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- PDB-2nrf: Crystal Structure of GlpG, a Rhomboid family intramembrane protease -

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Basic information

Entry
Database: PDB / ID: 2nrf
TitleCrystal Structure of GlpG, a Rhomboid family intramembrane protease
ComponentsProtein GlpG
KeywordsMEMBRANE PROTEIN / integral 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
Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWu, Z. / Yan, N. / Feng, L. / Yan, H. / Gu, L. / Shi, Y.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structural analysis of a rhomboid family intramembrane protease reveals a gating mechanism for substrate entry.
Authors: Wu, Z. / Yan, N. / Feng, L. / Oberstein, A. / Yan, H. / Baker, R.P. / Gu, L. / Jeffrey, P.D. / Urban, S. / Shi, Y.
History
DepositionNov 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Protein GlpG
B: Protein GlpG


Theoretical massNumber of molelcules
Total (without water)41,0572
Polymers41,0572
Non-polymers00
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-23 kcal/mol
Surface area17520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.458, 59.458, 118.048
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
DetailsEach asymmetric unit contains two molecules. They exhibit different conformations.

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Components

#1: Protein Protein GlpG


Mass: 20528.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glpG / Plasmid: pET-15b / Production host: Escherichia coli (E. coli) / Strain (production host): C43 (DE3) / References: UniProt: P09391
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.93 Å3/Da / Density % sol: 58.07 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: PEG 3000 7%, Li2S04 100 mM, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 13, 2006
RadiationMonochromator: a vertically focusing mirror and a horizontally focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twinType: hemihedral / Operator: h,-h-k,-l / Fraction: 0.4
ReflectionResolution: 2.6→100 Å / Num. all: 14363 / Num. obs: 14184 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 9 % / Rmerge(I) obs: 0.071 / Χ2: 1.033 / Net I/σ(I): 15.1
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.508 / Num. unique all: 1373 / Χ2: 0.446 / % possible all: 93.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
CBASSdata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2IC8

2ic8


Resolution: 2.6→100 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 1247 8.7 %Random
Rwork0.262 ---
all0.285 14360 --
obs0.285 13455 93.7 %-
Solvent computationBsol: 90.08 Å2
Displacement parametersBiso mean: 102.891 Å2
Baniso -1Baniso -2Baniso -3
1-12.766 Å20.768 Å20 Å2
2--12.766 Å20 Å2
3----25.532 Å2
Refinement stepCycle: LAST / Resolution: 2.6→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 0 26 2861
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.017
X-RAY DIFFRACTIONr_angle_refined_deg1.837
LS refinement shellResolution: 2.6→50 Å
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param

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