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- PDB-2xtv: Structure of E.coli rhomboid protease GlpG, active site mutant, S... -

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Basic information

Entry
Database: PDB / ID: 2xtv
TitleStructure of E.coli rhomboid protease GlpG, active site mutant, S201T, orthorhombic crystal form
ComponentsRHOMBOID PROTEASE GLPG
KeywordsHYDROLASE / 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 family / Rhomboid-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE / Rhomboid protease GlpG
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVinothkumar, K.R.
CitationJournal: J. Mol. Biol. / Year: 2011
Title: Structure of rhomboid protease in a lipid environment.
Authors: Vinothkumar, K.R.
History
DepositionOct 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 27, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)29,74715
Polymers20,2561
Non-polymers9,49114
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.630, 58.870, 91.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RHOMBOID PROTEASE GLPG / INTRAMEMBRANE SERINE PROTEASE / GLPG


Mass: 20256.033 Da / Num. of mol.: 1 / Fragment: CORE TM DOMAIN, RESIDUES 93-272 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: P09391, rhomboid protease
#2: Chemical
ChemComp-MC3 / 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE


Mass: 677.933 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C36H72NO8P / Comment: phospholipid*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, SER 201 TO THR
Nonpolymer detailsIN THE PRESENT MODEL LIPIDS (MC3) MOLECULES 504, 505, 508, 511, 513 AND 514 COULD ALSO REPRESENT ...IN THE PRESENT MODEL LIPIDS (MC3) MOLECULES 504, 505, 508, 511, 513 AND 514 COULD ALSO REPRESENT DETERGENT NONYL GLUCOSIDE USED FOR PURIFICATION OF PROTEIN.

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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: 2.41 Å3/Da / Density % sol: 48.94 % / Description: NONE
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.5M NACL, 0.1M BIS-TRIS, PH7, 2% DMPC/CHAPSO, (ADDED ONLY TO THE PROTEIN), 298K, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 29, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→45.54 Å / Num. obs: 22469 / % possible obs: 95.8 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 3.2 / % possible all: 86.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XOV

2xov


Resolution: 1.7→28.009 Å / SU ML: 0.19 / σ(F): 0 / Phase error: 18.38 / Stereochemistry target values: ML
Details: RESIDUES 246 AND 247 ARE DISORDERED. HENCE THERE IS A GAP BETWEEN 245 AND 248.THERE IS A DENSITY ABOVE THE ACTIVE SITE WHICH HAS NOT BEEN MODELLED, AS NONE OF COMPONENTS OF CRYSTALLISATION ...Details: RESIDUES 246 AND 247 ARE DISORDERED. HENCE THERE IS A GAP BETWEEN 245 AND 248.THERE IS A DENSITY ABOVE THE ACTIVE SITE WHICH HAS NOT BEEN MODELLED, AS NONE OF COMPONENTS OF CRYSTALLISATION CAN EXPLAIN THE DENSITY.
RfactorNum. reflection% reflection
Rfree0.215 1148 5.1 %
Rwork0.1862 --
obs0.1877 22432 95.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.136 Å2 / ksol: 0.412 e/Å3
Displacement parametersBiso mean: 24.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.3931 Å20 Å20 Å2
2---2.5354 Å20 Å2
3---0.1423 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1410 0 296 79 1785
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061744
X-RAY DIFFRACTIONf_angle_d1.0412299
X-RAY DIFFRACTIONf_dihedral_angle_d17.144698
X-RAY DIFFRACTIONf_chiral_restr0.072226
X-RAY DIFFRACTIONf_plane_restr0.004253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.77740.26091280.22842293X-RAY DIFFRACTION84
1.7774-1.87110.23111420.19982634X-RAY DIFFRACTION96
1.8711-1.98830.23761520.17872655X-RAY DIFFRACTION97
1.9883-2.14170.20681330.16352683X-RAY DIFFRACTION96
2.1417-2.35720.18931520.1592720X-RAY DIFFRACTION98
2.3572-2.6980.22331580.1582718X-RAY DIFFRACTION98
2.698-3.39830.20851450.1782740X-RAY DIFFRACTION97
3.3983-28.01270.21361380.21252841X-RAY DIFFRACTION95

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