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- PDB-3mkl: Crystal structure of DNA-binding transcriptional dual regulator f... -

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Basic information

Entry
Database: PDB / ID: 3mkl
TitleCrystal structure of DNA-binding transcriptional dual regulator from Escherichia coli K-12
ComponentsHTH-type transcriptional regulator gadX
KeywordsTranscription regulator / PSI2 / MCSG / structural genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / DNA-binding protein / transcriptional dual regulator
Function / homology
Function and homology information


cis-regulatory region sequence-specific DNA binding => GO:0000987 / DNA-binding transcription activator activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity / DNA-templated transcription / DNA damage response / positive regulation of DNA-templated transcription
Similarity search - Function
Bacterial regulatory helix-turn-helix proteins, AraC family / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / Homeobox-like domain superfamily ...Bacterial regulatory helix-turn-helix proteins, AraC family / Transcription regulator HTH, AraC- type / HTH domain AraC-type, conserved site / Bacterial regulatory proteins, araC family signature. / DNA binding HTH domain, AraC-type / Helix-turn-helix domain / Bacterial regulatory proteins, araC family DNA-binding domain profile. / helix_turn_helix, arabinose operon control protein / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HTH-type transcriptional regulator GadX
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsChang, C. / Mack, J. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of DNA-binding transcriptional dual regulator from Escherichia coli K-12
Authors: Chang, C. / Mack, J. / Clancy, S. / Joachimiak, A.
History
DepositionApr 15, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HTH-type transcriptional regulator gadX
B: HTH-type transcriptional regulator gadX


Theoretical massNumber of molelcules
Total (without water)28,1172
Polymers28,1172
Non-polymers00
Water3,819212
1
A: HTH-type transcriptional regulator gadX


Theoretical massNumber of molelcules
Total (without water)14,0581
Polymers14,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: HTH-type transcriptional regulator gadX


Theoretical massNumber of molelcules
Total (without water)14,0581
Polymers14,0581
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.972, 81.856, 165.065
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein HTH-type transcriptional regulator gadX


Mass: 14058.467 Da / Num. of mol.: 2 / Fragment: sequence database residues 137-255
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K-12 substr. DH10B / Gene: gadX, yhiX, b3516, JW3484 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: P37639
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.52 Å3/Da / Density % sol: 51.21 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 3.5
Details: 0.1M Citric acid pH 3.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. all: 15966 / Num. obs: 15608 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 7.8 % / Biso Wilson estimate: 31.7 Å2 / Rmerge(I) obs: 0.124 / Net I/σ(I): 35.4
Reflection shellResolution: 2.15→2.19 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 6.96 / Num. unique all: 769 / % possible all: 97.1

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
MLPHAREphasing
DMmodel building
RESOLVEmodel building
Cootmodel building
ARP/wARPmodel building
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.919 / SU B: 13.415 / SU ML: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.244 / ESU R Free: 0.199
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24681 740 4.8 %RANDOM
Rwork0.20651 ---
all0.20846 15505 --
obs0.20846 15505 97.32 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.996 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2---2.96 Å20 Å2
3---2.09 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 0 212 1950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221799
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2671.9552435
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0475219
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.50621.85281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39415328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4361520
X-RAY DIFFRACTIONr_chiral_restr0.0860.2277
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211337
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6591.51091
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.25621772
X-RAY DIFFRACTIONr_scbond_it2.1313708
X-RAY DIFFRACTIONr_scangle_it3.3534.5663
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.151→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 56 -
Rwork0.25 1075 -
obs-1131 96.75 %
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)
12.97110.013-0.89036.24140.78652.39360.0367-0.06630.0739-0.2504-0.04920.2060.06680.01830.01250.058-0.034-0.00060.0353-0.01250.090418.73587.773220.0482
24.6119-6.4301-2.69339.35344.52456.21180.53160.17320.178-1.1003-0.3467-0.1074-0.34190.1768-0.18480.5170.0909-0.07030.1455-0.0240.178528.4773-3.28818.7476
311.0919-1.2804-0.43434.74220.69923.78930.18180.3783-0.4886-0.2062-0.3226-0.00330.20830.30850.14080.0680.06060.05370.11770.02760.093629.2763-12.169610.1938
43.9490.8316-1.3983.3473-0.07363.87310.0218-0.03940.0083-0.1501-0.022-0.16270.0979-0.13780.00020.0465-0.04270.01070.0504-0.00570.065832.606726.642819.348
55.3154-0.5143-2.58640.52970.46897.07610.0151-0.34020.04170.0489-0.0687-0.0842-0.52120.00930.05360.0762-0.0381-0.01330.1237-0.02370.07518.373127.636331.8317
68.1450.3952-0.95495.8016-0.9686.1344-0.1857-0.1291-0.1910.1560.25560.3099-0.0265-0.4217-0.06990.0219-0.00780.02450.0971-0.02310.058910.145223.451930.2155
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A140 - 185
2X-RAY DIFFRACTION2A186 - 217
3X-RAY DIFFRACTION3A218 - 245
4X-RAY DIFFRACTION4B140 - 185
5X-RAY DIFFRACTION5B186 - 217
6X-RAY DIFFRACTION6B218 - 245

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