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- PDB-2nr9: Crystal structure of GlpG, Rhomboid Peptidase from Haemophilus in... -

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Basic information

Entry
Database: PDB / ID: 2nr9
TitleCrystal structure of GlpG, Rhomboid Peptidase from Haemophilus influenzae
ComponentsProtein glpG homolog
KeywordsMEMBRANE PROTEIN / intramembrane peptidase / rhomboid protease
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
Chem-PA6 / 3,6,12,15,18,21,24-HEPTAOXAHEXATRIACONTAN-1-OL / Rhomboid protease GlpG
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLemieux, M.J. / Fischer, S.J. / Cherney, M.M. / Bateman, K.S. / James, M.N.G.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2007
Title: The crystal structure of the rhomboid peptidase from Haemophilus influenzae provides insight into intramembrane proteolysis.
Authors: Lemieux, M.J. / Fischer, S.J. / Cherney, M.M. / Bateman, K.S. / James, M.N.G.
History
DepositionNov 1, 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: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein glpG homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0676
Polymers22,1411
Non-polymers1,9265
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: Protein glpG homolog
hetero molecules

A: Protein glpG homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,13412
Polymers44,2822
Non-polymers3,85210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area8490 Å2
ΔGint-88 kcal/mol
Surface area19690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.288, 35.047, 52.931
Angle α, β, γ (deg.)90.00, 104.02, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Protein glpG homolog / GlpG / Rhomboid peptidase


Mass: 22140.916 Da / Num. of mol.: 1 / Mutation: K2E, L24I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: 86-028NP / Gene: glpG / Plasmid: pBAD-MycHisA / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: P44783, rhomboid protease
#2: Chemical ChemComp-PA6 / (R)-2-(FORMYLOXY)-3-(PHOSPHONOOXY)PROPYL PENTANOATE / PHOSPHATIDIC ACID / Phosphatidic acid


Mass: 284.200 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H17O8P
#3: Chemical ChemComp-PQE / 3,6,12,15,18,21,24-HEPTAOXAHEXATRIACONTAN-1-OL / ANAPOE-C12E8


Mass: 536.782 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H60O8
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 50.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG4000, 0.1M Citrate, pH 6.0, 0.8M Ammonium Acetate, 15% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 14, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 12949 / Num. obs: 12248 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 13.5
Reflection shellHighest resolution: 2.1 Å / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 1.85 / % possible all: 93.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2IC8

2ic8


Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 11.003 / SU ML: 0.14 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.397 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.29535 513 4.8 %RANDOM
Rwork0.23282 ---
all0.23591 10147 --
obs0.23591 10147 94.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 67.424 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20.16 Å2
2--0.14 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1529 0 128 62 1719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0221732
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9922.0182318
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.5865191
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.21923.28467
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.50115264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.835154
X-RAY DIFFRACTIONr_chiral_restr0.0880.2256
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021190
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2880.3939
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3440.51183
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2290.5128
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4060.355
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3270.55
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2692978
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.9631543
X-RAY DIFFRACTIONr_scbond_it1.0712851
X-RAY DIFFRACTIONr_scangle_it1.1993775
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 33 -
Rwork0.241 733 -
obs--94.8 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.14861.84513.82752.45044.481711.6729-0.0388-0.3133-0.26530.2537-0.15740.25860.2963-0.62210.1962-0.0255-0.02360.0305-0.1125-0.02760.0312-35.276-10.29128.521
25.45642.5565-2.32884.7541-1.154.2152-0.13410.63660.1683-0.24960.1446-0.0456-0.2296-0.2895-0.0105-0.0243-0.0138-0.0444-0.02580.0022-0.1319-28.74-2.50512.245
33.63772.02932.3762.50373.99556.8685-0.2552-0.3108-0.59590.2959-0.0150.1070.45850.24810.27020.00560.01520.0362-0.1780.03280.0365-25.588-13.90931.304
45.0282-0.3076-3.12720.02760.43898.8908-0.1210.19390.03890.021-0.01710.0837-0.18170.06970.13810.0216-0.0249-0.0281-0.1150.0033-0.0396-18.941-2.88321.737
54.0287-0.02480.13430.0046-0.14024.3305-0.1485-0.1444-0.4135-0.2576-0.10580.13350.20630.44150.25430.00170.010.0129-0.06220.0378-0.0398-16.341-10.1630.154
65.1081-2.1035-4.74054.84562.56014.49230.02880.0294-0.39840.95270.24320.47972.4731.1238-0.27210.4052-0.06480.09240.40960.08240.1306-15.4-19.32729.48
70.56790.81790.57532.37692.62697.5816-0.0465-0.2711-0.2835-0.0259-0.01680.0743-0.24630.50480.0632-0.09-0.01940.0180.10230.0069-0.1398-10.031-2.30636.815
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 284 - 28
2X-RAY DIFFRACTION2AA29 - 6129 - 61
3X-RAY DIFFRACTION3AA62 - 8562 - 85
4X-RAY DIFFRACTION4AA86 - 11086 - 110
5X-RAY DIFFRACTION5AA111 - 133111 - 133
6X-RAY DIFFRACTION6AA134 - 166134 - 166
7X-RAY DIFFRACTION7AA167 - 195167 - 195

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