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- PDB-3ubb: The crystal structure of GlpG in complex with a phosphonofluorida... -

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Basic information

Entry
Database: PDB / ID: 3ubb
TitleThe crystal structure of GlpG in complex with a phosphonofluoridate inhibitor
ComponentsRhomboid protease glpG
KeywordsHYDROLASE/INHIBITOR / HELIX BUNDLE / MEMBRANE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


rhomboid protease / endopeptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Rhomboid-like fold / Rhomboid-like / Peptidase S54, GlpG peptidase, N-terminal / Rhomboid protease GlpG / GlpG peptidase, N-terminal domain superfamily / Cytoplasmic N-terminal domain of rhomboid serine protease / Peptidase S54, rhomboid domain / Rhomboid family / Rhomboid-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-3UB / Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.601 Å
AuthorsXue, Y. / Ha, Y.
CitationJournal: Biochemistry / Year: 2012
Title: Conformational Change in Rhomboid Protease GlpG Induced by Inhibitor Binding to Its S' Subsites.
Authors: Xue, Y. / Chowdhury, S. / Liu, X. / Akiyama, Y. / Ellman, J. / Ha, Y.
History
DepositionOct 24, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhomboid protease glpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,8302
Polymers20,5281
Non-polymers3011
Water54030
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Rhomboid protease glpG
hetero molecules

A: Rhomboid protease glpG
hetero molecules

A: Rhomboid protease glpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,4896
Polymers61,5853
Non-polymers9043
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area7170 Å2
ΔGint-38 kcal/mol
Surface area22970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.722, 111.722, 121.810
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Rhomboid protease glpG / Intramembrane serine protease


Mass: 20528.312 Da / Num. of mol.: 1 / Fragment: UNP residues 91-272
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: glpG, b3424, JW5687 / Plasmid: pET41b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09391, rhomboid protease
#2: Chemical ChemComp-3UB / propan-2-yl hydrogen (S)-[(1R)-1-{[(benzyloxy)carbonyl]amino}ethyl]phosphonate


Mass: 301.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20NO5P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 3.6 Å3/Da / Density % sol: 65.85 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7 / Details: 3M NaCl, pH 7, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 7, 2011 / Details: Si111
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 10287 / Num. obs: 10287 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 99

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
REFMACrefinement
CBASSdata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.601→44.961 Å / SU ML: 0.28 / σ(F): 1.4 / Phase error: 22.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2289 444 4.85 %
Rwork0.2112 --
obs0.212 9147 99.73 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.4091 Å2-0 Å2-0 Å2
2---5.4091 Å20 Å2
3---10.8181 Å2
Refinement stepCycle: LAST / Resolution: 2.601→44.961 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1398 0 19 30 1447
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081467
X-RAY DIFFRACTIONf_angle_d1.1152003
X-RAY DIFFRACTIONf_dihedral_angle_d14.803472
X-RAY DIFFRACTIONf_chiral_restr0.068216
X-RAY DIFFRACTIONf_plane_restr0.004239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.601-2.97690.26591600.20062828X-RAY DIFFRACTION100
2.9769-3.75030.2031360.17752906X-RAY DIFFRACTION100
3.7503-44.96770.23071480.22892969X-RAY DIFFRACTION99

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