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- PDB-3r4k: Crystal structure of a putative ICLR transcriptional regulator (T... -

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Basic information

Entry
Database: PDB / ID: 3r4k
TitleCrystal structure of a putative ICLR transcriptional regulator (TM1040_3717) from SILICIBACTER SP. TM1040 at 2.46 A resolution
ComponentsTranscriptional regulator, IclR familyTranscriptional regulation
KeywordsDNA BINDING PROTEIN / DNA/RNA-binding 3-helical bundle / Profilin-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-biology
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily / Beta-Lactamase ...helix_turn_helix isocitrate lyase regulation / Bacterial transcriptional regulator / Transcription regulator IclR, N-terminal / Transcription regulator IclR, C-terminal / IclR helix-turn-helix domain / IclR-type HTH domain profile. / IclR effector binding domain profile. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator, IclR family
Similarity search - Component
Biological speciesRuegeria sp. TM1040 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.46 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative ICLR transcriptional regulator (TM1040_3717) from SILICIBACTER SP. TM1040 at 2.46 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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, IclR family
B: Transcriptional regulator, IclR family
C: Transcriptional regulator, IclR family
D: Transcriptional regulator, IclR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,9069
Polymers111,5954
Non-polymers3105
Water5,206289
1
A: Transcriptional regulator, IclR family
B: Transcriptional regulator, IclR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9224
Polymers55,7982
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4300 Å2
ΔGint-25 kcal/mol
Surface area22360 Å2
MethodPISA
2
C: Transcriptional regulator, IclR family
D: Transcriptional regulator, IclR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9845
Polymers55,7982
Non-polymers1863
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-23 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)203.983, 75.523, 77.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

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


Mass: 27898.793 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruegeria sp. TM1040 (bacteria) / Gene: TM1040_3717 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q1GKY2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 289 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.20M CaAcetate, 20.0% PEG-3350, No Buffer pH 7.3, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9116,0.9796,0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2011
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91161
20.97961
30.97941
ReflectionResolution: 2.46→29.14 Å / Num. all: 41482 / Num. obs: 41482 / % possible obs: 94.3 % / Redundancy: 3.5 % / Rsym value: 0.14 / Net I/σ(I): 7.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.46-2.523.60.8251.71108331070.82597.1
2.52-2.593.50.68221077230530.68297.6
2.59-2.673.50.6182.21046129610.61897.7
2.67-2.753.50.5242.6999028850.52496.8
2.75-2.843.30.462.8921827520.4695.7
2.84-2.943.30.3993.2825824930.39989.9
2.94-3.053.40.3064.2790622920.30686.7
3.05-3.183.50.2485.2903425580.24898.3
3.18-3.323.50.1836.8850624310.18397.8
3.32-3.483.50.1368.6803522870.13696.1
3.48-3.673.40.11110754121860.11195.7
3.67-3.893.40.09311.8631618510.09386.2
3.89-4.163.60.06914.5669218740.06992.7
4.16-4.493.60.06315.8675318820.06398.6
4.49-4.923.50.05916599716960.05996.4
4.92-5.53.40.06614510914850.06691.7
5.5-6.353.50.07413.1413811910.07484
6.35-7.783.60.05616.3417711710.05695.4
7.78-113.40.0420.628588470.0486.6
11-29.143.50.0421.617044800.0485.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.15data scaling
BUSTER-TNT2.8.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.46→29.14 Å / Cor.coef. Fo:Fc: 0.9281 / Cor.coef. Fo:Fc free: 0.9042 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 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. 1,2-ETHANEDIOL (EDO) MOLECULES FROM THE CRYOPROTECTION SOLUTION ARE MODELED. 5. NCS RESTRAINTS WERE USED DURING REFINEMENT VIA THE AUTONCS OPTION. 6. MAD PHASE RESTRAINTS (HL COEFFICIENTS) WERE USED DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2312 2098 5.06 %RANDOM
Rwork0.1901 ---
obs0.1922 41435 --
Displacement parametersBiso max: 140.99 Å2 / Biso mean: 44.073 Å2 / Biso min: 11.11 Å2
Baniso -1Baniso -2Baniso -3
1-7.0048 Å20 Å20 Å2
2---6.8744 Å20 Å2
3----0.1304 Å2
Refinement stepCycle: LAST / Resolution: 2.46→29.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7553 0 20 289 7862
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3637SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes147HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1187HARMONIC5
X-RAY DIFFRACTIONt_it7778HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1070SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8955SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7778HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10581HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion2.84
X-RAY DIFFRACTIONt_other_torsion2.89
LS refinement shellResolution: 2.46→2.52 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2802 186 6 %
Rwork0.2176 2916 -
all0.2213 3102 -
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)
14.9736-0.3154-2.98690.1102-0.01732.42220.41960.60520.6294-0.053-0.04280.0467-0.3852-0.3623-0.3769-0.1130.04380.0584-0.14350.0697-0.0917135.48725.413925.8378
21.44230.79360.06371.58930.32871.0890.01220.0974-0.11830.0020.0645-0.10980.06930.0165-0.0767-0.12250.04420.025-0.01710.0288-0.1163149.337-0.84120.0975
31.2564-0.70770.64031.2402-0.80231.1412-0.0852-0.07010.07150.110.05950.0281-0.1555-0.02420.0257-0.0521-0.0110.0144-0.0866-0.007-0.0697115.06318.510362.5199
40.88490.0795-0.10530.2780.40561.6323-0.02260.0857-0.0654-0.0377-0.041-0.0280.05490.03060.0636-0.0432-0.01930.0016-0.06520.0231-0.0668120.149-7.578250.0556
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|255 }A1 - 255
2X-RAY DIFFRACTION2{ B|2 - B|255 }B2 - 255
3X-RAY DIFFRACTION3{ C|1 - C|255 }C1 - 255
4X-RAY DIFFRACTION4{ D|1 - D|255 }D1 - 255

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