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- PDB-4cgr: Structure of Regulator Protein SCO3201 from Streptomyces coelicolor -

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Basic information

Entry
Database: PDB / ID: 4cgr
TitleStructure of Regulator Protein SCO3201 from Streptomyces coelicolor
ComponentsPUTATIVE TETR-FAMILY TRANSCRIPTIONAL REGULATOR
KeywordsTRANSCRIPTION / REGULATOR / TETR
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
Tetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Bacterial regulatory proteins, tetR family / DNA-binding HTH domain, TetR-type / TetR-type HTH domain profile. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / TetR-family transcriptional regulator
Similarity search - Component
Biological speciesSTREPTOMYCES COELICOLOR (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsWaack, P. / Werten, S. / Hinrichs, W.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2014
Title: Structure and Regulatory Targets of Sco3201, a Highly Promiscuous Tetr-Like Regulator of Streptomyces Coelicolor M145.
Authors: Xu, D. / Waack, P. / Zhang, Q. / Werten, S. / Hinrichs, W. / Virolle, M.
History
DepositionNov 26, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.method / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PUTATIVE TETR-FAMILY TRANSCRIPTIONAL REGULATOR
B: PUTATIVE TETR-FAMILY TRANSCRIPTIONAL REGULATOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0033
Polymers46,9082
Non-polymers951
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-14.1 kcal/mol
Surface area19500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.680, 79.630, 95.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.970304, -0.238294, -0.041539), (-0.133006, 0.382179, 0.914466), (-0.202036, 0.892836, -0.402524)
Vector: 7.49188, 15.84406, -18.1361)

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Components

#1: Protein PUTATIVE TETR-FAMILY TRANSCRIPTIONAL REGULATOR / SCO3201


Mass: 23454.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STREPTOMYCES COELICOLOR (bacteria) / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: Q9KYU4
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / 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: 2.52 Å3/Da / Density % sol: 51.3 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 5
Details: HANGING DROP VAPOR DIFFUSION 0.1 M (NH4)H2PO4, 0.1 M TRIS/HCL PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.97549
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 6, 2013 / Details: MIRRORS
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97549 Å / Relative weight: 1
ReflectionResolution: 2.1→61.3 Å / Num. obs: 25127 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 51 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.77 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXCDEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.1→61.28 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.936 / SU B: 14.76 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.237 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.26893 1282 5.1 %RANDOM
Rwork0.22699 ---
obs0.22922 23803 99.84 %-
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: 67.899 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å20 Å20 Å2
2---3.03 Å20 Å2
3---0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.1→61.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2872 0 5 31 2908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0192930
X-RAY DIFFRACTIONr_bond_other_d0.0010.022810
X-RAY DIFFRACTIONr_angle_refined_deg1.6851.9543987
X-RAY DIFFRACTIONr_angle_other_deg0.85436376
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5755382
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.22421.121116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49115416
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1071535
X-RAY DIFFRACTIONr_chiral_restr0.0870.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213338
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02687
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_it2.7223.6351546
X-RAY DIFFRACTIONr_mcbond_other2.7213.6341545
X-RAY DIFFRACTIONr_mcangle_it3.7195.431922
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4783.9841384
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 80 -
Rwork0.324 1743 -
obs--99.95 %
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)
15.1681.9592-2.29875.3274-0.89936.052-0.22610.2266-0.1487-0.09010.1555-0.36640.3499-0.16160.07060.0728-0.0477-0.02920.2059-0.07540.143121.312.7948-6.3018
22.65832.1381-0.71345.18071.83894.4431-0.0047-0.18090.17830.15440.05130.17580.01440.358-0.04660.17910.03210.10430.1626-0.04010.092113.7041-4.6257-24.102
37.7402-1.2228-0.594111.24432.79515.01080.1383-0.1382-0.06520.0364-0.12920.39750.296-0.1018-0.00920.0772-0.05430.08270.1473-0.02270.2829-14.1587.1575-9.2711
47.6772-1.4744-2.60625.28640.39934.0749-0.4152-0.0007-0.90870.34150.14760.68690.8344-0.28980.26760.3931-0.03270.24770.2167-0.04440.3531-2.4128-13.978-16.596
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 86
2X-RAY DIFFRACTION1A127 - 139
3X-RAY DIFFRACTION2A87 - 126
4X-RAY DIFFRACTION2A140 - 230
5X-RAY DIFFRACTION3B6 - 86
6X-RAY DIFFRACTION3B127 - 139
7X-RAY DIFFRACTION4B87 - 126
8X-RAY DIFFRACTION4B140 - 229

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