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- PDB-4h1d: Cocrystal structure of GlpG and DFP -

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Basic information

Entry
Database: PDB / ID: 4h1d
TitleCocrystal structure of GlpG and DFP
ComponentsRhomboid protease GlpG
KeywordsHYDROLASE / intramembrane protease / serine protease / DFP / membrane protein
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 domain / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8975 Å
AuthorsXue, Y. / Ha, Y.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Large lateral movement of transmembrane helix s5 is not required for substrate access to the active site of rhomboid intramembrane protease.
Authors: Xue, Y. / Ha, Y.
History
DepositionSep 10, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
Water48627
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Rhomboid protease GlpG
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)122,28112
Polymers121,2846
Non-polymers9976
Water1086
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
crystal symmetry operation10_455y-1/3,x+1/3,-z+1/31
crystal symmetry operation11_565x-y+2/3,-y+4/3,-z+1/31
crystal symmetry operation12_555-x+2/3,-x+y+1/3,-z+1/31
Buried area11500 Å2
ΔGint-129 kcal/mol
Surface area43470 Å2
MethodPISA
3
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 area4650 Å2
ΔGint-57 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.073, 110.073, 123.995
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-413-

HOH

21A-424-

HOH

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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


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 65.6 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 7
Details: 0.1 M bis-tris propane 1.5 M NH4Cl, pH 7, EVAPORATION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 1, 2011
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8975→40 Å / Num. all: 6580 / Num. obs: 6580 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
CBASSdata collection
CCP4model building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8975→37.787 Å / SU ML: 0.36 / σ(F): 1.92 / Phase error: 32.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 311 4.73 %RANDOM
Rwork0.2322 ---
obs0.2339 6580 99.71 %-
all-6580 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.251 Å2 / ksol: 0.296 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--14.6827 Å20 Å20 Å2
2---14.6827 Å20 Å2
3---29.3653 Å2
Refinement stepCycle: LAST / Resolution: 2.8975→37.787 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1354 0 10 27 1391
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091410
X-RAY DIFFRACTIONf_angle_d1.1581922
X-RAY DIFFRACTIONf_dihedral_angle_d17.293461
X-RAY DIFFRACTIONf_chiral_restr0.068210
X-RAY DIFFRACTIONf_plane_restr0.005226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8975-3.65010.26681620.20873064X-RAY DIFFRACTION100
3.6501-37.79010.27021490.23913205X-RAY DIFFRACTION100

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