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- PDB-3txt: Crystal structure of GlpG in complex with inhibitor DFP -

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Basic information

Entry
Database: PDB / ID: 3txt
TitleCrystal structure of GlpG in complex with inhibitor DFP
ComponentsRhomboid protease glpG
KeywordsHYDROLASE/INHIBITOR / serine protease / intramembrane protease / 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
DIISOPROPYL PHOSPHONATE / Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsXue, Y. / Ha, Y.
CitationJournal: To be Published
Title: The crystal structure of rhomboid protease GlpG in complex with a mechanism-based inhibitor
Authors: Xue, Y. / Ha, Y.
History
DepositionSep 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: 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)20,3802
Polymers20,2141
Non-polymers1661
Water41423
1
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)61,1416
Polymers60,6423
Non-polymers4983
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 area5850 Å2
ΔGint-44 kcal/mol
Surface area22710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.667, 109.667, 125.097
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: 20214.020 Da / Num. of mol.: 1 / Fragment: UNP residues 92-270
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: glpG, b3424, JW5687 / Production host: Escherichia coli (E. coli) / References: UniProt: P09391, rhomboid protease
#2: Chemical ChemComp-DFP / DIISOPROPYL PHOSPHONATE


Mass: 166.155 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15O3P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 3.58 Å3/Da / Density % sol: 65.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 3M NaCl, 0.1 M bis-tris propane, pH7, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 12996 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.1_743)refinement
REFMACrefinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→23.327 Å / SU ML: 0.35 / σ(F): 0 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2384 634 4.88 %
Rwork0.2188 --
obs0.2199 12988 99.28 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 79.262 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.3685 Å2-0 Å20 Å2
2---14.3685 Å20 Å2
3---28.737 Å2
Refinement stepCycle: LAST / Resolution: 2.3→23.327 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1389 0 10 23 1422
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071447
X-RAY DIFFRACTIONf_angle_d0.9851969
X-RAY DIFFRACTIONf_dihedral_angle_d17.072481
X-RAY DIFFRACTIONf_chiral_restr0.066213
X-RAY DIFFRACTIONf_plane_restr0.004232
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.47490.26541320.26072375X-RAY DIFFRACTION97
2.4749-2.72360.27291360.2182452X-RAY DIFFRACTION100
2.7236-3.11690.28461200.21232481X-RAY DIFFRACTION100
3.1169-3.92390.2321330.19962481X-RAY DIFFRACTION100
3.9239-23.32830.21851130.22542565X-RAY DIFFRACTION99

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