[English] 日本語
Yorodumi
- PDB-2r2c: Crystal structure of a domain of the outer membrane lipoprotein O... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r2c
TitleCrystal structure of a domain of the outer membrane lipoprotein Omp28 from Porphyromonas gingivalis
Components28 kDa outer membrane protein Omp28
KeywordsMEMBRANE PROTEIN / Lipoprotein / Omp28 / structural genomics / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homology
Function and homology information


: / cysteine-type peptidase activity
Similarity search - Function
Outer membrane protein Omp28 / Outer membrane protein Omp28 / Thioredoxin-like superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
28 kDa outer membrane protein Omp28
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsZhang, R. / Hatzos, C. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a domain of the outer membrane lipoprotein Omp28 from Porphyromonas gingivalis.
Authors: Zhang, R. / Hatzos, C. / Moy, S. / Joachimiak, A.
History
DepositionAug 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 28 kDa outer membrane protein Omp28
B: 28 kDa outer membrane protein Omp28


Theoretical massNumber of molelcules
Total (without water)41,9062
Polymers41,9062
Non-polymers00
Water6,305350
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.831, 110.342, 90.730
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsAuthors state that this protein exists as dimer. The deposited Mol.A and Mol.B represent the dimer in the asymmetric unit

-
Components

#1: Protein 28 kDa outer membrane protein Omp28 / Outer membrane lipoprotein Omp28


Mass: 20953.047 Da / Num. of mol.: 2 / Fragment: Domain: Residues 108-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: omp28, PG_2173 / Plasmid: pDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9S3Q1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.2M Sodium citrate tribasic dihydrate, 20% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2007 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→63.63 Å / Num. all: 34652 / Num. obs: 34354 / % possible obs: 99.14 % / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Biso Wilson estimate: 30 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 37.5
Reflection shellResolution: 1.8→1.848 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 2 / Num. unique all: 2670 / % possible all: 94.46

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→63.63 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.734 / SU ML: 0.061 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.094 / ESU R Free: 0.094
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20076 1801 5 %RANDOM
Rwork0.17392 ---
all0.17527 34354 --
obs0.17527 34354 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.219 Å2
Baniso -1Baniso -2Baniso -3
1-0.78 Å20 Å20 Å2
2---0.07 Å20 Å2
3----0.7 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.042 Å0.04 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 1.8→63.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1846 0 0 350 2196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221885
X-RAY DIFFRACTIONr_angle_refined_deg1.3861.9482560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.935225
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.3125.47684
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47815321
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.675152
X-RAY DIFFRACTIONr_chiral_restr0.1170.2297
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021390
X-RAY DIFFRACTIONr_nbd_refined0.2150.2886
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21301
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1160.237
X-RAY DIFFRACTIONr_mcbond_it1.2081.51166
X-RAY DIFFRACTIONr_mcangle_it1.85921859
X-RAY DIFFRACTIONr_scbond_it2.6773830
X-RAY DIFFRACTIONr_scangle_it4.2284.5701
LS refinement shellResolution: 1.8→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 127 -
Rwork0.266 2395 -
obs-2522 94.46 %
Refinement TLS params.Method: refined / Origin x: 25.208 Å / Origin y: 19.522 Å / Origin z: 35.044 Å
111213212223313233
T0.0084 Å2-0.002 Å2-0.0015 Å2--0.0192 Å2-0.0132 Å2---0.0729 Å2
L0.4295 °20.4078 °2-0.3693 °2-0.9222 °2-0.7738 °2--0.7512 °2
S-0.0205 Å °0.0398 Å °0.0143 Å °-0.0381 Å °0.052 Å °0.0251 Å °0.0594 Å °-0.0065 Å °-0.0315 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA36 - 4536 - 45
2X-RAY DIFFRACTION1AA53 - 9653 - 96
3X-RAY DIFFRACTION1AA114 - 150114 - 150
4X-RAY DIFFRACTION1AA151 - 180151 - 180
5X-RAY DIFFRACTION1BB53 - 9553 - 95
6X-RAY DIFFRACTION1BB115 - 150115 - 150
7X-RAY DIFFRACTION1BB151 - 180151 - 180

+
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