[English] 日本語
Yorodumi
- PDB-6pwy: Structure of C. elegans ZK177.8, SAMHD1 ortholog -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6pwy
TitleStructure of C. elegans ZK177.8, SAMHD1 ortholog
ComponentsZK177.8
KeywordsHYDROLASE / deoxynucleoside triphosphate triphosphohydrolase / dNTPase
Function / homology
Function and homology information


Nucleotide catabolism / dGTPase activity / dGTP catabolic process / nucleus
Similarity search - Function
HD domain profile. / HD domain / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / SUCCINIC ACID / Uncharacterized protein ZK177.8
Similarity search - Component
Biological speciesCaenorhabditis elegans (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.81 Å
AuthorsLim, C.S. / Maehigashi, T. / Wade, L.R. / Bowen, N. / Knecht, K. / Xiong, Y. / Kim, B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)AI150451 United States
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)AI136581 United States
CitationJournal: To Be Published
Title: ZK177.8 of Caenorhabditis elegans: Aicardi-Goutieres Syndrome SAMHD1 Ortholog
Authors: Maehigashi, T. / Lim, C. / Wade, L.R. / Bowen, N. / Knecht, K. / Schinazi, R.F. / Xiong, Y. / Kim, B.
History
DepositionJul 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ZK177.8
B: ZK177.8
D: ZK177.8
C: ZK177.8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,09726
Polymers239,2694
Non-polymers6,82822
Water26,6981482
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking, Formaldehyde crosslinking, followed by SDS-PAGE analysis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29900 Å2
ΔGint1 kcal/mol
Surface area74480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.681, 90.557, 93.357
Angle α, β, γ (deg.)65.580, 65.490, 86.220
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22D
13A
23C
14B
24D
15B
25C
16D
26C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A21 - 539
2010B21 - 539
1020A21 - 540
2020D21 - 540
1030A21 - 539
2030C21 - 539
1040B21 - 540
2040D21 - 540
1050B21 - 546
2050C21 - 546
1060D21 - 540
2060C21 - 540

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

-
Protein , 1 types, 4 molecules ABDC

#1: Protein
ZK177.8


Mass: 59817.262 Da / Num. of mol.: 4 / Fragment: UNP residues 41-565
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: ZK177.8 / Plasmid: pET14b / Production host: Escherichia coli (E. coli) / References: UniProt: Q09374

-
Non-polymers , 5 types, 1504 molecules

#2: Chemical
ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical
ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H6O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1482 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.84 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 8 / Details: 0.1 M SPG, pH 5.5, 20% w/v PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2019
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 209546 / % possible obs: 94.1 % / Redundancy: 2 % / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.082 / Rrim(I) all: 0.129 / Χ2: 1.201 / Net I/σ(I): 9.8 / Num. measured all: 417412
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.8320.728101140.1630.6140.9560.96191.3
1.83-1.8620.654101560.2640.5510.8590.95491.6
1.86-1.920.648102310.3190.5450.850.99491.4
1.9-1.9420.532102200.2780.4510.7011.21392.2
1.94-1.981.90.445102660.5610.3760.5850.94992.2
1.98-2.0320.379103760.6480.3210.4990.96192.9
2.03-2.0820.339103240.6390.2880.4461.22593.1
2.08-2.1320.273103440.7880.2320.361.04593
2.13-2.21.90.24104440.8340.2050.3171.06992.9
2.2-2.271.80.21102180.8220.1830.281.68692.4
2.27-2.351.90.17104440.9140.1450.2251.14494.2
2.35-2.441.90.146106190.940.1250.1931.13994.7
2.44-2.5520.127106450.9430.1070.1661.20296
2.55-2.692.10.107107920.9640.090.1411.19596.7
2.69-2.862.10.087107360.9790.0720.1141.20896.7
2.86-3.082.10.071107720.9860.0580.0921.3296.7
3.08-3.392.10.06106710.9890.0490.0781.48895.9
3.39-3.8820.052106630.990.0420.0671.4695.9
3.88-4.881.80.046106670.9920.0380.061.49795.7
4.88-502.30.045108440.9940.0340.0571.25997.3

-
Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
BUCCANEERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4BZB

4bzb


Resolution: 1.81→46.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.948 / SU B: 7.386 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.13 / ESU R Free: 0.119
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 10556 5 %RANDOM
Rwork0.1822 ---
obs0.1835 198955 93.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 129.95 Å2 / Biso mean: 30.921 Å2 / Biso min: 8.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.36 Å2-0.1 Å2-0.02 Å2
2---0.07 Å2-0.1 Å2
3---0.16 Å2
Refinement stepCycle: final / Resolution: 1.81→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16225 0 420 1482 18127
Biso mean--26.44 38.19 -
Num. residues----2033
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01317054
X-RAY DIFFRACTIONr_bond_other_d0.0020.01715849
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.64823070
X-RAY DIFFRACTIONr_angle_other_deg1.441.58236936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92552051
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22122.847878
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.914153129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.56515100
X-RAY DIFFRACTIONr_chiral_restr0.0940.22222
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0218625
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023395
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A161970.09
12B161970.09
21A168450.04
22D168450.04
31A161790.09
32C161790.09
41B162050.1
42D162050.1
51B171080.04
52C171080.04
61D161870.1
62C161870.1
LS refinement shellResolution: 1.81→1.852 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.325 692 -
Rwork0.335 13023 -
obs--82.73 %
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)
10.31090.1484-0.01020.33770.01760.1590.0095-0.0699-0.03750.0948-0.0078-0.09550.02270.0665-0.00170.0786-0.004-0.04030.05510.01420.038712.684-37.3065-23.1115
20.28010.02320.08830.3773-0.07510.1791-0.0123-0.09530.00650.1082-0.00340.0162-0.0372-0.06310.01570.1062-0.011-0.00920.0556-0.00330.005-22.4348-19.5724-18.9106
30.44310.17140.00640.2343-0.01470.1607-0.01080.0997-0.1038-0.06230.02-0.02080.07430.0132-0.00910.0971-0.007-0.00220.0302-0.02560.039-4.8396-53.6905-52.5928
40.3756-0.0056-0.08970.24330.08220.1415-0.00260.11930.0242-0.0885-0.01080.0062-0.0703-0.03970.01350.1048-0.0144-0.02140.06470.00850.0074-20.2227-17.5131-56.8271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 900
2X-RAY DIFFRACTION2B1 - 900
3X-RAY DIFFRACTION3D1 - 900
4X-RAY DIFFRACTION4C1 - 900

+
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://pdbjlvh1.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