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- PDB-2grm: Crystal structure of PrgX/iCF10 complex -

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Basic information

Entry
Database: PDB / ID: 2grm
TitleCrystal structure of PrgX/iCF10 complex
Components
  • PrgX
  • peptide
KeywordsTRANSCRIPTION / receptor / inhibitor
Function / homologySerine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #400 / lambda repressor-like DNA-binding domains / 434 Repressor (Amino-terminal Domain) / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsShi, K. / Kozlowicz, B.K. / Gu, Z.Y. / Ohlendorf, D.H. / Earhart, C.A. / Dunny, G.M.
CitationJournal: Mol.Microbiol. / Year: 2006
Title: Molecular basis for control of conjugation by bacterial pheromone and inhibitor peptides.
Authors: Kozlowicz, B.K. / Shi, K. / Gu, Z.Y. / Ohlendorf, D.H. / Earhart, C.A. / Dunny, G.M.
History
DepositionApr 24, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PrgX
B: PrgX
C: PrgX
D: peptide
E: peptide


Theoretical massNumber of molelcules
Total (without water)112,8135
Polymers112,8135
Non-polymers00
Water86548
1
A: PrgX
D: peptide

A: PrgX
D: peptide

A: PrgX
D: peptide

A: PrgX
D: peptide


Theoretical massNumber of molelcules
Total (without water)151,4708
Polymers151,4708
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
crystal symmetry operation3_456-x-1,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
2
B: PrgX
C: PrgX
E: peptide

B: PrgX
C: PrgX
E: peptide


Theoretical massNumber of molelcules
Total (without water)149,8906
Polymers149,8906
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_455-x-1/2,-y+1/2,z1
Unit cell
Length a, b, c (Å)93.459, 134.748, 192.478
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

21A-322-

HOH

31A-323-

HOH

41A-331-

HOH

51A-332-

HOH

61B-322-

HOH

71B-325-

HOH

DetailsThe second part of the biological assembly is generated by the two fold axis: -x, -y, z+1/2.

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Components

#1: Protein PrgX


Mass: 37077.516 Da / Num. of mol.: 3 / Mutation: Y231C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Production host: Escherichia coli (E. coli) / References: GenBank: 150553
#2: Protein/peptide peptide


Mass: 790.002 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.68 Å3/Da / Density % sol: 54.16 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.6 / Details: LiCl, pH 5.6, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2005
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 24750 / Num. obs: 24503 / % possible obs: 98.2 % / Observed criterion σ(I): 5.1
Reflection shellResolution: 3→3.18 Å / % possible all: 95.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→39.62 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2749067.19 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.285 1184 4.8 %RANDOM
Rwork0.238 ---
all0.248 24750 --
obs0.238 24503 99 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5006 Å2 / ksol: 0.315236 e/Å3
Displacement parametersBiso mean: 100.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.45 Å20 Å20 Å2
2---11.52 Å20 Å2
3---15.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.53 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.74 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 3→39.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7732 0 0 50 7782
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 3→3.19 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.47 188 4.7 %
Rwork0.377 3773 -
obs--97.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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