[English] 日本語
Yorodumi
- PDB-2nr9: Crystal structure of GlpG, Rhomboid Peptidase from Haemophilus in... -

+
Open data


ID or keywords:

Loading...

-
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 domain / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more