[English] 日本語
Yorodumi
- PDB-6vtf: Naegleria gruberi RNA ligase with PPi -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6vtf
TitleNaegleria gruberi RNA ligase with PPi
ComponentsRNA ligase
KeywordsLIGASE / RNA repair / adenylyltransferase
Function / homologyRNA ligase, DRB0094 / PHA02142 OB-fold domain / RNA ligase domain, REL/Rln2 / RNA ligase / ATP binding / PYROPHOSPHATE 2- / Predicted protein
Function and homology information
Biological speciesNaegleria gruberi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsUnciuleac, M.C. / Goldgur, Y. / Shuman, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM126945 United States
CitationJournal: Nucleic Acids Res. / Year: 2020
Title: Caveat mutator: alanine substitutions for conserved amino acids in RNA ligase elicit unexpected rearrangements of the active site for lysine adenylylation.
Authors: Unciuleac, M.C. / Goldgur, Y. / Shuman, S.
History
DepositionFeb 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 10, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 11, 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: RNA ligase
B: RNA ligase
C: RNA ligase
D: RNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,3518
Polymers154,6474
Non-polymers7044
Water2,090116
1
A: RNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8382
Polymers38,6621
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: RNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8382
Polymers38,6621
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: RNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8382
Polymers38,6621
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: RNA ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8382
Polymers38,6621
Non-polymers1761
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)124.745, 104.896, 120.073
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: ARG / End label comp-ID: ARG / Auth seq-ID: 3 - 339 / Label seq-ID: 4 - 340

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

-
Components

#1: Protein
RNA ligase /


Mass: 38661.832 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naegleria gruberi (eukaryote) / Gene: NAEGRDRAFT_82186 / Production host: Escherichia coli (E. coli) / References: UniProt: D2W2Z5
#2: Chemical
ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H2O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: NgRnl wild type (10 mg/ml) was adjusted to 1 mM PPi and incubated for 15 min on ice before aliquots of the protein solution (1 ul) were mixed on a coverslip with an equal volume of ...Details: NgRnl wild type (10 mg/ml) was adjusted to 1 mM PPi and incubated for 15 min on ice before aliquots of the protein solution (1 ul) were mixed on a coverslip with an equal volume of precipitant solution containing 0.1 M HEPES pH 6.5, 30% PEG6000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.7→30.21 Å / Num. obs: 41889 / % possible obs: 97.4 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.049 / Rrim(I) all: 0.101 / Χ2: 1.098 / Net I/σ(I): 5.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.7-2.753.60.41920440.7560.2510.4910.83597.3
2.75-2.83.40.37620330.8060.2250.4410.86596.8
2.8-2.853.90.3420870.8560.1890.3910.86197.4
2.85-2.9140.29821050.8880.1650.3420.90698.7
2.91-2.9740.26320720.9070.1470.3030.96398.7
2.97-3.043.90.23321110.9240.1310.2691.0298.9
3.04-3.123.90.19820880.9490.1110.2281.03998.3
3.12-3.23.90.18420940.9520.1030.2121.06698.5
3.2-3.293.90.15520900.9610.0880.1791.15498.2
3.29-3.43.60.13620580.9740.080.1591.25497.4
3.4-3.523.90.12220940.9790.0680.141.25197.2
3.52-3.664.20.11520820.9810.0620.1311.32397.8
3.66-3.834.10.10720920.9840.0580.1221.33398.1
3.83-4.034.10.09521170.9870.0520.1081.35597.8
4.03-4.2840.08120930.9920.0440.0931.28297.1
4.28-4.613.80.06920670.9930.0390.0791.26495.7
4.61-5.074.20.06821240.9920.0360.0781.198.2
5.07-5.84.20.06421110.9940.0340.0720.99996.6
5.8-7.33.90.05721100.9950.0320.0660.92595.2
7.3-3040.04422170.9980.0240.051.07194.9

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5COT

5cot


Resolution: 2.71→30.21 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.45
RfactorNum. reflection% reflection
Rfree0.274 1974 4.72 %
Rwork0.2176 --
obs0.2202 41850 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 138.74 Å2 / Biso mean: 63.2337 Å2 / Biso min: 18.08 Å2
Refinement stepCycle: final / Resolution: 2.71→30.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10796 0 36 116 10948
Biso mean--96.61 51.4 -
Num. residues----1348
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4124X-RAY DIFFRACTION7.938TORSIONAL
12B4124X-RAY DIFFRACTION7.938TORSIONAL
13C4124X-RAY DIFFRACTION7.938TORSIONAL
14D4124X-RAY DIFFRACTION7.938TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.71-2.780.38531110.29852292240379
2.78-2.850.37691430.29452842298597
2.85-2.930.37991340.29162874300899
2.93-3.030.34641530.28262881303499
3.03-3.140.33061410.27162876301798
3.14-3.260.35031440.2512926307099
3.26-3.410.30071450.24622840298598
3.41-3.590.26881440.22792863300798
3.59-3.820.26951440.21852891303598
3.82-4.110.25311390.20192909304898
4.11-4.520.23111370.16662880301796
4.52-5.170.20871400.16662913305398
5.17-6.50.2341490.20782911306097
6.51-30.210.2731500.20992978312894
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)
13.0429-0.5853-1.7893.65110.61514.13420.0195-0.15570.13990.24510.0290.10610.2734-0.01290.0350.27840.013-0.01190.435-0.00480.4752-44.36961.9712-8.194
20.6706-0.0529-1.11152.792-1.80037.06770.1313-0.04960.1103-0.0924-0.0597-0.36630.19080.4422-0.09610.43170.0712-0.02670.4865-0.05010.4993-37.63174.942-37.1836
32.8242-0.78480.74943.60920.38553.00760.06370.2323-0.2337-0.0007-0.11240.0216-0.0259-0.01150.02280.2479-0.00770.02640.26740.00630.2745-46.207349.3121-54.1497
41.17850.86590.25930.6655-0.80753.48540.1134-0.061-0.07530.42-0.22650.0069-0.4993-0.04350.03590.56550.0420.05080.4212-0.01150.2784-43.251446.1037-31.8581
52.6373-0.53660.86193.4241-0.69223.46140.1802-0.0251-0.20.3474-0.1836-0.2407-0.59350.2988-0.02980.6316-0.05990.01770.45840.08220.2508-36.660842.2144-18.6514
64.50881.47930.16422.3906-0.72743.8238-0.2886-0.0853-0.1640.4912-0.0951-0.1176-0.99690.45080.21090.7673-0.02050.00090.37480.05250.293-39.797958.2558-32.9481
71.9881-1.67341.3561.9147-0.15133.7621-0.36140.13430.13930.54820.16210.3738-0.23770.05620.10920.4532-0.03210.19060.38270.04510.2718-42.898529.7229-76.5445
82.6838-0.01331.13412.4908-0.90951.3881-0.10740.0023-0.4312-0.38630.0669-0.21720.48030.37980.06070.5124-0.02180.1330.3194-0.03560.2734-44.914417.7514-72.8437
96.71163.6628-0.12052.54520.31181.41070.147-0.3136-0.52820.0659-0.1382-0.1415-0.0557-0.10250.020.23180.02990.04170.32250.02460.4361-73.515517.9207-65.6054
105.81040.9672-0.15062.54020.20093.9136-0.0933-0.47310.91820.12-0.1802-0.07-0.2207-0.23820.10790.3872-0.11210.04180.2803-0.0390.3818-62.048931.5667-66.1532
112.94710.4353-0.06123.53810.26183.1590.1005-0.223-0.10650.2227-0.2462-0.1708-0.44020.77320.14450.3953-0.0837-0.02640.47390.09960.276-41.24929.339613.1452
124.212-1.0710.85372.87980.08151.8165-0.03050.03290.4579-0.0956-0.24080.533-0.1203-0.14150.24390.2812-0.04210.00040.4133-0.10870.648-69.494731.73635.3304
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 119 )A3 - 119
2X-RAY DIFFRACTION2chain 'A' and (resid 120 through 339 )A120 - 339
3X-RAY DIFFRACTION3chain 'B' and (resid 3 through 119 )B3 - 119
4X-RAY DIFFRACTION4chain 'B' and (resid 120 through 173 )B120 - 173
5X-RAY DIFFRACTION5chain 'B' and (resid 174 through 284 )B174 - 284
6X-RAY DIFFRACTION6chain 'B' and (resid 285 through 339 )B285 - 339
7X-RAY DIFFRACTION7chain 'C' and (resid 3 through 29 )C3 - 29
8X-RAY DIFFRACTION8chain 'C' and (resid 30 through 137 )C30 - 137
9X-RAY DIFFRACTION9chain 'C' and (resid 138 through 284 )C138 - 284
10X-RAY DIFFRACTION10chain 'C' and (resid 285 through 339 )C285 - 339
11X-RAY DIFFRACTION11chain 'D' and (resid 3 through 119 )D3 - 119
12X-RAY DIFFRACTION12chain 'D' and (resid 120 through 339 )D120 - 339

+
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