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- PDB-3sxk: Zn2+-bound FCD domain of TM0439, a putative transcriptional regulator -

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Basic information

Entry
Database: PDB / ID: 3sxk
TitleZn2+-bound FCD domain of TM0439, a putative transcriptional regulator
ComponentsTranscriptional regulator, GntR family
KeywordsTRANSCRIPTION REGULATOR / TRANSCRIPTION FACTOR / TRANSCRIPTION / METAL-BINDING / Structural Genomics / PSI-2 / Protein Structure Initiative / Integrated Center for Structure and Function Innovation / ISFI / FADR-C / FADR / GNTR / TRANSCRIPTIONAL REGULATOR / TRANSCRIPTION REPRESSOR / ZINC-BINDING / NICKEL-BINDING / DNA-BINDING / SURFACE ENTROPY REDUCTION
Function / homology
Function and homology information


cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / 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 DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
BICARBONATE ION / Transcriptional regulator, GntR family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsCzelakowski, G.P. / Derewenda, Z.S. / Integrated Center for Structure and Function Innovation (ISFI)
Citation
Journal: To be Published
Title: Zn2+-bound FCD domain of TM0439, a putative transcriptional regulator
Authors: Czelakowski, G.P. / Derewenda, Z.S.
#1: Journal: 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
DepositionJul 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.2Sep 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_atom_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_atom_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: Transcriptional regulator, GntR family
B: Transcriptional regulator, GntR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,49510
Polymers32,9192
Non-polymers5768
Water5,188288
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-178 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.697, 79.977, 49.223
Angle α, β, γ (deg.)90.000, 115.080, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'A' and (resseq 72:118 or resseq 121:211 ) and (not element H)A0
211chain 'B' and (resseq 72:118 or resseq 121:211 ) and (not element H)B0

NCS oper: (Code: given
Matrix: (-0.536423, 0.006519, 0.843924), (0.001839, -0.999959, 0.008893), (0.843947, 0.006323, 0.536389)
Vector: 0.097316, -3.49212, 0.005457)
Detailsbiological unit is the same as asym.

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Components

#1: Protein Transcriptional regulator, GntR family


Mass: 16459.686 Da / Num. of mol.: 2 / Fragment: Sequence database residues 75-211 / Mutation: E118A, K119A, K122A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / DSM 3109 / JCM 10099 / Gene: TM_0439 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9WYS0
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.47 Å3/Da / Density % sol: 50.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mM Tris pH 8.0, 100 mM NaCl, 200 mM (NH4)2SO4, 100 mM BisTris pH 5.5, 25% PEG 3350, 0.1 mM ZnCl2, 2 mM DTT , VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 20, 2010 / Details: Mirrors Rh/Pt coated
RadiationMonochromator: Si(220) Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.63→45 Å / Num. all: 39975 / Num. obs: 38096 / % possible obs: 95.3 % / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.041 / Χ2: 1.012 / Net I/σ(I): 26.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.63-1.663.30.18112780.992165.7
1.66-1.693.40.1614830.999173.7
1.69-1.723.40.15616451.039184
1.72-1.763.70.14119530.988196.2
1.76-1.794.10.11919151.012198.3
1.79-1.844.20.119861.02198.3
1.84-1.884.20.08919601.045198.7
1.88-1.934.20.07619611.013198.7
1.93-1.994.20.06120111.022198.9
1.99-2.054.20.05419560.986198.9
2.05-2.134.20.0519790.995199
2.13-2.214.20.04219681.023199
2.21-2.314.20.0419900.984199.4
2.31-2.434.20.03519830.968199.4
2.43-2.594.20.03519790.984199.5
2.59-2.794.20.03620001.038199.5
2.79-3.074.20.04120071.055199.8
3.07-3.514.20.05320111.087199.9
3.51-4.424.10.03720021.037199.8
4.42-454.10.02720290.948198.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIXdev_817refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB: 3FMS, Chain A: 72-211

3fms


Resolution: 1.63→39.922 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8657 / SU ML: 0.34 / σ(F): 1.34 / Phase error: 20.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1923 1017 2.67 %SCALEPACK2MTZ FREEFAC 0.05, RANDOM
Rwork0.1701 ---
obs0.1707 38057 95.19 %-
all-39980 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.428 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 125.25 Å2 / Biso mean: 27.8605 Å2 / Biso min: 9.01 Å2
Baniso -1Baniso -2Baniso -3
1-1.5556 Å20 Å2-4.9651 Å2
2---7.6176 Å2-0 Å2
3---6.1102 Å2
Refinement stepCycle: LAST / Resolution: 1.63→39.922 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 22 288 2611
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0292408
X-RAY DIFFRACTIONf_angle_d1.7623240
X-RAY DIFFRACTIONf_chiral_restr0.093352
X-RAY DIFFRACTIONf_plane_restr0.007417
X-RAY DIFFRACTIONf_dihedral_angle_d13.327932
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1103X-RAY DIFFRACTIONPOSITIONAL0.336
12B1103X-RAY DIFFRACTIONPOSITIONAL0.336
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6299-1.71590.30061140.23364010412473
1.7159-1.82340.23321610.20255433559497
1.8234-1.96420.20091270.16565449557699
1.9642-2.16180.20151640.15815461562599
2.1618-2.47460.17271330.15185538567199
2.4746-3.11750.2011590.165555435702100
3.1175-39.93360.1761590.17455606576599

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