[English] 日本語
Yorodumi
- PDB-5ixu: Crystal structure of an uncharacterized NIPSNAP domain protein fr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5ixu
TitleCrystal structure of an uncharacterized NIPSNAP domain protein from Burkholderia xenovorans
ComponentsUncharacterized protein
KeywordsStructural Genomics/Unknown Function / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / Structural Genomics-Unknown Function complex
Function / homologyNIPSNAP / : / NIPSNAP / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / NIPSNAP domain-containing protein
Function and homology information
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an uncharacterized protein from Burkholderia xenovorans
Authors: Mayclin, S.J. / Delker, S.L. / Lorimer, D.D. / Edwards, T.E.
History
DepositionMar 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8442
Polymers13,7481
Non-polymers961
Water28816
1
A: Uncharacterized protein
hetero molecules

A: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6874
Polymers27,4952
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation13_556y,x,-z+11
Buried area2890 Å2
ΔGint-46 kcal/mol
Surface area10150 Å2
MethodPISA
2
A: Uncharacterized protein
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)110,74916
Polymers109,9808
Non-polymers7698
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_556-x,y,-z+11
crystal symmetry operation4_556x,-y,-z+11
crystal symmetry operation13_556y,x,-z+11
crystal symmetry operation14_556-y,-x,-z+11
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
Buried area19670 Å2
ΔGint-247 kcal/mol
Surface area32490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.620, 94.620, 94.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number207
Space group name H-MP432

-
Components

#1: Protein Uncharacterized protein


Mass: 13747.516 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_B0070 / Plasmid: BuxeA.00127.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q13J81
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.57 Å3/Da / Density % sol: 52 % / Mosaicity: 0.27 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: JCSG+ E4: 1.26 M Ammonium sulfate, 0.1 M Tris pH 8.5; protein conc. 19.1mg/mL; 20% EG cryo; puck bbt8-3

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 16, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 5419 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 26.79 % / Biso Wilson estimate: 50.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.063 / Net I/σ(I): 43.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.5-2.570.5696.651100
2.57-2.640.4838.081100
2.64-2.710.38510.051100
2.71-2.80.31212.581100
2.8-2.890.21618.181100
2.89-2.990.19919.421100
2.99-3.10.1427.141100
3.1-3.230.10934.211100
3.23-3.370.08144.911100
3.37-3.540.06552.871100
3.54-3.730.06557.04196.1
3.73-3.950.05563.51199.6
3.95-4.230.04279199.6
4.23-4.570.03488.981100
4.57-50.0397.81100
5-5.590.03192.341100
5.59-6.460.03484.351100
6.46-7.910.0386.011100
7.91-11.180.02397.49199.2
11.18-500.02366.23195.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
Cootmodel building
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vqs

1vqs


Resolution: 2.5→50 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.59
RfactorNum. reflection% reflectionSelection details
Rfree0.2646 542 10.02 %Random selection
Rwork0.1923 ---
obs0.199 5407 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 137.82 Å2 / Biso mean: 50.0019 Å2 / Biso min: 25 Å2
Refinement stepCycle: final / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms811 0 5 16 832
Biso mean--134.61 44.44 -
Num. residues----102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008846
X-RAY DIFFRACTIONf_angle_d0.931163
X-RAY DIFFRACTIONf_chiral_restr0.053125
X-RAY DIFFRACTIONf_plane_restr0.006149
X-RAY DIFFRACTIONf_dihedral_angle_d16.426484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5004-2.7520.33861310.240411661297100
2.752-3.150.32461480.24411731321100
3.15-3.96810.28761260.18661214134099
3.9681-38.6330.20941370.17091312144999
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)
13.3279-2.2019-2.47757.40073.79586.5130.13391.0602-0.4253-0.3796-0.5948-0.7212-0.281-0.31030.5670.40210.10550.06650.55840.12960.41113.0388.69129.6747
27.4203-4.2640.59837.58050.45612.87580.16530.12320.9179-0.6413-0.1944-0.8022-0.30210.54070.02540.3859-0.04950.05060.54440.12260.548915.452322.090334.0384
35.1044-5.8828-0.92459.16840.43430.42780.34860.16950.2554-0.3789-0.4671-0.27730.00740.05370.0210.3728-0.0187-0.01150.44060.12840.360313.386211.085740.5855
46.1317-2.9662.23592.5372-3.97719.05360.0122-0.45770.99720.8496-0.0132-0.6647-0.7155-0.4417-0.01410.53880.17-0.01440.5095-0.00730.59364.676429.13643.2589
51.9578-0.79320.12545.39461.91782.58190.46320.43790.3646-0.5811-0.3695-0.9488-0.4687-0.4966-0.07720.67880.176-0.05350.62570.18210.49655.441225.280927.2278
62.48590.2968-0.18512.74281.66935.57210.14870.1957-0.09860.0481-0.1462-0.45550.2429-0.1386-0.0160.44820.0618-0.06790.37180.04360.37618.473715.233641.5622
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 15 through 28 )A15 - 28
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 46 )A29 - 46
3X-RAY DIFFRACTION3chain 'A' and (resid 47 through 62 )A47 - 62
4X-RAY DIFFRACTION4chain 'A' and (resid 63 through 72 )A63 - 72
5X-RAY DIFFRACTION5chain 'A' and (resid 73 through 86 )A73 - 86
6X-RAY DIFFRACTION6chain 'A' and (resid 87 through 116 )A87 - 116

+
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