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- PDB-3sxy: Metal-free full-length structure of Tm0439, a metal-binding FCD f... -

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Basic information

Entry
Database: PDB / ID: 3sxy
TitleMetal-free full-length structure of Tm0439, a metal-binding FCD family 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


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
Transcriptional regulator, GntR family
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.647 Å
AuthorsCzelakowski, G.P. / Derewenda, Z.S. / Integrated Center for Structure and Function Innovation (ISFI)
Citation
Journal: To be Published
Title: Metal-free full-length structure of Tm0439, a metal-binding FCD family 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)50,9912
Polymers50,9912
Non-polymers00
Water7,062392
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-10 kcal/mol
Surface area19010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.512, 69.822, 63.980
Angle α, β, γ (deg.)90.000, 95.440, 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 10:210 ) and (not element H)A0
211chain 'B' and (resseq 10:210 ) and (not element H)B0

NCS oper: (Code: given
Matrix: (0.699328, 0.65339, 0.289865), (0.656376, -0.74757, 0.101538), (0.283038, 0.119252, -0.951666)
Vector: -153.947006, 425.652008, -59.4258)
Detailsbiological unit is the same as asym.

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Components

#1: Protein Transcriptional regulator, GntR family


Mass: 25495.463 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 392 / 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: 2.42 Å3/Da / Density % sol: 49.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50 mM Tris pH 8.0, 300 mM NaCl, 17% PEG 3350, 200 mM NH4NO3, 10mM EDTA, 2mM DTT, vapor diffusion, sitting drop, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 1, 2009 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Si 111. Rosenbaum-Rock double-crystal monochromator: liquid nitrogen cooled; sagitally focusing 2nd crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→43 Å / Num. all: 56846 / Num. obs: 56675 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 22.9 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 12.28
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allDiffraction-ID% possible all
1.7-1.742.90.5073784199.8
1.74-1.7830.4453731199.8
1.78-1.833.10.3993744199.8
1.83-1.893.20.36537771100
1.89-1.953.30.3263765199.9
1.95-2.023.30.2573786199.9
2.02-2.13.40.1793766199.9
2.1-2.193.40.1443765199.9
2.19-2.313.30.1143785199.9
2.31-2.453.40.0843783199.8
2.45-2.643.40.073781199.9
2.64-2.913.40.0643788199.8
2.91-3.333.40.0573800199.9
3.33-4.193.40.0523817199.8
4.19-433.20.0663803197.7

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Processing

Software
NameVersionClassificationNB
PHENIXdev_817refinement
PDB_EXTRACT3.1data extraction
SERGUIdata collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb: 3fms, Chain A 6-211

3fms


Resolution: 1.647→34.65 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8909 / SU ML: 0.37 / σ(F): 1.33 / Phase error: 18.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1798 1170 2.07 %SCALE2MTZ FREERFRAC 0.02, RANDOM
Rwork0.1769 ---
obs0.177 56587 96.07 %-
all-58902 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.732 Å2 / ksol: 0.391 e/Å3
Displacement parametersBiso max: 93.22 Å2 / Biso mean: 28.2109 Å2 / Biso min: 9.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.0459 Å20 Å2-1.9477 Å2
2--0.7964 Å20 Å2
3----0.7505 Å2
Refinement stepCycle: LAST / Resolution: 1.647→34.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3314 0 0 392 3706
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0233441
X-RAY DIFFRACTIONf_angle_d1.7044631
X-RAY DIFFRACTIONf_chiral_restr0.113530
X-RAY DIFFRACTIONf_plane_restr0.014593
X-RAY DIFFRACTIONf_dihedral_angle_d13.0751367
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1598X-RAY DIFFRACTIONPOSITIONAL0.88
12B1598X-RAY DIFFRACTIONPOSITIONAL0.88
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6468-1.72180.24671050.2445121522671
1.7218-1.81260.23791570.227371207277100
1.8126-1.92610.24231430.223971917334100
1.9261-2.07480.21811650.182971347299100
2.0748-2.28360.16381420.167771887330100
2.2836-2.61390.17261350.160972277362100
2.6139-3.29280.16711700.164271987368100
3.2928-34.65760.16651530.17487238739199
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)
17.1452-0.92253.5139.0339-2.13567.9386-0.0807-0.7901-0.13420.40920.01210.3501-0.2692-0.30970.13660.1398-0.05820.0420.24350.02860.1902-28.5357229.5264-4.2349
24.5917-0.48241.77522.4164-0.89262.6028-0.02570.1467-0.53750.1190.11470.25510.1328-0.2336-0.02750.1997-0.02630.03330.1483-0.00260.1778-29.8621225.2699-11.809
31.34791.33350.39534.9432-0.10852.4488-0.0132-0.0230.0411-0.18990.02760.1333-0.13550.0218-0.01340.08050.0126-0.00020.14520.0180.115-7.0327244.6268-9.4307
41.6540.3107-0.03441.83880.21092.2240.0264-0.35350.00290.24030.05450.1026-0.0194-0.1468-0.06360.08840.02870.01660.15010.00220.1094-14.7138244.1875-1.7072
58.45561.1869-3.13343.1371-4.90998.21770.0055-0.4127-0.28570.2543-0.0493-0.1140.18760.14040.08330.1915-0.0048-0.00130.1598-0.02970.0925-6.0726242.56166.9574
63.59163.608-0.28647.8052-0.90690.76410.0422-0.1833-0.16660.291-0.055-0.3425-0.01220.14420.07460.12830.0251-0.03960.1487-0.00930.0982-1.8574240.5181-0.476
73.49654.5563-4.13556.0344-5.45544.9795-0.19450.7048-0.4118-0.57060.0376-0.59680.57940.39240.21640.18330.0373-0.00340.275-0.03880.2284-23.0655231.6128-34.4345
83.11341.6789-0.91852.7316-0.72511.304-0.09510.19780.2035-0.15160.03130.19190.0834-0.04430.0790.07610.0239-0.00980.1449-0.00180.1321-30.9626237.1615-31.4705
91.7868-0.44550.26112.2076-0.82861.92880.06070.2258-0.1721-0.2978-0.035-0.10930.21150.1377-0.02840.13810.01620.02040.1574-0.03230.1399-3.311236.1064-30.893
106.9571-6.55813.50997.9466-3.49862.83450.0022-0.14740.47720.0425-0.0612-0.746-0.10280.26490.04810.0961-0.00570.040.2072-0.00870.21255.6524242.5426-27.6816
114.18050.82935.28257.56153.19377.4035-0.00750.6810.128-1.0263-0.184-0.80860.04750.8529-0.01410.23190.00760.07310.22390.05770.2459-9.0336251.6729-37.3783
123.8014-3.25660.78953.77770.8063.95680.20340.82920.8042-1.0109-0.4740.3597-1.6502-1.2620.1990.39070.0333-0.050.25330.02980.3216-15.2945254.477-38.9025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 13:32)A13 - 32
2X-RAY DIFFRACTION2(chain A and resid 33:77)A33 - 77
3X-RAY DIFFRACTION3(chain A and resid 78:107)A78 - 107
4X-RAY DIFFRACTION4(chain A and resid 108:164)A108 - 164
5X-RAY DIFFRACTION5(chain A and resid 165:177)A165 - 177
6X-RAY DIFFRACTION6(chain A and resid 178:215)A178 - 215
7X-RAY DIFFRACTION7(chain B and resid 14:23)B14 - 23
8X-RAY DIFFRACTION8(chain B and resid 24:76)B24 - 76
9X-RAY DIFFRACTION9(chain B and resid 77:179)B77 - 179
10X-RAY DIFFRACTION10(chain B and resid 180:201)B180 - 201
11X-RAY DIFFRACTION11(chain B and resid 202:207)B202 - 207
12X-RAY DIFFRACTION12(chain B and resid 208:215)B208 - 215

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