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- PDB-3crj: Crystal structure of a TetR transcription regulator from Haloarcu... -

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Basic information

Entry
Database: PDB / ID: 3crj
TitleCrystal structure of a TetR transcription regulator from Haloarcula marismortui ATCC 43049
ComponentsTranscription regulator
KeywordsTRANSCRIPTION REGULATOR / APC88200 / TetR / Haloarcula marismortui ATCC 43049 / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


regulation of biosynthetic process / regulation of primary metabolic process / DNA binding
Similarity search - Function
BetI-type transcriptional repressor, C-terminal / BetI-type transcriptional repressor, C-terminal / 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. / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
TetR family transcriptional regulator
Similarity search - Component
Biological speciesHaloarcula marismortui ATCC 43049 (Halophile)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.6 Å
AuthorsTan, K. / Zhou, M. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a TetR transcription regulator from Haloarcula marismortui ATCC 43049.
Authors: Tan, K. / Zhou, M. / Freeman, L. / Joachimiak, A.
History
DepositionApr 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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: Transcription regulator
B: Transcription regulator
C: Transcription regulator
D: Transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,1055
Polymers92,0704
Non-polymers351
Water00
1
A: Transcription regulator
B: Transcription regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,0703
Polymers46,0352
Non-polymers351
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-21.5 kcal/mol
Surface area17350 Å2
MethodPISA
2
C: Transcription regulator
D: Transcription regulator


Theoretical massNumber of molelcules
Total (without water)46,0352
Polymers46,0352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-21 kcal/mol
Surface area17240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.494, 103.361, 167.898
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS EXPERIMENTALLY UNKNOWN AND THE CHAINS A,B AND C,D ARE EXPECTED TO FORM DIMERS, RESPECTIVELY.

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Components

#1: Protein
Transcription regulator


Mass: 23017.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haloarcula marismortui ATCC 43049 (Halophile)
Species: Haloarcula marismortui / Strain: DSM 3752 / JCM 8966 / Gene: tetR, pNG7308 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q5V649
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.15M DL-malic acid, 20% w/v PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97918 Å
DetectorType: SBC-3 / Detector: CCD / Date: Oct 13, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→35.99 Å / Num. all: 32786 / Num. obs: 32786 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.116 / Net I/σ(I): 18.76
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.606 / Mean I/σ(I) obs: 1.35 / Num. unique all: 1603 / % possible all: 72.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.6→35.99 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.891 / SU B: 28.873 / SU ML: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.565 / ESU R Free: 0.338 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. The N-terminal DNA-binding domain region of chain C (residues MET 1 to LEU 58) is partially disordered. Only main chain was built in ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. The N-terminal DNA-binding domain region of chain C (residues MET 1 to LEU 58) is partially disordered. Only main chain was built in most part of this region.
RfactorNum. reflection% reflectionSelection details
Rfree0.28789 1652 5.1 %RANDOM
Rwork0.23355 ---
all0.23628 30998 --
obs0.23628 30998 95.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.313 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20 Å2
2--0 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.6→35.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5904 0 1 0 5905
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226011
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9658165
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6025746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.00724.406320
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.923151008
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9671550
X-RAY DIFFRACTIONr_chiral_restr0.1040.2942
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024635
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.23013
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.24198
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2196
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.229
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1930.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6121.53807
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.01525978
X-RAY DIFFRACTIONr_scbond_it1.732421
X-RAY DIFFRACTIONr_scangle_it2.7434.52184
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.667 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 94 -
Rwork0.309 1519 -
obs-1613 65.62 %
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)
18.8792.0676-1.126410.3248-1.93569.17510.026-0.4498-0.2861.3153-0.026-0.09490.40850.13780-0.0902-0.13020.0261-0.22520.0554-0.1342-7.78368.492103.955
22.28081.72390.69192.89650.35862.93520.0123-0.0562-0.11640.33050.0186-0.07970.19880.1449-0.0309-0.1957-0.068-0.0396-0.2140.0132-0.21957.55389.631102.166
316.34099.46535.558410.84580.705713.55080.8476-3.10292.17030.5003-1.35631.0005-0.4117-0.4460.5087-0.2275-0.03310.09060.5895-0.4360.4073-25.56594.92782.833
43.07692.4059-0.14714.0351-0.58612.68720.0076-0.05370.3849-0.1963-0.00560.6133-0.4518-0.3728-0.002-0.2083-0.0305-0.0665-0.1260.0357-0.15180.051101.98186.006
533.4098-15.4568-6.69967.7635.159814.27991.15110.7864-0.5426-0.07610.59353.8398-0.6687-1.2189-1.74470.66510.4508-0.20120.7996-0.25731.1035-20.117129.47262.761
60.85621.0161-0.12843.3345-0.43199.0245-0.0086-0.16740.32030.4410.15370.7433-0.4953-1.1379-0.1451-0.09450.02770.0949-0.10210.0752-0.10182.126113.23460.895
76.3244-8.7412-5.212727.30521.390112.4638-1.3744-1.2120.29611.56791.6023-0.85870.59471.0014-0.22790.0930.4314-0.15730.0528-0.1797-0.05973.773146.13542.716
82.5217-1.2852-0.25713.9373-1.23976.03150.12030.01710.4795-0.0810.0121-0.2261-0.6918-0.0511-0.1324-0.0531-0.02670.1243-0.19720.0388-0.14212.754120.71944.098
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA7 - 5610 - 59
2X-RAY DIFFRACTION2AA57 - 19660 - 199
3X-RAY DIFFRACTION3BB9 - 5612 - 59
4X-RAY DIFFRACTION4BB57 - 19660 - 199
5X-RAY DIFFRACTION5CC11 - 5614 - 59
6X-RAY DIFFRACTION6CC57 - 19660 - 199
7X-RAY DIFFRACTION7DD8 - 5611 - 59
8X-RAY DIFFRACTION8DD57 - 19660 - 199

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