[English] 日本語
Yorodumi
- PDB-3jvc: Crystal Structure of the Lipoprotein_17 domain from Q9PRA0_UREPA ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3jvc
TitleCrystal Structure of the Lipoprotein_17 domain from Q9PRA0_UREPA protein of Ureaplasma parvum. Northeast Structural Genomics Consortium Target UuR17a.
ComponentsConserved hypothetical membrane lipoprotein
KeywordsLIPID BINDING PROTEIN / lipoprotein-17 / Q9PRA0 / PF04200 / DUF1976 / UuR17a / NESG. / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / Lipoprotein
Function / homology
Function and homology information


Nuclear Transport Factor 2; Chain: A, - #270 / Lipoprotein-associated domain / Lipoprotein associated domain / Uncharacterised protein family MG067 / Mycoplasma peptidase DUF31 / Mycoplasma peptidase (DUF31) / Nuclear Transport Factor 2; Chain: A, / Prokaryotic membrane lipoprotein lipid attachment site profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Membrane-associated lipoprotein
Similarity search - Component
Biological speciesUreaplasma parvum serovar 3 str. ATCC 700970 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.69 Å
AuthorsVorobiev, S. / Neely, H. / Lee, D. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the Lipoprotein_17 domain from Q9PRA0_UREPA protein of Ureaplasma parvum.
Authors: Vorobiev, S. / Neely, H. / Lee, D. / Ciccosanti, C. / Mao, L. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 29, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Conserved hypothetical membrane lipoprotein
B: Conserved hypothetical membrane lipoprotein
C: Conserved hypothetical membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)44,3483
Polymers44,3483
Non-polymers00
Water72140
1
A: Conserved hypothetical membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)14,7831
Polymers14,7831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Conserved hypothetical membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)14,7831
Polymers14,7831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Conserved hypothetical membrane lipoprotein


Theoretical massNumber of molelcules
Total (without water)14,7831
Polymers14,7831
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.560, 76.829, 214.589
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Detailsmonomer according to gel-filtration

-
Components

#1: Protein Conserved hypothetical membrane lipoprotein


Mass: 14782.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ureaplasma parvum serovar 3 str. ATCC 700970 (bacteria)
Strain: ATCC 700970 / Serovar 3 / Gene: UU045 / Plasmid: pET 21-23C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) +Magic / References: UniProt: Q9PRA0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 40 / 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: 2.35 Å3/Da / Density % sol: 47.65 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 7.5
Details: 24% PEG 20000, 0.1M RbCl, 0.1M HEPES, pH 7.5, microbatch under paraffin oil, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97914 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 19, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97914 Å / Relative weight: 1
ReflectionResolution: 2.69→50 Å / Num. all: 22432 / Num. obs: 22095 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.9 % / Biso Wilson estimate: 48.5 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 52.2
Reflection shellResolution: 2.69→2.79 Å / Redundancy: 9.8 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 14.2 / Num. unique all: 2184 / % possible all: 94

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SHELXDEphasing
RESOLVEmodel building
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.69→38.42 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 161344.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1057 4.8 %RANDOM
Rwork0.23 ---
obs0.23 21846 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.4848 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---4.24 Å20 Å2
3---4.22 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.36 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.69→38.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2704 0 0 40 2744
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.8
X-RAY DIFFRACTIONc_improper_angle_d0.89
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.69→2.86 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.331 140 4.1 %
Rwork0.271 3296 -
obs--92.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

+
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