[English] 日本語
Yorodumi
- PDB-5u8j: Crystal structure of a protein of unknown function ECL_02571 invo... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5u8j
TitleCrystal structure of a protein of unknown function ECL_02571 involved in membrane biogenesis from Enterobacter cloacae
ComponentsUPF0502 protein BFJ73_07745
KeywordsUNKNOWN FUNCTION / membrane biogenesis / alpha/beta protein / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homologyWinged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha / :
Function and homology information
Biological speciesEnterobacter cloacae (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.52 Å
AuthorsStogios, P.J. / Skarina, T. / Sandoval, J. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: Crystal structure of a protein of unknown function ECL_02571 involved in membrane biogenesis from Enterobacter cloacae
Authors: Stogios, P.J.
History
DepositionDec 14, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UPF0502 protein BFJ73_07745
B: UPF0502 protein BFJ73_07745
C: UPF0502 protein BFJ73_07745
D: UPF0502 protein BFJ73_07745
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,4256
Polymers79,3544
Non-polymers712
Water3,999222
1
A: UPF0502 protein BFJ73_07745
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8742
Polymers19,8381
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UPF0502 protein BFJ73_07745


Theoretical massNumber of molelcules
Total (without water)19,8381
Polymers19,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UPF0502 protein BFJ73_07745
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8742
Polymers19,8381
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: UPF0502 protein BFJ73_07745


Theoretical massNumber of molelcules
Total (without water)19,8381
Polymers19,8381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.170, 53.890, 90.000
Angle α, β, γ (deg.)90.00, 100.04, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
UPF0502 protein BFJ73_07745


Mass: 19838.465 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacter cloacae (bacteria) / Gene: BFJ73_07745 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: A0A1B3EZY2
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.62 Å3/Da / Density % sol: 53.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 20% PEG3350, 0.2 M potassium dihydrogen phosphate, 1% sucrose, 0.1 M phosphate citrate pH 4.2

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.52→30 Å / Num. obs: 28186 / % possible obs: 98.2 % / Redundancy: 5 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 19.84
Reflection shellResolution: 2.52→2.56 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.922 / Mean I/σ(I) obs: 2.17 / CC1/2: 0.664 / % possible all: 94.6

-
Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BZ6

3bz6


Resolution: 2.52→29.564 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2737 1361 4.92 %RANDOM
Rwork0.2126 ---
obs0.2157 27685 98.27 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.52→29.564 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5326 0 2 222 5550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035419
X-RAY DIFFRACTIONf_angle_d0.6547313
X-RAY DIFFRACTIONf_dihedral_angle_d23.6342087
X-RAY DIFFRACTIONf_chiral_restr0.042831
X-RAY DIFFRACTIONf_plane_restr0.003962
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5201-2.61010.34351180.28252582X-RAY DIFFRACTION97
2.6101-2.71450.36721490.28032555X-RAY DIFFRACTION97
2.7145-2.8380.3661560.29072549X-RAY DIFFRACTION97
2.838-2.98750.35041010.26632647X-RAY DIFFRACTION98
2.9875-3.17440.32031270.24872613X-RAY DIFFRACTION98
3.1744-3.41920.27791270.22162630X-RAY DIFFRACTION99
3.4192-3.76270.27491390.21392641X-RAY DIFFRACTION99
3.7627-4.30570.25571460.17522661X-RAY DIFFRACTION99
4.3057-5.41930.20521440.1762695X-RAY DIFFRACTION99
5.4193-29.56560.25911540.1972751X-RAY DIFFRACTION100
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)
11.80791.79321.46753.69272.86612.23110.6870.6549-0.5374-0.39350.1002-0.23980.28360.75491.28481.3072-0.30830.35580.3516-0.62030.11991.05544.335417.3629
22.90391.56670.57345.12470.86091.656-0.38560.08880.3001-0.38440.39380.7266-0.2985-0.28650.00030.4484-0.0729-0.01640.40030.04350.4144-10.90388.502328.1457
31.0288-1.399-0.80411.91691.07510.61680.11481.17111.0921-2.6050.60470.9966-0.96210.11180.1861.0171-0.1912-0.06770.6940.19460.481-10.8834-3.653115.7631
43.0911-0.0023-0.46474.76620.58971.4273-0.33440.0126-0.50610.36950.6917-0.90840.29650.43040.00140.4861-0.0115-0.04960.4963-0.17090.55071.6968-9.489130.2105
52.00264.0258-1.42562.2869-0.91050.3781-0.26180.9063-2.1854-0.4485-0.8987-0.8571.1483-0.2244-0.21771.2448-0.03520.3590.3333-0.07860.75926.31211.065516.256
64.37710.2411-1.18031.33090.41642.7828-0.1844-0.0815-0.05960.13690.2256-0.06160.1136-0.0168-00.4377-0.07450.02160.3724-0.05790.35877.812624.028323.6398
73.9292-0.0824-2.66872.32512.01723.59520.10550.38750.1634-0.2902-0.0492-0.31030.0881-0.35850.00060.4279-0.13340.03310.4734-0.02110.42313.465724.607610.0825
80.70280.3266-0.97031.436-0.05561.33060.49320.19670.2453-0.58530.1346-0.00870.4144-0.57120.00040.6954-0.1652-0.0290.7542-0.0150.41783.963616.98671.5928
91.55071.14720.44073.2288-1.39822.6503-0.28990.2403-0.1253-0.30950.39390.25420.2341-0.268800.4234-0.13290.00860.49320.04120.4505-28.2618-16.782821.0171
101.2301-0.39910.62020.7182-0.08250.40090.19420.2966-0.0711-0.5194-0.03590.4006-0.6679-0.1069-0.00190.5612-0.1144-0.06960.60550.11930.5622-28.172-6.062915.1574
114.95230.46070.1312.45852.13864.35210.0262-0.4473-0.25490.4276-0.0570.0120.3523-0.49590.00140.4831-0.0760.00950.50010.1120.4133-27.674-12.967639.8348
124.4286-2.1187-4.31934.37122.58434.29560.1434-1.5597-0.66911.7132-0.23581.65910.7954-1.7801-0.15570.5818-0.13840.05231.39050.28360.8138-41.2935-14.910735.4346
13-00.00420.0070.00110.01670.04560.4577-0.47990.19830.66290.39070.5858-0.6019-0.1587-01.00570.01690.3671.0134-0.09360.951538.627841.621327.1438
143.5732-0.11590.58582.76380.77050.9143-0.02390.3-0.0460.1057-0.0461-0.0227-0.06050.320200.4261-0.178-0.04880.5760.05340.574636.787229.827415.5965
153.0138-0.2233-0.75873.30371.75331.1530.07610.05861.6741-0.2125-0.32610.1963-0.1102-0.1938-0.00010.4682-0.0224-0.16570.58310.13671.090823.807643.101414.3065
161.1318-0.8203-0.09191.243-0.43450.398-0.58270.22951.75180.26670.17350.3984-0.5591-0.029-0.03910.6341-0.2738-0.23770.24160.13351.90331.124550.154219.7806
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:5)
2X-RAY DIFFRACTION2(chain A and resid 6:84)
3X-RAY DIFFRACTION3(chain A and resid 85:94)
4X-RAY DIFFRACTION4(chain A and resid 95:171)
5X-RAY DIFFRACTION5(chain B and resid 1:7)
6X-RAY DIFFRACTION6(chain B and resid 8:71)
7X-RAY DIFFRACTION7(chain B and resid 72:141)
8X-RAY DIFFRACTION8(chain B and resid 142:173)
9X-RAY DIFFRACTION9(chain C and resid 2:63)
10X-RAY DIFFRACTION10(chain C and resid 64:86)
11X-RAY DIFFRACTION11(chain C and resid 87:166)
12X-RAY DIFFRACTION12(chain C and resid 167:172)
13X-RAY DIFFRACTION13(chain D and resid 1:5)
14X-RAY DIFFRACTION14(chain D and resid 6:86)
15X-RAY DIFFRACTION15(chain D and resid 87:142)
16X-RAY DIFFRACTION16(chain D and resid 143:171)

+
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