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- PDB-4nel: Crystal structure of a putative transcriptional regulator from Sa... -

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Basic information

Entry
Database: PDB / ID: 4nel
TitleCrystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with N,N-dimethylmethanamine
ComponentsTranscriptional regulatorTranscriptional regulation
KeywordsTRANSCRIPTION REGULATOR / STRUCTURAL GENOMICS / PSI-BIOLOGY / MIDWEST CENTER FOR STRUCTURAL GENOMICS / MCSG
Function / homology
Function and homology information


regulation of DNA-templated transcription / DNA binding
Similarity search - Function
BetI-type transcriptional repressor, C-terminal / BetI-type transcriptional repressor, C-terminal / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. ...BetI-type transcriptional repressor, C-terminal / BetI-type transcriptional repressor, C-terminal / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / Tetracycline Repressor, domain 2 / Tetracyclin repressor-like, C-terminal domain superfamily / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Lambda repressor-like, DNA-binding domain superfamily / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
N,N-dimethylmethanamine / Transcriptional regulator
Similarity search - Component
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHalavaty, A.S. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with N,N-dimethylmethanamine
Authors: Halavaty, A.S. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionOct 29, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2013Group: Other
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3972
Polymers22,3381
Non-polymers591
Water55831
1
A: Transcriptional regulator
hetero molecules

A: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7944
Polymers44,6762
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area3240 Å2
ΔGint-14 kcal/mol
Surface area16820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.864, 109.240, 73.878
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-415-

HOH

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Components

#1: Protein Transcriptional regulator / Transcriptional regulation


Mass: 22338.117 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomonospora viridis (bacteria) / Strain: DSM 43017 / Gene: Svir_16270 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: C7MT25
#2: Chemical ChemComp-KEN / N,N-dimethylmethanamine / Trimethylamine


Mass: 59.110 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H9N
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPROTEIN WAS PROTEOLIZED DURING CRYSTALLIZATION EXPERIMENT. THE REPORTED SEQUENCE IS THE ONE ...PROTEIN WAS PROTEOLIZED DURING CRYSTALLIZATION EXPERIMENT. THE REPORTED SEQUENCE IS THE ONE OBSERVED IN THE STRUCTURE.

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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: 1.89 Å3/Da / Density % sol: 34.94 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: protein at 1.2 mg/mL in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME, 5 mM N,N-dimethylmethanamine, crystallization: The Classics II F12: 0.2 M NaCl, 0.1 M HEPES pH 7.5 25%(w/v) PEG3350, ...Details: protein at 1.2 mg/mL in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME, 5 mM N,N-dimethylmethanamine, crystallization: The Classics II F12: 0.2 M NaCl, 0.1 M HEPES pH 7.5 25%(w/v) PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 21, 2013 / Details: Be lenses
RadiationMonochromator: DIAMOND(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. all: 11143 / Num. obs: 11143 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.2 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 27.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 7.4 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 4.2 / Num. unique all: 541 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KWA

4kwa


Resolution: 2.05→26.86 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.931 / SU B: 12.751 / SU ML: 0.157 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.251 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25908 520 4.7 %RANDOM
Rwork0.18492 ---
obs0.18801 10449 99.63 %-
all-10449 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.416 Å2
Baniso -1Baniso -2Baniso -3
1-2.37 Å20 Å2-0 Å2
2---4.35 Å2-0 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.05→26.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1566 0 4 31 1601
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191646
X-RAY DIFFRACTIONr_bond_other_d0.0010.021602
X-RAY DIFFRACTIONr_angle_refined_deg1.6241.9462230
X-RAY DIFFRACTIONr_angle_other_deg0.82933646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.9215197
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.14422.15988
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45715284
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6531523
X-RAY DIFFRACTIONr_chiral_restr0.0920.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021870
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02423
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 45 -
Rwork0.225 769 -
obs-769 100 %
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)
14.2297-2.04851.15996.1327-1.08622.48720.1546-0.01180.1528-0.1254-0.18460.2777-0.2371-0.0860.030.1013-0.00720.00610.21440.00750.034-11.73215.63187.8862
20.9725-0.1027-0.162411.08263.43082.07490.13980.1671-0.0743-0.1397-0.32580.6854-0.0638-0.28190.18590.0363-0.01690.00160.2661-0.03010.1214-15.3958-15.075110.1407
32.0743-0.29910.28944.95873.993811.7935-0.0672-0.03290.03980.0324-0.07160.05460.080.00090.13870.0188-0.00750.02220.21430.04720.0517-5.3861-10.310412.6581
40.52591.1695-0.461315.41344.94313.69950.0542-0.1118-0.0540.0396-0.31660.546-0.0983-0.32270.26240.01-0.0140.02310.369-0.03170.3055-15.0689-22.140918.9916
53.08020.5836-0.29475.8984-1.23674.62510.0406-0.012-0.4246-0.2519-0.1102-0.1352-0.00040.20140.06970.03190.02010.03660.27360.00240.1475-1.7454-26.799712.7997
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A95 - 136
2X-RAY DIFFRACTION2A137 - 179
3X-RAY DIFFRACTION3A180 - 204
4X-RAY DIFFRACTION4A205 - 235
5X-RAY DIFFRACTION5A236 - 284

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