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- PDB-2w25: Crystal structure of Glu104Ala mutant -

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Basic information

Entry
Database: PDB / ID: 2w25
TitleCrystal structure of Glu104Ala mutant
ComponentsPROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
KeywordsTRANSCRIPTION / TRANSCRIPTION REGULATION / TRANSCRIPTIONAL REGULATOR / MUTANT / RV3291C / GLU104ALA / DNA-BINDING
Function / homology
Function and homology information


amino acid binding / protein homooligomerization / sequence-specific DNA binding / DNA binding
Similarity search - Function
AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain ...AsnC-type HTH domain profile. / Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain / Transcription regulator AsnC-like / helix_turn_helix ASNC type / AsnC-type HTH domain / Transcription regulator AsnC/Lrp, ligand binding domain / Lrp/AsnC ligand binding domain / Winged helix-turn-helix DNA-binding / Dimeric alpha-beta barrel / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Alpha-Beta Plaits / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Leucine-responsive regulatory protein
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsShrivastava, T. / RAmachandran, R.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Ligand-Induced Structural Transitions, Mutational Analysis, and 'Open' Quaternary Structure of the M. Tuberculosis Feast/Famine Regulatory Protein (Rv3291C).
Authors: Shrivastava, T. / Dey, A. / Ramachandran, R.
History
DepositionOct 24, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 17, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_status / reflns_shell
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details ..._exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _reflns_shell.Rmerge_I_obs
Revision 1.4Dec 13, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)32,9452
Polymers32,9452
Non-polymers00
Water1,29772
1
A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN

A: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN
B: PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN


Theoretical massNumber of molelcules
Total (without water)131,7808
Polymers131,7808
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Buried area33270 Å2
ΔGint-137.32 kcal/mol
Surface area48950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.650, 100.650, 99.306
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212
Components on special symmetry positions
IDModelComponents
11B-2014-

HOH

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Components

#1: Protein PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN / LEUCINE-RESPONSIVE REGULATORY PROTEIN / RV3291C


Mass: 16472.561 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PET21D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P96896
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 104 TO ALA ENGINEERED RESIDUE IN CHAIN B, GLU 104 TO ALA

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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: 3.9 Å3/Da / Density % sol: 68.22 % / Description: NONE
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.0, reservoir: 100 mM 4-morpholineethanesulfonic acid (Mes), pH 6.0, 0.75 M lithium acetate (LiAc)

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→20 Å / Num. obs: 25538 / % possible obs: 91.3 % / Observed criterion σ(I): 2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 12.9
Reflection shellResolution: 2.15→2.32 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.2 / % possible all: 94.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALEPACKdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IVM

2ivm


Resolution: 2.15→71.25 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.951 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 1367 5.1 %RANDOM
Rwork0.217 ---
obs0.217 24011 94.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.15→71.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2231 0 0 72 2303
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0222259
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2691.9733077
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8915292
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.69622.277101
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.47215366
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.5461530
X-RAY DIFFRACTIONr_chiral_restr0.2420.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021706
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2430.2792
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21530
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.278
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3820.243
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2780.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1811.51467
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.23422361
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.8243792
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.614.5716
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.361 93
Rwork0.329 1931

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