[English] 日本語
Yorodumi
- PDB-5eqz: Crystal structure of a Rev protein from Borrelia burgdorferi at 1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5eqz
TitleCrystal structure of a Rev protein from Borrelia burgdorferi at 1.80 A resolution
ComponentsRev protein
KeywordsTRANSCRIPTION / SSGCID / Borellia burgdorferi / Rev protein / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyBorrelia REV / Borrelia burgdorferi REV protein / Transcription elongation factor S-II, central domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / DNA-templated transcription / Rev protein
Function and homology information
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a Rev protein from Borrelia burgdorferi at 1.80 A resolution
Authors: Yano, J.K. / Sullivan, A.H. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2017Group: Data collection / Derived calculations / Category: pdbx_struct_oper_list / reflns_shell
Item: _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.2Mar 6, 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: Rev protein


Theoretical massNumber of molelcules
Total (without water)16,3821
Polymers16,3821
Non-polymers00
Water1,964109
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.970, 42.510, 64.140
Angle α, β, γ (deg.)90.000, 109.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-259-

HOH

-
Components

#1: Protein Rev protein


Mass: 16381.591 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (strain ATCC 35210 / B31 / CIP 102532 / DSM 4680) (bacteria)
Strain: ATCC 35210 / B31 / CIP 102532 / DSM 4680 / Gene: BB_M27 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9S0B8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.51 Å3/Da / Density % sol: 51.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 5
Details: native crystal, MCSG1 condition F03: 20% PEG 3350,0.2 M Ammonium Citrate Dibasic, pH 5.0, BobuA.18943.a.B2.PS02467 at 19.33 mg/ml, cryo 20% EG, tray 266003F3, puck pla5-11. Iodide data ...Details: native crystal, MCSG1 condition F03: 20% PEG 3350,0.2 M Ammonium Citrate Dibasic, pH 5.0, BobuA.18943.a.B2.PS02467 at 19.33 mg/ml, cryo 20% EG, tray 266003F3, puck pla5-11. Iodide data set,JCSG+ condition A03: 20% Peg 3350, 200 mM Ammonium Citrate Tribasic, BobuA.18943.a.B2.PS02467 at 19.33 mg/ml, cryo 30% EG, 1.5 M NaI, tray 266002A3, puck pla5-6

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceTypeIDWavelength (Å)
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT11.5418
ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT21.5418
Detector
TypeIDDetectorDate
RIGAKU SATURN 944+1CCDSep 25, 2015
RIGAKU SATURN 944+2CCDSep 24, 2015
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
2Rigaku VariMaxSINGLE WAVELENGTHMx-ray1
1Rigaku VariMaxSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNumber: 292969 / Rmerge(I) obs: 0.034 / Χ2: 1.8 / D res high: 2 Å / Num. obs: 21278 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
8.945023410.029
6.328.9443110.023
5.166.3254710.026
4.475.1668010.024
44.4777410.021
3.65484510.023
3.383.6591910.025
3.163.3896910.027
2.983.16103710.029
2.832.98113110.034
2.72.83117610.04
2.582.7122310.046
2.482.58128510.055
2.392.48128510.062
2.312.39140610.066
2.242.31141110.08
2.172.24145410.097
2.112.17150910.108
2.052.11150710.138
22.05145510.168
ReflectionResolution: 1.8→50 Å / Num. obs: 15025 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 6.7 % / Biso Wilson estimate: 24.15 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.032 / Χ2: 1.015 / Net I/σ(I): 34.87 / Num. measured all: 101069
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.854.90.9520.5193.495115113810530.57892.5
1.85-1.90.960.4134.314976108510180.45993.8
1.9-1.950.980.2955.795082105310120.32896.1
1.95-2.010.9870.2287.475291107010330.25396.5
2.01-2.080.9910.14311.7849179609520.15999.2
2.08-2.150.9940.10914.8751349799690.12199
2.15-2.230.9960.08618.4651519519500.09599.9
2.23-2.320.9980.06425.5351478868880.07100
2.32-2.430.9980.0627.452448608550.06599.4
2.43-2.550.9990.05231.6953798378370.057100
2.55-2.680.9990.04238.4854347967950.04699.9
2.68-2.850.9990.03845.5953407337340.041100
2.85-3.0410.03155.1456577217150.03499.2
3.04-3.2910.02768.3457086496470.02999.7
3.29-3.610.02587.1464646076070.026100
3.6-4.0210.02193.6859915535520.02299.8
4.02-4.6510.01899.3753944934940.019100
4.65-5.6910.01994.1643694074020.0298.8
5.69-8.0510.01988.9735243353330.0299.4
8.05-500.9990.01898.4617521851790.01996.8

-
Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.8→50 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 1474 9.81 %
Rwork0.2034 13545 -
obs0.2071 15019 98.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.44 Å2 / Biso mean: 33.2544 Å2 / Biso min: 14.27 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1054 0 0 109 1163
Biso mean---37.59 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061067
X-RAY DIFFRACTIONf_angle_d0.7161436
X-RAY DIFFRACTIONf_chiral_restr0.045169
X-RAY DIFFRACTIONf_plane_restr0.004186
X-RAY DIFFRACTIONf_dihedral_angle_d14.25667
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85810.29621220.26151156X-RAY DIFFRACTION93
1.8581-1.92450.32891430.26091194X-RAY DIFFRACTION95
1.9245-2.00150.29981360.24891159X-RAY DIFFRACTION96
2.0015-2.09260.27231240.2261240X-RAY DIFFRACTION99
2.0926-2.20290.25651200.22341244X-RAY DIFFRACTION100
2.2029-2.34090.29371450.22251239X-RAY DIFFRACTION100
2.3409-2.52160.27121420.21061247X-RAY DIFFRACTION100
2.5216-2.77530.2541380.21451251X-RAY DIFFRACTION100
2.7753-3.17660.26221340.21031258X-RAY DIFFRACTION100
3.1766-4.00130.21221330.17931256X-RAY DIFFRACTION100
4.0013-500.18551370.17731301X-RAY DIFFRACTION99
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)
12.4134-0.1784-0.32721.8757-1.05312.2980.0175-0.0295-0.17810.184-0.07990.14280.0808-0.39550.07890.1531-0.0145-0.0130.2169-0.03630.178523.0664-0.4923-4.0531
20.7474-0.7855-0.67621.3349-0.43912.2760.37490.37620.1403-0.1438-0.0175-0.0574-1.415-1.04920.07590.28390.10650.01540.31580.01440.203823.3077.5238-21.4655
32.93110.2187-1.99043.01241.0887.7310.00950.20940.0542-0.4225-0.0133-0.37780.0996-0.2912-0.09410.19360.00970.03060.2498-0.00150.179830.6708-0.6148-39.9417
46.8403-0.7801-5.14962.62340.00764.2329-0.09190.5212-0.3486-0.0148-0.20120.39140.0634-1.74830.03680.20260.0188-0.02230.7385-0.10650.278519.1846-0.7288-32.9913
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 20 through 68 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 69 through 108 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 109 through 135 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 136 through 157 )A0

+
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