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- PDB-3ihu: Crystal structure of DNA binding protein (YP_298823.1) from Ralst... -

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Basic information

Entry
Database: PDB / ID: 3ihu
TitleCrystal structure of DNA binding protein (YP_298823.1) from Ralstonia eutropha JMP134 at 1.92 A resolution
ComponentsTranscriptional regulator, GntR familyTranscriptional regulation
KeywordsTRANSCRIPTION REGULATOR / YP_298823.1 / DNA binding protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / DNA-binding / Transcription / Transcription regulation / FCD domain
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
GntR ligand-binding domain-like / FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Four Helix Bundle (Hemerythrin (Met), subunit A) ...GntR ligand-binding domain-like / FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, GntR family
Similarity search - Component
Biological speciesRalstonia eutropha (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of DNA binding protein (YP_298823.1) from Ralstonia eutropha JMP134 at 1.92 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / 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, GntR family
B: Transcriptional regulator, GntR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0295
Polymers48,8662
Non-polymers1633
Water3,639202
1
A: Transcriptional regulator, GntR family


Theoretical massNumber of molelcules
Total (without water)24,4331
Polymers24,4331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transcriptional regulator, GntR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5964
Polymers24,4331
Non-polymers1633
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.646, 79.135, 103.244
Angle α, β, γ (deg.)90.000, 102.080, 90.000
Int Tables number5
Space group name H-MC121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Transcriptional regulator, GntR family / Transcriptional regulation


Mass: 24432.787 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia eutropha (bacteria) / Strain: JMP134 / Gene: Reut_B4629, YP_298823.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q46SA5
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS 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: 2.23 Å3/Da / Density % sol: 44.93 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.17
Details: 24.0000% polyethylene glycol 6000, 1.0000M lithium chloride, 0.1M TRIS pH 8.17, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97862,0.97799
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 16, 2009 / 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
20.978621
30.977991
ReflectionResolution: 1.92→29.361 Å / Num. obs: 32709 / % possible obs: 99.6 % / Redundancy: 2.7 % / Biso Wilson estimate: 34.581 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 12.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.92-1.972.70.5561.4655824160.556100
1.97-2.022.70.4151.8650823750.415100
2.02-2.082.70.2972.5626622900.297100
2.08-2.152.70.2213.4601221920.221100
2.15-2.222.70.1674.5598521830.167100
2.22-2.292.70.1345.5582821290.134100
2.29-2.382.70.116.7547219900.11100
2.38-2.482.70.0937.9532919420.093100
2.48-2.592.80.0828.7518618820.082100
2.59-2.722.80.0798.4485917650.079100
2.72-2.862.70.0768.4469317080.07699.9
2.86-3.042.70.0648.7442816200.06499.9
3.04-3.252.70.05410.6409214900.05499.9
3.25-3.512.80.04612.8384513970.04699.7
3.51-3.842.80.0414.5357812900.0499.7
3.84-4.292.80.03318.8324711740.03399.6
4.29-4.962.80.03219.1287710390.03299.4
4.96-6.072.70.03915.824048760.03998.9
6.07-8.592.70.03916.217906570.03997.9
8.59-29.362.40.04115.47092940.04174.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.92→29.361 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 10.003 / SU ML: 0.128 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.154
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. 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. 4. CHLORIDE ION AND GLYCEROL MOLECULE FROM THE CRYSTALLIZATION/CRYOPROTECTION SOLUTIONS ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1662 5.1 %RANDOM
Rwork0.199 ---
obs0.201 32709 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 66.26 Å2 / Biso mean: 24.792 Å2 / Biso min: 6.63 Å2
Baniso -1Baniso -2Baniso -3
1-1.53 Å20 Å2-0.65 Å2
2---1.3 Å20 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.92→29.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3117 0 8 202 3327
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0213267
X-RAY DIFFRACTIONr_bond_other_d0.0010.022262
X-RAY DIFFRACTIONr_angle_refined_deg1.4891.9554431
X-RAY DIFFRACTIONr_angle_other_deg0.96735459
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9535437
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62722.222162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.73615570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5371548
X-RAY DIFFRACTIONr_chiral_restr0.0890.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023745
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02714
X-RAY DIFFRACTIONr_mcbond_it0.871.52066
X-RAY DIFFRACTIONr_mcbond_other0.2321.5853
X-RAY DIFFRACTIONr_mcangle_it1.54723298
X-RAY DIFFRACTIONr_scbond_it2.58231201
X-RAY DIFFRACTIONr_scangle_it4.1344.51118
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.307 127 -
Rwork0.266 2287 -
all-2414 -
obs--99.88 %
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)
11.10210.4437-0.71882.5557-1.57521.440.1326-0.0449-0.0564-0.0841-0.07260.15120.0347-0.1573-0.060.14710.0373-0.03250.2321-0.05530.1967-6.7353.41335.401
21.79780.66341.21071.41510.48552.23510.02210.1735-0.1084-0.34-0.0184-0.17920.0182-0.0291-0.00360.26430.19120.06790.20880.02070.17979.066-7.66616.167
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 219
2X-RAY DIFFRACTION2B15 - 218

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