[English] 日本語
Yorodumi
- PDB-2guk: Crystal Structure of the Conserved Protein of Unknown Function fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2guk
TitleCrystal Structure of the Conserved Protein of Unknown Function from Porphyromonas gingivalis
Componentshypothetical protein PG1857
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta / alpha-helical bundle / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyPG1857-like / PG1857-like / Domain of unknown function DUF2023 / PG1857-like superfamily / Protein of unknown function (DUF2023) / 2-Layer Sandwich / Alpha Beta / : / DUF2023 domain-containing protein
Function and homology information
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.91 Å
AuthorsKim, Y. / Quartey, P. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of the Conserved Hypothetical Protein from Porphyromonas gingivalis
Authors: Kim, Y. / Quartey, P. / Moy, S. / Joachimiak, A.
History
DepositionMay 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Oct 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
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
Remark 300THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THERE IS NO ...THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). THERE IS NO EXPERIMENTAL EVIDENCE ABOUT THE BIOLOGICAL UNIT. THE BIOLOGICAL UNIT COULD BE A DIMER (AS IN THE ASYMMETRIC UNIT) OR A TETRAMER. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S).

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: hypothetical protein PG1857
B: hypothetical protein PG1857


Theoretical massNumber of molelcules
Total (without water)28,3872
Polymers28,3872
Non-polymers00
Water2,378132
1
A: hypothetical protein PG1857
B: hypothetical protein PG1857

A: hypothetical protein PG1857
B: hypothetical protein PG1857


Theoretical massNumber of molelcules
Total (without water)56,7734
Polymers56,7734
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Unit cell
Length a, b, c (Å)50.028, 50.028, 186.912
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein hypothetical protein PG1857


Mass: 14193.339 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Strain: W83 / Gene: PG1587, GeneID:2551814 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: GenBank: 34541468, UniProt: Q7MTT4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 275 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 5% iso-propanol, 0.1 M HEPES 7.5, 10 % PEG 4K, VAPOR DIFFUSION, SITTING DROP, temperature 275K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 24, 2006 / Details: mirrors
RadiationMonochromator: double crystal monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.91→34.76 Å / Num. all: 20138 / Num. obs: 19279 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.7 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 10.5
Reflection shellResolution: 1.91→1.98 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1825 / % possible all: 96.7

-
Processing

Software
NameVersionClassification
REFMAC5.2.0000refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
MLPHAREphasing
RESOLVEphasing
SHELXEmodel building
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.91→34.76 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.435 / SU ML: 0.153 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.22 / ESU R Free: 0.192
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.28056 1953 10.2 %RANDOM
Rwork0.23253 ---
all0.23742 17168 --
obs0.23742 17168 98.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.333 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 1.91→34.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1826 0 0 132 1958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221959
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9642652
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4075239
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.09322.264106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.23815355
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8831527
X-RAY DIFFRACTIONr_chiral_restr0.1270.2278
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021541
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2390.21004
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2133
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.261
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9571.51199
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.48421902
X-RAY DIFFRACTIONr_scbond_it2.2193840
X-RAY DIFFRACTIONr_scangle_it3.3324.5750
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.96 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.394 137
Rwork0.309 1192
obs-1192
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)
12.20190.8366-1.36840.61910.0121.78980.02690.10720.21080.01150.04160.09840.00530.0815-0.06850.0362-0.0464-0.04630.01650.0819-0.069731.97228.361110.458
20.42580.3546-1.06960.3164-1.0914.596-0.0224-0.0013-0.0625-0.04720.06560.03920.32660.2014-0.04320.03390.00240.02560.06180.0116-0.033548.32326.26186.336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 1147 - 117
2X-RAY DIFFRACTION2BB6 - 1179 - 120

+
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