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- PDB-4hdd: Domain swapping in the cytoplasmic domain of the Escherichia coli... -

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Basic information

Entry
Database: PDB / ID: 4hdd
TitleDomain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease
ComponentsRhomboid protease GlpG
KeywordsHYDROLASE / domain swapping / peptidase / rhomboid protease / intramembrane protease / membrane
Function / homology
Function and homology information


rhomboid protease / endopeptidase activity / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
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
Similarity search - Domain/homology
ACETATE ION / Rhomboid protease GlpG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsLazareno-Saez, C. / Arutyunova, E. / Coquelle, N. / Lemieux, M.J.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Domain swapping in the cytoplasmic domain of the Escherichia coli rhomboid protease.
Authors: Lazareno-Saez, C. / Arutyunova, E. / Coquelle, N. / Lemieux, M.J.
History
DepositionOct 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Oct 30, 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_ref_seq_dif / 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_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Rhomboid protease GlpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1722
Polymers9,1131
Non-polymers591
Water1,18966
1
A: Rhomboid protease GlpG
hetero molecules

A: Rhomboid protease GlpG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3444
Polymers18,2262
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556-x,y,-z+11
Buried area5100 Å2
ΔGint-29 kcal/mol
Surface area7910 Å2
MethodPISA
2
A: Rhomboid protease GlpG
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)73,37516
Polymers72,9028
Non-polymers4728
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_556-x,y,-z+11
crystal symmetry operation6_556x,-y,-z+11
crystal symmetry operation7_556y,x,-z+11
crystal symmetry operation8_556-y,-x,-z+11
Buried area29320 Å2
ΔGint-173 kcal/mol
Surface area22700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.760, 51.760, 91.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Rhomboid protease GlpG / Intramembrane serine protease


Mass: 9112.795 Da / Num. of mol.: 1 / Fragment: N-terminal cytoplasmic domain (UNP residues 2-74)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: TOP10 / Gene: b3424, glpG, JW5687 / Plasmid: pBad Myc/HisA / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: P09391, rhomboid protease
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
11.6826.89
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2981vapor diffusion, hanging drop6.90.49M sodium phosphate monobasic monohydrate - 0.91M potassium phosphate dibasic, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 298K
2982vapor diffusion, hanging drop4.6100mM sodium acetate trihydrate, 0.2M ammonium sulfate, 25% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 12.3.110.9793, 1.116
SYNCHROTRONCLSI 08ID-120.9795
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDSep 8, 2011
RAYONIX MX-3002CCDOct 6, 2011
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)MADMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
21.1161
30.97951
ReflectionResolution: 1.35→45.058 Å / Num. all: 25782 / Num. obs: 25782 / % possible obs: 98.6 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.595 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 14.83
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.35-1.390.4812.073748188298.5
1.39-1.420.3792.513796188799
1.42-1.460.2743.313752184699.2
1.46-1.510.1834.713563174399.1
1.51-1.560.1545.843501169799.2
1.56-1.610.1227.343467165999.2
1.61-1.670.0929.223423161699.3
1.67-1.740.07111.173204151999.5
1.74-1.820.05713.723103147499.1
1.82-1.910.04516.382976140599.1
1.91-2.010.03819.942843133699.5
2.01-2.130.0323.492683126298.7
2.13-2.280.02726.252494117597.7
2.28-2.460.02428.482395112999.3
2.46-2.70.02431.62181100798.7
2.7-3.020.02232.32197991899
3.02-3.490.02135.28174280096.9
3.49-4.270.02336.92145066696.2
4.27-6.040.02637.5108549092.8
6.040.02937.5759527187.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
MxDCdata collection
XDSdata reduction
PHENIX(1.7.3_928)phasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→45.058 Å / Occupancy max: 1 / Occupancy min: 0.42 / FOM work R set: 0.8858 / SU ML: 0.18 / σ(F): -3 / Phase error: 17.61 / Stereochemistry target values: phased maximum-likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.182 704 5.03 %RANDOM
Rwork0.1618 ---
obs0.1629 14001 99.41 %-
all-14001 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.668 Å2 / ksol: 0.434 e/Å3
Displacement parametersBiso max: 74.93 Å2 / Biso mean: 21.7243 Å2 / Biso min: 8.59 Å2
Baniso -1Baniso -2Baniso -3
1--1.1799 Å2-0 Å20 Å2
2---1.1799 Å20 Å2
3---2.3598 Å2
Refinement stepCycle: LAST / Resolution: 1.35→45.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms522 0 4 66 592
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014553
X-RAY DIFFRACTIONf_angle_d1.437756
X-RAY DIFFRACTIONf_chiral_restr0.09186
X-RAY DIFFRACTIONf_plane_restr0.007102
X-RAY DIFFRACTIONf_dihedral_angle_d16.056204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3501-1.45430.30671370.203226002737100
1.4543-1.60070.21351380.152926252763100
1.6007-1.83230.1881410.145226622803100
1.8323-2.30850.16541400.135526572797100
2.3085-45.08360.16971480.17352753290198

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