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- PDB-1z77: Crystal structure of transcriptional regulator protein from Therm... -

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Basic information

Entry
Database: PDB / ID: 1z77
TitleCrystal structure of transcriptional regulator protein from Thermotoga maritima.
Componentstranscriptional regulator (TetR family)
KeywordsTRANSCRIPTION / transcriptional regulator / TetR family / structural genomics / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
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
Transcriptional regulator, TetR family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD/SAD / Resolution: 2 Å
AuthorsKoclega, K.D. / Chruszcz, M. / Zimmerman, M.D. / Cymborowski, M. / Kudritska, M. / Minor, W. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Struct.Biol. / Year: 2007
Title: Crystal structure of a transcriptional regulator TM1030 from Thermotoga maritima solved by an unusual MAD experiment.
Authors: Koclega, K.D. / Chruszcz, M. / Zimmerman, M.D. / Cymborowski, M. / Evdokimova, E. / Minor, W.
History
DepositionMar 24, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 7, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details ..._pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression
Revision 1.5Apr 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 / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). THE BIOLOGICAL MOLECULE IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: transcriptional regulator (TetR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3383
Polymers24,2141
Non-polymers1242
Water64936
1
A: transcriptional regulator (TetR family)
hetero molecules

A: transcriptional regulator (TetR family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6766
Polymers48,4282
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area3110 Å2
ΔGint-5 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.043, 65.684, 55.694
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein transcriptional regulator (TetR family)


Mass: 24213.879 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Plasmid: PET-15B / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3)pLysS / References: UniProt: Q9X0C0
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 36 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.05M Na citrate, 30% w/v PEG 2K MME, 0.1M KSCN, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.91932
SYNCHROTRONAPS 19-BM20.97932
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 11, 2005
SBC-32CCDFeb 10, 2005
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
2SI 111 CHANNELSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.919321
20.979321
ReflectionResolution: 1.95→50 Å / Num. obs: 15569 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 8.1 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 24.84
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.539 / Mean I/σ(I) obs: 3.3 / Num. unique all: 1531 / Rsym value: 0.471 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
CCP4phasing
RefinementMethod to determine structure: SAD/SAD / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.918 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26671 715 5 %RANDOM
Rwork0.22944 ---
all0.23129 14438 --
obs0.23129 13472 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.765 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å20 Å2
2--1.53 Å20 Å2
3---0.75 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1596 0 8 36 1640
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221632
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.972192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1535199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92124.53375
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89215298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.246157
X-RAY DIFFRACTIONr_chiral_restr0.1120.2244
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021204
X-RAY DIFFRACTIONr_nbd_refined0.2190.2786
X-RAY DIFFRACTIONr_nbtor_refined0.310.21179
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.265
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.258
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1760.210
X-RAY DIFFRACTIONr_mcbond_it1.4541.51045
X-RAY DIFFRACTIONr_mcangle_it1.88821584
X-RAY DIFFRACTIONr_scbond_it3.6313703
X-RAY DIFFRACTIONr_scangle_it4.9164.5608
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 61 -
Rwork0.23 996 -
obs--100 %

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