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- PDB-4ndw: Crystal STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ESX-1 SECRETED PR... -

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Basic information

Entry
Database: PDB / ID: 4ndw
TitleCrystal STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS ESX-1 SECRETED PROTEIN REGULATOR (EspR)
ComponentsNucleoid-associated protein EspR
KeywordsTRANSCRIPTION / ALL HELICAL / HELIX-TURN-HELIX MOTIF / TRANSACTIONAL REGULATOR / DNA BINDING
Function / homology
Function and homology information


response to host immune response / nucleoid / regulation of protein secretion / peptidoglycan-based cell wall / positive regulation of DNA-templated transcription / DNA binding / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
lambda repressor-like DNA-binding domains / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Nucleoid-associated protein EspR / Nucleoid-associated protein EspR
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsGangwar, S.P. / Meena, S.R. / Saxena, A.K.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2014
Title: Comparison of four different crystal forms of the Mycobacterium tuberculosis ESX-1 secreted protein regulator EspR
Authors: Gangwar, S.P. / Meena, S.R. / Saxena, A.K.
History
DepositionOct 28, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif
Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoid-associated protein EspR
B: Nucleoid-associated protein EspR


Theoretical massNumber of molelcules
Total (without water)34,0622
Polymers34,0622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-28 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.890, 83.890, 130.750
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Nucleoid-associated protein EspR


Mass: 17031.234 Da / Num. of mol.: 2 / Fragment: ESX-1 SECRETED PROTEIN REGULATOR
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37RV / Gene: espR, MT3964, Rv3849, RV3849C / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P96228, UniProt: P9WJB7*PLUS

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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: 68.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 24% PEG 3350, 0.2M SODIUM MALONATE, 0.1M BIS-TRIS PROPANE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97833 Å
DetectorType: MAR CCD 225 / Detector: CCD / Date: Apr 21, 2011
RadiationMonochromator: Si(111) monochromator. / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97833 Å / Relative weight: 1
ReflectionResolution: 3.3→48.6 Å / Num. obs: 8435 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.8 % / Biso Wilson estimate: 99.7 Å2 / Rmerge(I) obs: 0.159 / Net I/σ(I): 11
Reflection shellResolution: 3.3→3.48 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 2.6 / % possible all: 100

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHENIXAUTOSOLmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
SCALAdata scaling
PHENIXAUTOSOLphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→43.583 Å / σ(F): 1.34 / Phase error: 34.72 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.324 399 4.74 %
Rwork0.266 --
obs0.2683 8411 100 %
all-1210 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-15.0292 Å20 Å2-0 Å2
2--15.0292 Å2-0 Å2
3----30.0584 Å2
Refinement stepCycle: LAST / Resolution: 3.3→43.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2020 0 0 0 2020
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092058
X-RAY DIFFRACTIONf_angle_d1.2292781
X-RAY DIFFRACTIONf_dihedral_angle_d17.447775
X-RAY DIFFRACTIONf_chiral_restr0.072303
X-RAY DIFFRACTIONf_plane_restr0.005368
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3019-3.77920.36811340.30082597X-RAY DIFFRACTION95
3.7792-4.75950.26241360.25262630X-RAY DIFFRACTION95
4.7595-35.30520.33741290.25952766X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: -84.7282 Å / Origin y: 103.2205 Å / Origin z: 2.7739 Å
111213212223313233
T1.2576 Å20.0928 Å20.0584 Å2-0.5684 Å20.0116 Å2--0.7548 Å2
L1.3 °2-0.3806 °2-0.741 °2-0.9314 °2-0.6796 °2--1.5312 °2
S-0.5793 Å °-0.2835 Å °-0.1573 Å °-0.1624 Å °0.1623 Å °-0.2759 Å °0.5414 Å °0.2277 Å °0.3882 Å °
Refinement TLS groupSelection details: all

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