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

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Basic information

Entry
Database: PDB / ID: 4jnn
TitleCrystal structure of a putative transcriptional regulator from Saccharomonospora viridis in complex with benzamidine
ComponentsTranscriptional regulatorTranscriptional regulation
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / TetR family
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
BENZAMIDINE / BETA-MERCAPTOETHANOL / Transcriptional regulator
Similarity search - Component
Biological speciesSaccharomonospora viridis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsFilippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / 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 benzamidine
Authors: Filippova, E.V. / Minasov, G. / Shuvalova, L. / Kiryukhina, O. / Endres, M. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
History
DepositionMar 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 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)23,0003
Polymers22,8021
Non-polymers1982
Water25214
1
A: Transcriptional regulator
hetero molecules

A: Transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0006
Polymers45,6032
Non-polymers3974
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_557-x,y,-z+5/21
Buried area4480 Å2
ΔGint-2 kcal/mol
Surface area17180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.791, 109.952, 76.875
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Transcriptional regulator / Transcriptional regulation


Mass: 22801.633 Da / Num. of mol.: 1
Fragment: DNA binding domain and regulatory domain (UNP residues 94-287)
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-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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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: 1.98 Å3/Da / Density % sol: 37.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.3
Details: 0.2 M tri-Potassium Citrate, 20% PEG3350, pH 8.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07815 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 12, 2012 / Details: MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07815 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. all: 7525 / Num. obs: 7525 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 57 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 53.4
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 17.7 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ICH

4ich


Resolution: 2.35→27.85 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.915 / SU B: 24.882 / SU ML: 0.273 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.685 / ESU R Free: 0.304 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26586 344 4.6 %RANDOM
Rwork0.19836 ---
obs0.20167 7166 95.79 %-
all-7166 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 59.308 Å2
Baniso -1Baniso -2Baniso -3
1-2.25 Å20 Å20 Å2
2---3.03 Å2-0 Å2
3---0.78 Å2
Refinement stepCycle: LAST / Resolution: 2.35→27.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1568 0 13 14 1595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191610
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.9472177
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4345190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.21322.47185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.61915279
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5571521
X-RAY DIFFRACTIONr_chiral_restr0.1090.2242
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021226
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.354→2.415 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 27 -
Rwork0.237 522 -
obs--96.65 %
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)
17.0952-3.0997-3.689810.48931.06075.0140.0583-0.0402-0.76660.1877-0.1825-0.8398-0.08940.340.12430.24660.0186-0.08870.2135-0.02620.288811.6576104.054586.1248
24.4918-0.974-0.17337.9334-1.88293.58030.5530.99080.9647-0.652-0.4251-1.00710.2690.1504-0.12790.27670.10910.12630.50570.20550.3915.5359128.87985.0654
35.32720.41070.36731.87350.13081.57710.47950.23451.0137-0.0987-0.3094-0.13260.10740.0669-0.17010.2140.05960.15030.22010.07680.28886.6049131.482792.1651
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A94 - 143
2X-RAY DIFFRACTION2A144 - 180
3X-RAY DIFFRACTION3A181 - 284

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