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- PDB-3ni7: Crystal structure of the TetR transcriptional regulator from Nitr... -

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Basic information

Entry
Database: PDB / ID: 3ni7
TitleCrystal structure of the TetR transcriptional regulator from Nitrosomonas europaea ATCC 19718
ComponentsBacterial regulatory proteins, TetR family
KeywordsTRANSCRIPTION REGULATOR / TetR / transcriptional regulator / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


COQ9 / COQ9 / 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
Bacterial regulatory proteins, TetR family
Similarity search - Component
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.78 Å
AuthorsKnapik, A. / Chruszcz, M. / Cymborowski, M. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of the TetR transcriptional regulator from Nitrosomonas europaea ATCC 19718
Authors: Knapik, A. / Chruszcz, M. / Cymborowski, M. / Xu, X. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Minor, W.
History
DepositionJun 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Bacterial regulatory proteins, TetR family
B: Bacterial regulatory proteins, TetR family


Theoretical massNumber of molelcules
Total (without water)51,2062
Polymers51,2062
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-25 kcal/mol
Surface area17660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.222, 75.378, 98.079
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A6 - 190
2111B6 - 190

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Components

#1: Protein Bacterial regulatory proteins, TetR family


Mass: 25602.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Gene: NE0300 / Plasmid: P15TV LIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 DE3 GOLD MAGIC / References: UniProt: Q82XH4
Has protein modificationY

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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: 2.32 Å3/Da / Density % sol: 46.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES, 0.65M MGFORMATE, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 13, 2006 / Details: MIRROR
RadiationMonochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979371
20.9791
ReflectionResolution: 2.8→50 Å / Num. all: 12269 / Num. obs: 12269 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 69.8 Å2 / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 19.797
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.708 / Mean I/σ(I) obs: 2.1 / Rsym value: 0.708 / % possible all: 94.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-3000phasing
MLPHAREphasing
DMmodel building
SHELXDphasing
RESOLVEmodel building
ARP/wARPmodel building
BUCCANEERmodel building
REFMAC5.5.0109refinement
Cootmodel building
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing
BUCCANEERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.78→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.916 / SU B: 55.82 / SU ML: 0.466 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 1.319 / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.279 590 4.8 %RANDOM
Rwork0.249 ---
all0.25 12316 --
obs0.25 12223 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 81.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--0.29 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 2.78→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2727 0 0 0 2727
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0212787
X-RAY DIFFRACTIONr_bond_other_d00.021829
X-RAY DIFFRACTIONr_angle_refined_deg1.6371.9313781
X-RAY DIFFRACTIONr_angle_other_deg4.16934408
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6275343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.4422.377122
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.87315468
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2191526
X-RAY DIFFRACTIONr_chiral_restr0.0840.2444
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023073
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02613
X-RAY DIFFRACTIONr_mcbond_it0.6831.51735
X-RAY DIFFRACTIONr_mcbond_other0.9031.5691
X-RAY DIFFRACTIONr_mcangle_it1.33422763
X-RAY DIFFRACTIONr_scbond_it2.83431052
X-RAY DIFFRACTIONr_scangle_it4.3494.51018
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 2187 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
tight positional0.240.05
tight thermal0.30.5
LS refinement shellResolution: 2.78→2.86 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 45 -
Rwork0.361 797 -
obs--94.82 %
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)
16.05371.7979-3.015811.8113-1.7158.38180.40260.30880.07890.7215-0.18850.7955-0.56760.3664-0.21411.52280.0167-0.16870.2404-0.03030.518839.53843.64347.395
20.34070.13930.282111.33782.3946.2745-0.1447-0.0142-0.07490.0042-0.0520.4358-0.06670.0760.19681.4670.0435-0.2290.21930.01870.71340.03823.49533.522
37.66730.385-1.112714.12763.118311.1391-0.08120.6464-0.02240.7394-0.25440.65590.2708-0.33810.33571.52260.0301-0.09080.25050.00730.57488.918-0.00831.401
44.68082.9765-2.379212.6013-1.48342.59820.07030.123-0.05510.85490.0858-0.2017-0.1911-0.1052-0.15611.68990.0295-0.26790.23360.0080.626719.94920.64423.336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 50
2X-RAY DIFFRACTION2A51 - 188
3X-RAY DIFFRACTION3B6 - 50
4X-RAY DIFFRACTION4B51 - 188

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