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- PDB-3fms: Crystal structure of TM0439, a GntR transcriptional regulator -

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Basic information

Entry
Database: PDB / ID: 3fms
TitleCrystal structure of TM0439, a GntR transcriptional regulator
ComponentsTranscriptional regulator, GntR family
KeywordsTRANSCRIPTION REGULATOR / GNTR FAMILY / TRANSCRIPTIONAL REGULATOR / STRUCTURAL GENOMICS / SURFACE ENTROPY REDUCTION / PSI-2 / PROTEIN STRUCTURE INITIATIVE / INTEGRATED CENTER FOR STRUCTURE AND FUNCTION INNOVATION / ISFI / DNA-BINDING / TRANSCRIPTION REGULATION / Transcription
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding / metal ion binding
Similarity search - Function
GntR ligand-binding domain-like / FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Four Helix Bundle (Hemerythrin (Met), subunit A) ...GntR ligand-binding domain-like / FCD / GntR, C-terminal / FCD domain / Transcription regulator FadR/GntR, C-terminal / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Four Helix Bundle (Hemerythrin (Met), subunit A) / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / NICKEL (II) ION / Transcriptional regulator, GntR family
Similarity search - Component
Biological speciesThermotoga maritima MSB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsZheng, M. / Cooper, D.R. / Yu, M. / Hung, L.-W. / Derewenda, U. / Derewenda, Z.S. / Integrated Center for Structure and Function Innovation (ISFI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of Thermotoga maritima TM0439: implications for the mechanism of bacterial GntR transcription regulators with Zn2+-binding FCD domains.
Authors: Zheng, M. / Cooper, D.R. / Grossoehme, N.E. / Yu, M. / Hung, L.W. / Cieslik, M. / Derewenda, U. / Lesley, S.A. / Wilson, I.A. / Giedroc, D.P. / Derewenda, Z.S.
History
DepositionDec 22, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 10, 2009ID: 3DBW
Revision 1.0Feb 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Nov 1, 2017Group: Refinement description / Category: software
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Oct 20, 2021Group: 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
Revision 1.6Oct 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

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Assembly

Deposited unit
A: Transcriptional regulator, GntR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,6904
Polymers24,5141
Non-polymers1773
Water1,45981
1
A: Transcriptional regulator, GntR family
hetero molecules

A: Transcriptional regulator, GntR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3818
Polymers49,0272
Non-polymers3546
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1920 Å2
ΔGint-11.4 kcal/mol
Surface area18900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.188, 71.718, 43.323
Angle α, β, γ (deg.)90.000, 104.590, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-229-

HOH

21A-281-

HOH

31A-284-

HOH

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Components

#1: Protein Transcriptional regulator, GntR family


Mass: 24513.697 Da / Num. of mol.: 1 / Mutation: E118A, K119A, K122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima MSB8 (bacteria) / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0439 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q9WYS0
#2: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O
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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 35% 2-methyl-2,4-pentanediol, 0.1 M Sodium acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97960, 0.95370, 0.97980
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 10, 2007
RadiationMonochromator: KOHZU: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.95371
30.97981
ReflectionRedundancy: 7 % / Number: 68034 / Rmerge(I) obs: 0.059 / Χ2: 1.63 / D res high: 2.4 Å / D res low: 40 Å / Num. obs: 9724 / % possible obs: 98.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.174099.910.0392.1497.5
4.15.1799.910.0391.8327.3
3.584.110010.062.6437.3
3.263.5899.910.0722.2877.4
3.023.2699.910.0871.6177.5
2.853.0210010.1041.3137.5
2.72.8510010.141.067.3
2.592.799.610.1850.9966.8
2.492.599710.2080.9426
2.42.4988.710.2190.9115.1
ReflectionResolution: 2.2→40 Å / Num. obs: 12695 / % possible obs: 98.4 % / Redundancy: 7 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 46.3
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.228 / Mean I/σ(I) obs: 5.1 / % possible all: 88.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→36.163 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.39 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: AUTHORS USED TLS
RfactorNum. reflection% reflection
Rfree0.228 620 4.93 %
Rwork0.157 --
obs0.161 12586 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.545 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 118.97 Å2 / Biso mean: 38.632 Å2 / Biso min: 11.03 Å2
Baniso -1Baniso -2Baniso -3
1--2.729 Å2-0 Å23.637 Å2
2--0.865 Å2-0 Å2
3---1.864 Å2
Refinement stepCycle: LAST / Resolution: 2.2→36.163 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1713 0 9 81 1803
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173499
X-RAY DIFFRACTIONf_angle_d1.316351
X-RAY DIFFRACTIONf_chiral_restr0.108270
X-RAY DIFFRACTIONf_plane_restr0.007515
X-RAY DIFFRACTIONf_dihedral_angle_d14.195895
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.4210.2771460.1672764291091
2.421-2.7720.2551690.1530373206100
2.772-3.4910.2351490.14730693218100
3.491-36.1670.2051560.15630963252100
Refinement TLS params.Method: refined / Origin x: 10.2423 Å / Origin y: 44.5731 Å / Origin z: 10.2735 Å
111213212223313233
T0.2202 Å2-0.0018 Å2-0.0112 Å2-0.2641 Å20.014 Å2--0.2348 Å2
L0.6846 °2-0.5198 °2-0.1357 °2-1.273 °2-0.0437 °2--0.8469 °2
S-0.0519 Å °-0.1237 Å °-0.0735 Å °0.1136 Å °-0.0118 Å °-0.0123 Å °0.0659 Å °0.0181 Å °0.0581 Å °
Refinement TLS groupSelection details: all

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