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- PDB-3s2w: The crystal structure of a MarR transcriptional regulator from Me... -

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Basic information

Entry
Database: PDB / ID: 3s2w
TitleThe crystal structure of a MarR transcriptional regulator from Methanosarcina mazei Go1
ComponentsTranscriptional regulator, MarR family
KeywordsTRANSCRIPTION REGULATOR / structural genomics / PSI-Biology / protein structure initiative / MCSG / Midwest Center for Structural Genomics
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / 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 ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Transcriptional regulator, MarR family
Similarity search - Component
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.453 Å
AuthorsTan, K. / Li, H. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a MarR transcriptional regulator from Methanosarcina mazei Go1
Authors: Tan, K. / Li, H. / Gu, M. / Joachimiak, A.
History
DepositionMay 17, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcriptional regulator, MarR family
B: Transcriptional regulator, MarR family
C: Transcriptional regulator, MarR family
D: Transcriptional regulator, MarR family
E: Transcriptional regulator, MarR family
F: Transcriptional regulator, MarR family
G: Transcriptional regulator, MarR family
H: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,74122
Polymers150,3978
Non-polymers1,34514
Water1,67593
1
A: Transcriptional regulator, MarR family
B: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9836
Polymers37,5992
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6050 Å2
ΔGint-88 kcal/mol
Surface area14640 Å2
MethodPISA
2
C: Transcriptional regulator, MarR family
D: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,9836
Polymers37,5992
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-88 kcal/mol
Surface area14230 Å2
MethodPISA
3
E: Transcriptional regulator, MarR family
F: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8875
Polymers37,5992
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5850 Å2
ΔGint-93 kcal/mol
Surface area14240 Å2
MethodPISA
4
G: Transcriptional regulator, MarR family
H: Transcriptional regulator, MarR family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8875
Polymers37,5992
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-68 kcal/mol
Surface area14080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.943, 300.077, 55.711
Angle α, β, γ (deg.)90.00, 111.13, 90.00
Int Tables number4
Space group name H-MP1211
DetailsExperimentally unknown. It is predicted that the chains A and B, C and D, E and F, G and H form dimers, respectively.

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Components

#1: Protein
Transcriptional regulator, MarR family


Mass: 18799.574 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Strain: Go1 / Gene: MM_1863 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8PVU7
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 2.23 Å3/Da / Density % sol: 44.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Li Sulfate, 0.1M Bis-Tris, 25% w/v PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97926, 0.97940
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 25, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystals / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.97941
ReflectionResolution: 2.45→47 Å / Num. all: 47529 / Num. obs: 47529 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 21.4
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.677 / Mean I/σ(I) obs: 1.5 / Num. unique all: 2286 / % possible all: 96.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.453→46.113 Å / SU ML: 0.36 / σ(F): 0 / Phase error: 27.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2462 2291 5.07 %random
Rwork0.1794 ---
all0.1828 45223 --
obs0.1828 45223 94.59 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.972 Å2 / ksol: 0.326 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.7898 Å20 Å2-1.8728 Å2
2--1.2172 Å20 Å2
3----3.007 Å2
Refinement stepCycle: LAST / Resolution: 2.453→46.113 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9148 0 70 93 9311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089367
X-RAY DIFFRACTIONf_angle_d1.1212505
X-RAY DIFFRACTIONf_dihedral_angle_d16.8263633
X-RAY DIFFRACTIONf_chiral_restr0.081271
X-RAY DIFFRACTIONf_plane_restr0.0041588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.453-2.54060.33242020.26643643X-RAY DIFFRACTION80
2.5406-2.64240.36042270.24054017X-RAY DIFFRACTION90
2.6424-2.76260.31491990.234159X-RAY DIFFRACTION92
2.7626-2.90820.29822170.22394326X-RAY DIFFRACTION95
2.9082-3.09040.31032240.21814399X-RAY DIFFRACTION96
3.0904-3.3290.27362240.20614437X-RAY DIFFRACTION98
3.329-3.66380.25792570.18224416X-RAY DIFFRACTION99
3.6638-4.19370.20792690.14984485X-RAY DIFFRACTION99
4.1937-5.28240.21352380.14254532X-RAY DIFFRACTION99
5.2824-46.12140.21712340.16994518X-RAY DIFFRACTION99
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)
11.5090.14960.77990.4838-0.11721.4455-0.0713-0.11180.12030.0654-0.0649-0.0049-0.0621-0.05260.10620.13370.03230.03570.1734-0.00330.1181-8.0146113.9699-15.393
21.4491-0.4412-0.35631.07430.4391.226-0.01110.0548-0.14820.0276-0.03240.02810.13980.01460.04030.318-0.00940.00570.3096-0.01870.2712-34.765674.05595.7899
31.5774-0.3309-0.37580.63360.28070.81220.01070.04630.1468-0.01830.0776-0.09750.074-0.0722-0.07860.2350.01-0.07660.2701-0.00110.2355-38.1378149.5496.5304
42.0444-0.135-0.10250.999-0.93631.7878-0.1283-0.0750.30650.23910.33730.0107-0.3699-0.1244-0.12990.51360.0848-0.04820.3697-0.03410.4209-35.8428181.9208-21.4409
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A or chain B
2X-RAY DIFFRACTION2chain C or chain D
3X-RAY DIFFRACTION3chain E or chain F
4X-RAY DIFFRACTION4chain G or chain H

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