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- PDB-3odj: Crystal structure of H. influenzae rhomboid GlpG with disordered ... -

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Basic information

Entry
Database: PDB / ID: 3odj
TitleCrystal structure of H. influenzae rhomboid GlpG with disordered loop 4, helix 5 and loop 5
ComponentsRhomboid protease glpG
KeywordsHYDROLASE / rhomboid peptidase / membrane protein
Function / homology
Function and homology information


rhomboid protease / serine-type endopeptidase activity / proteolysis / identical protein binding / plasma membrane
Similarity search - Function
Rhomboid-like fold / Rhomboid-like / Peptidase S54, rhomboid domain / Rhomboid family / Rhomboid-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Rhomboid protease GlpG
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsBrooks, C.L. / Lazareno-Saez, C. / Lamoureux, J.S. / Mak, M.W. / Lemieux, M.J.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Insights into Substrate Gating in H. influenzae Rhomboid.
Authors: Brooks, C.L. / Lazareno-Saez, C. / Lamoureux, J.S. / Mak, M.W. / Lemieux, M.J.
History
DepositionAug 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 22, 2017Group: Database references / Category: pdbx_database_related / Item: _pdbx_database_related.db_id
Revision 1.4Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rhomboid protease glpG


Theoretical massNumber of molelcules
Total (without water)22,1411
Polymers22,1411
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Rhomboid protease glpG

A: Rhomboid protease glpG


Theoretical massNumber of molelcules
Total (without water)44,2822
Polymers44,2822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area1430 Å2
ΔGint-13 kcal/mol
Surface area16790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.927, 35.190, 52.672
Angle α, β, γ (deg.)90.000, 104.060, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Rhomboid protease glpG / Intramembrane serine protease


Mass: 22140.916 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: glpG, HI_0618 / Plasmid: pBAD myc His A / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: P44783, rhomboid protease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6
Details: PEG 4000, NaCl, Ethanol, glycerol, pH 6.0, vapour diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.84→50 Å / Num. obs: 5066 / % possible obs: 96.9 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.069 / Χ2: 1.047 / Net I/σ(I): 11.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.84-2.952.10.425091.0998.8
2.95-3.072.10.2544931.06998.2
3.07-3.212.10.2235171.0898.7
3.21-3.382.10.1454981.0698
3.38-3.592.10.1225091.05997.7
3.59-3.872.10.0685081.00797.1
3.87-4.262.10.0495001.05296.9
4.26-4.872.10.0415131.02396.6
4.87-6.142.10.0485030.97995.1
6.14-5020.0225161.05192

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.84→50 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.886 / Occupancy max: 1 / Occupancy min: 0.35 / SU B: 18.797 / SU ML: 0.374 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.446 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2966 231 4.6 %RANDOM
Rwork0.2434 ---
obs0.246 5066 96.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 82.81 Å2 / Biso mean: 45.2444 Å2 / Biso min: 23.05 Å2
Baniso -1Baniso -2Baniso -3
1--2.57 Å20 Å20.11 Å2
2--4.03 Å20 Å2
3----1.4 Å2
Refinement stepCycle: LAST / Resolution: 2.84→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 0 18 1277
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221294
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9451757
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1475155
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47923.27355
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.5715212
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.002154
X-RAY DIFFRACTIONr_chiral_restr0.1220.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02956
X-RAY DIFFRACTIONr_mcbond_it0.681.5774
X-RAY DIFFRACTIONr_mcangle_it1.2921248
X-RAY DIFFRACTIONr_scbond_it1.5583520
X-RAY DIFFRACTIONr_scangle_it2.5254.5509
LS refinement shellResolution: 2.841→2.915 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 19 -
Rwork0.285 326 -
all-345 -
obs--88.69 %

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