[English] 日本語
Yorodumi
- PDB-3nm7: Crystal Structure of Borrelia burgdorferi Pur-alpha -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3nm7
TitleCrystal Structure of Borrelia burgdorferi Pur-alpha
ComponentsUncharacterized protein
KeywordsNUCLEIC ACID BINDING PROTEIN / Pur-alpha / Pur repeat / Pur domain / PURA / Whirly fold / RNA binding / DNA binding
Function / homology
Function and homology information


purine-rich negative regulatory element binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / metal ion binding
Similarity search - Function
Protein of unknown function DUF3276 / Protein of unknown function (DUF3276) / Nuclear Transport Factor 2; Chain: A, - #700 / Purine-rich element binding protein family / DNA/RNA-binding repeats in PUR-alpha/beta/gamma and in hypothetical proteins from spirochetes and the Bacteroides-Cytophaga-Flexibacter bacteria. / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
DUF3276 family protein
Similarity search - Component
Biological speciesBorrelia burgdorferi (Lyme disease spirochete)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsGraebsch, A. / Roche, S. / Kostrewa, D. / Niessing, D.
Citation
Journal: Plos One / Year: 2010
Title: Of Bits and Bugs - on the use of bioinformatics and a bacterial crystal structure to solve a eukaryotic repeat-protein structure.
Authors: Graebsch, A. / Roche, S. / Kostrewa, D. / Soeding, S. / Niessing, D.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: X-ray structure of Pur-alpha reveals a Whirly-like fold and an unusual nucleic-acid binding surface
Authors: Graebsch, A. / Roche, S. / Niessing, D.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6757
Polymers59,5274
Non-polymers1483
Water2,792155
1
A: Uncharacterized protein
B: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9125
Polymers29,7632
Non-polymers1483
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4280 Å2
ΔGint-25 kcal/mol
Surface area10070 Å2
MethodPISA
2
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)29,7632
Polymers29,7632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-32 kcal/mol
Surface area9120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.790, 57.750, 142.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31B
41D
12A
22C
13B
23D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A3 - 13
2111C3 - 13
3111B3 - 13
4111D3 - 13
1211A19 - 40
2211C19 - 40
3211B19 - 40
4211D19 - 40
1311A49 - 54
2311C49 - 54
3311B49 - 54
4311D49 - 54
1411A56 - 77
2411C56 - 77
3411B56 - 77
4411D56 - 77
1121A14 - 18
2121C14 - 18
1221A41 - 48
2221C41 - 48
1321A55
2321C55
1131B14 - 18
2131D14 - 18
1231B41 - 48
2231D41 - 48

NCS ensembles :
ID
1
2
3

-
Components

#1: Protein
Uncharacterized protein


Mass: 14881.649 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Borrelia burgdorferi (Lyme disease spirochete)
Gene: BB_0047 / Plasmid: pGEX6p1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: O51076
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 1.65 Å3/Da / Density % sol: 25.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 125 mM NaCl, 100 mM Hepes pH 7.2, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9724 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2008
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9724 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 20614 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 35.32 Å2 / Rmerge(I) obs: 0.162 / Rsym value: 0.074 / Net I/σ(I): 14.99
Reflection shellResolution: 2.21→2.34 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.695 / Mean I/σ(I) obs: 2.48 / Rsym value: 0.522 / % possible all: 97.6

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.5.0044refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
SCALAdata scaling
BUSTER2.9.2refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3N8B

3n8b


Resolution: 2.2→23.11 Å / Cor.coef. Fo:Fc: 0.9068 / Cor.coef. Fo:Fc free: 0.8927 / Occupancy max: 1 / Occupancy min: 0 / SU B: 17.343 / SU ML: 0.193 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 1053 5.11 %RANDOM
Rwork0.2168 ---
obs0.219 20602 99.67 %-
all-20602 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.47 Å2
Baniso -1Baniso -2Baniso -3
1--16.7686 Å20 Å20 Å2
2--8.1936 Å20 Å2
3---8.575 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.2→23.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2588 0 9 155 2752
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012670HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.173574HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d988SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes85HARMONIC2
X-RAY DIFFRACTIONt_gen_planes381HARMONIC5
X-RAY DIFFRACTIONt_it2670HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.11
X-RAY DIFFRACTIONt_other_torsion19.63
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact
LS refinement shellResolution: 2.2→2.32 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3052 153 5.22 %
Rwork0.2564 2780 -
all0.2587 2933 -
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)
10.5528-0.8055-0.30024.8099-0.02833.58110.0468-0.0999-0.0771-0.60050.05570.16610.4975-0.1602-0.10250.407-0.0451-0.0740.1090.0340.1807-4.398-5.78421.922
22.42980.6418-2.07299.82874.437911.4270.0518-0.09370.6292-0.99-0.03260.17310.14170.2438-0.01920.42360.03-0.01620.10220.00090.2923-6.2610.58414.359
33.3548-1.5398-0.05210.08640.5674.80920.09390.06330.0259-0.9308-0.13241.6060.4426-0.76920.03850.3999-0.0437-0.19760.20240.04710.4816-15.4555.23116.878
46.1697-3.9465-7.93147.12727.099315.8770.1343-0.2030.1985-0.45040.1451-0.3796-0.21070.0448-0.27940.2249-0.01640.01740.03170.01930.17841.0214.63118.808
51.3781-1.28661.1035.8785-1.4734.8527-0.002-0.08770.147-0.69550.0840.1485-0.26290.1041-0.08190.4399-0.0406-0.00530.0667-0.00840.15141.839-22.58221.387
65.2332-1.20863.968111.742-5.76145.116-0.591-0.1668-0.339-0.89720.637-0.2603-0.1981-0.4401-0.0460.93090.1167-0.00920.1832-0.0640.22011.911-38.50512.983
77.31924.7348-2.26038.7112-0.06332.4894-0.84620.2638-1.1374-2.68910.4082-2.0144-0.00910.38460.4381.12880.00430.59690.1494-0.00790.625611.423-33.65414.067
813.8124-6.629311.88657.4175-7.389513.7729-0.00780.2349-0.2924-0.54320.14650.44120.06710.1242-0.13870.2799-0.0597-0.06760.02320.01540.2215-4.176-32.95219.375
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 56
2X-RAY DIFFRACTION2A57 - 77
3X-RAY DIFFRACTION3B3 - 56
4X-RAY DIFFRACTION4B57 - 77
5X-RAY DIFFRACTION5C3 - 56
6X-RAY DIFFRACTION6C57 - 77
7X-RAY DIFFRACTION7D3 - 56
8X-RAY DIFFRACTION8D57 - 77

+
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