DIFFRACTIONr_scbond_it4.4678687
X-RAY DIFFRACTIONr_scangle_it6.28311598
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 92 -
Rwork0.247 1547 -
all-1639 -
obs--99.76 %

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