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- PDB-3r0a: Possible transcriptional regulator from Methanosarcina mazei Go1 ... -

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Basic information

Entry
Database: PDB / ID: 3r0a
TitlePossible transcriptional regulator from Methanosarcina mazei Go1 (gi 21227196)
ComponentsPutative transcriptional regulator
KeywordsTranscription regulator / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / possible transcriptional regulator
Function / homology: / DnaD N-terminal 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 / Putative transcriptional regulator
Function and homology information
Biological speciesMethanosarcina mazei (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.31 Å
AuthorsJoachimiak, A. / Duke, N.E.C. / Li, H. / Gu, M. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Possible transcriptional regulator from Methanosarcina mazei Go1 (gi 21227196)
Authors: Joachimiak, A. / Duke, N.E.C. / Li, H. / Gu, M.
History
DepositionMar 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 23, 2013Group: Other
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative transcriptional regulator
B: Putative transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)28,6742
Polymers28,6742
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-31 kcal/mol
Surface area14090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.126, 67.059, 72.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative transcriptional regulator


Mass: 14337.048 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina mazei (archaea) / Gene: MM_1094 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21magic / References: UniProt: Q8PXX2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.13 Å3/Da / Density % sol: 42.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Index screen, conditions #92 (H-8), 0.1M magnesium formate dihydrate, 15% w/v polyethylene glycol 3350, pH approximately 6.0 cryoprotected using Paratone-N, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 25, 2010
Details: double crystal Si(111) monochromator, sagitally bent mirror
RadiationMonochromator: double crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 11225 / Num. obs: 8825 / % possible obs: 78.6 % / Observed criterion σ(I): 3.8 / Redundancy: 9.8 %

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.31→49.32 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.868 / SU B: 13.482 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R: 0.566 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.36314 534 4.8 %RANDOM
Rwork0.26623 ---
obs0.27083 10635 99.38 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.191 Å2
Baniso -1Baniso -2Baniso -3
1-2.69 Å20 Å20 Å2
2---2.52 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.31→49.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1981 0 0 54 2035
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222011
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.9542702
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3135241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.57125.75899
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.81915408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9641510
X-RAY DIFFRACTIONr_chiral_restr0.0990.2299
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021468
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_it0.8651.51205
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63821944
X-RAY DIFFRACTIONr_scbond_it2.1153806
X-RAY DIFFRACTIONr_scangle_it3.5874.5758
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.31→2.37 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 39 -
Rwork0.289 700 -
obs--92.72 %

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