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- PDB-1zkg: Crystal structure of Transcriptional regulator, TETR family (tm10... -

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Basic information

Entry
Database: PDB / ID: 1zkg
TitleCrystal structure of Transcriptional regulator, TETR family (tm1030) from Thermotoga maritima at 2.30 A resolution
Componentstranscriptional regulator, TetR family
KeywordsTRANSCRIPTION REGULATOR / tm1030 / Transcriptional regulator / TETR family / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
: / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / 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. ...: / Tetracyclin repressor-like, C-terminal domain / DNA-binding HTH domain, TetR-type, conserved site / TetR-type HTH domain signature. / 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. / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Unknown ligand / Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2007
Title: Crystal structure of TM1030 from Thermotoga maritima at 2.3 A resolution reveals molecular details of its transcription repressor function.
Authors: Premkumar, L. / Rife, C.L. / Sri Krishna, S. / McMullan, D. / Miller, M.D. / Abdubek, P. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Canaves, J.M. / Carlton, D. / Chiu, H.J. / Clayton, T. ...Authors: Premkumar, L. / Rife, C.L. / Sri Krishna, S. / McMullan, D. / Miller, M.D. / Abdubek, P. / Ambing, E. / Astakhova, T. / Axelrod, H.L. / Canaves, J.M. / Carlton, D. / Chiu, H.J. / Clayton, T. / DiDonato, M. / Duan, L. / Elsliger, M.A. / Feuerhelm, J. / Floyd, R. / Grzechnik, S.K. / Hale, J. / Hampton, E. / Han, G.W. / Haugen, J. / Jaroszewski, L. / Jin, K.K. / Klock, H.E. / Knuth, M.W. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Levin, I. / McPhillips, T.M. / Morse, A.T. / Nigoghossian, E. / Okach, L. / Oommachen, S. / Paulsen, J. / Quijano, K. / Reyes, R. / Rezezadeh, F. / Rodionov, D. / Schwarzenbacher, R. / Spraggon, G. / van den Bedem, H. / White, A. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionMay 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGIMERIZATION STATE.
Remark 999SEQUENCE: THIS GENE USES AN ALTERNATE INITIATION CODON THAT RESULTS IN A VALINE AT POSITION 1 WHEN ...SEQUENCE: THIS GENE USES AN ALTERNATE INITIATION CODON THAT RESULTS IN A VALINE AT POSITION 1 WHEN EXPRESSED AS A FUSION

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: transcriptional regulator, TetR family
B: transcriptional regulator, TetR family


Theoretical massNumber of molelcules
Total (without water)51,2874
Polymers51,2872
Non-polymers02
Water1,00956
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-22 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.518, 87.109, 59.156
Angle α, β, γ (deg.)90.000, 110.730, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: LEU / End label comp-ID: LYS / Refine code: 5 / Auth seq-ID: 2 - 200 / Label seq-ID: 14 - 212

Dom-IDAuth asym-IDLabel asym-ID
1BB
2AA

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Components

#1: Protein transcriptional regulator, TetR family


Mass: 25643.451 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm1030 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X0C0
#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.6 Å3/Da / Density % sol: 52.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.5
Details: 30.0% PEG-8000, 0.2M MgNO3, 0.1M Citrate pH 4.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.918370, 0.979508
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 3, 2005 / Details: Flat mirror
RadiationMonochromator: single crystal Si(111) bent monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.9795081
ReflectionResolution: 2.3→29.18 Å / Num. obs: 21323 / % possible obs: 99.5 % / Redundancy: 5 % / Rsym value: 0.093 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured obsRsym valueDiffraction-ID% possible all
2.3-2.363.71.215070.612195.8
2.36-2.423.61.515310.513199.9
2.42-2.493.71.814930.406199.9
2.49-2.573.62.314660.327199.6
2.57-2.663.62.813910.26199.9
2.66-2.753.63.513400.213199.8
2.75-2.853.64.113340.18199.7
2.85-2.973.65.212740.1411100
2.97-3.13.7611950.117199.4
3.1-3.257.33.211630.2111100
3.25-3.437.24.310980.1541100
3.43-3.647.3610620.1131100
3.64-3.897.27.59810.091100
3.89-4.27.18.89300.0761100
4.2-4.67.19.28480.0691100
4.6-5.146.99.87520.0651100
5.14-5.946.696830.0731100
5.94-7.276.68.65790.0741100
7.27-10.296.610.74500.0541100
10.29-29.185.712.22460.05196.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→29.18 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 17.312 / SU ML: 0.202 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.33 / ESU R Free: 0.251
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. DENSITY NEAR A89 AND B89 MODELED AS UNL BASED ON SIMILARITY TO PDB 1VI0 (LIKELY PART OF A COA MOIETY)
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1105 5.2 %RANDOM
Rwork0.201 ---
all0.204 ---
obs0.20399 20200 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.288 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å2-1.25 Å2
2---0.03 Å20 Å2
3---1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3268 0 19 56 3343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223333
X-RAY DIFFRACTIONr_bond_other_d0.0010.023102
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9734477
X-RAY DIFFRACTIONr_angle_other_deg0.8137183
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6475399
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.53524.161161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87715643
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1021520
X-RAY DIFFRACTIONr_chiral_restr0.080.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023648
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02716
X-RAY DIFFRACTIONr_nbd_refined0.2340.2885
X-RAY DIFFRACTIONr_nbd_other0.1610.22944
X-RAY DIFFRACTIONr_nbtor_refined0.1920.21667
X-RAY DIFFRACTIONr_nbtor_other0.0880.21936
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2280.270
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2620.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1110.24
X-RAY DIFFRACTIONr_mcbond_it2.51132179
X-RAY DIFFRACTIONr_mcbond_other0.6283815
X-RAY DIFFRACTIONr_mcangle_it3.16153190
X-RAY DIFFRACTIONr_scbond_it6.26481484
X-RAY DIFFRACTIONr_scangle_it8.497111286
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1181medium positional0.550.5
1942loose positional0.895
1181medium thermal1.092
1942loose thermal2.8910
LS refinement shellResolution: 2.301→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 85 -
Rwork0.237 1470 -
obs--99.11 %
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)
16.2907-2.01084.50640.9879-1.50123.2389-0.1128-0.2466-0.33940.08610.33660.1209-0.2274-0.1662-0.2237-0.0453-0.00290.0914-0.03070.0148-0.074934.77441.95112.28
23.95970.6848-1.36570.8507-0.65140.7065-0.1312-0.05860.3056-0.03190.18360.04440.0181-0.0121-0.05230.0339-0.0323-0.0729-0.0727-0.0505-0.070235.19957.528-12.676
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 20013 - 212
2X-RAY DIFFRACTION2BB2 - 20014 - 212

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