[English] 日本語
Yorodumi
- PDB-7p1y: A small alarmone hydrolase TdActApo2 mutant - T78N -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p1y
TitleA small alarmone hydrolase TdActApo2 mutant - T78N
ComponentsHD domain-containing protein
KeywordsHYDROLASE / small alarmone hydrolase
Function / homologyMetal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / metal ion binding / : / HD/PDEase domain-containing protein
Function and homology information
Biological speciesTreponema denticola (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsJin, Y. / Roth, C. / Rizkallah, P.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust209057/Z/17/Z United Kingdom
CitationJournal: To Be Published
Title: A small alarmone hydrolase TdActApo2 mutant - T78N
Authors: Jin, Y. / Roth, C. / Rizkallah, P.
History
DepositionJul 2, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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
BBB: HD domain-containing protein
DDD: HD domain-containing protein
CCC: HD domain-containing protein
AAA: HD domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,61710
Polymers106,3264
Non-polymers2916
Water1,56787
1
BBB: HD domain-containing protein
AAA: HD domain-containing protein
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, A dimer
  • 53.3 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)53,3095
Polymers53,1632
Non-polymers1453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-29 kcal/mol
Surface area15390 Å2
MethodPISA
2
DDD: HD domain-containing protein
hetero molecules

CCC: HD domain-containing protein
hetero molecules


  • defined by author&software
  • 53.3 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)53,3095
Polymers53,1632
Non-polymers1453
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.286, 69.189, 132.070
Angle α, β, γ (deg.)90.000, 93.015, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11BBB
21DDD
32BBB
42CCC
53BBB
63AAA
74DDD
84CCC
95DDD
105AAA
116CCC
126AAA

NCS domain segments:

Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 1 / Auth seq-ID: 17 - 192 / Label seq-ID: 44 - 219

Dom-IDComponent-IDEns-IDAuth asym-IDLabel asym-ID
111BBBA
211DDDB
322BBBA
422CCCC
533BBBA
633AAAD
744DDDB
844CCCC
955DDDB
1055AAAD
1166CCCC
1266AAAD

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

-
Components

#1: Protein
HD domain-containing protein


Mass: 26581.613 Da / Num. of mol.: 4 / Mutation: D78N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola (strain ATCC 35405 / DSM 14222 / CIP 103919 / JCM 8153 / KCTC 15104) (bacteria)
Strain: ATCC 35405 / DSM 14222 / CIP 103919 / JCM 8153 / KCTC 15104
Gene: TDE_1690 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q73M21
#2: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.63 Å3/Da / Density % sol: 53.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.22 mM TdRel-D78N protein in the buffer of 1 mM MnCl2, 25 mM Tris-HCl pH 8.0, and 200 mM NaCl was mixed 1:1 ratio with the precipitant containing 0.2 M NH4Cl and 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976238 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976238 Å / Relative weight: 1
ReflectionResolution: 2.38→61.345 Å / Num. obs: 44562 / % possible obs: 100 % / Redundancy: 11.7 % / CC1/2: 0.999 / Net I/σ(I): 10.4
Reflection shellResolution: 2.39→2.47 Å / Redundancy: 11.4 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4645 / CC1/2: 0.604 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3gni

3gni


Resolution: 2.38→61.278 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.171 / SU B: 8.981 / SU ML: 0.191 / Average fsc free: 0.8597 / Average fsc work: 0.8728 / Cross valid method: FREE R-VALUE / ESU R: 0.245 / ESU R Free: 0.2
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2269 2212 4.966 %
Rwork0.1907 42332 -
all0.193 --
obs-44544 99.978 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 63.939 Å2
Baniso -1Baniso -2Baniso -3
1-4.215 Å20 Å2-0.998 Å2
2---0.017 Å20 Å2
3----4.07 Å2
Refinement stepCycle: LAST / Resolution: 2.38→61.278 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5493 0 6 87 5586
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0135592
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175521
X-RAY DIFFRACTIONr_angle_refined_deg1.641.637530
X-RAY DIFFRACTIONr_angle_other_deg1.371.57912724
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2425687
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.48824.124274
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.968151087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4421522
X-RAY DIFFRACTIONr_chiral_restr0.0820.2749
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026188
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021196
X-RAY DIFFRACTIONr_nbd_refined0.2310.21263
X-RAY DIFFRACTIONr_symmetry_nbd_other0.170.24889
X-RAY DIFFRACTIONr_nbtor_refined0.1670.22768
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.22699
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.170.2108
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.4020.224
X-RAY DIFFRACTIONr_nbd_other0.1880.2109
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3820.25
X-RAY DIFFRACTIONr_mcbond_it6.6286.4712754
X-RAY DIFFRACTIONr_mcbond_other6.6296.4692752
X-RAY DIFFRACTIONr_mcangle_it9.439.6813430
X-RAY DIFFRACTIONr_mcangle_other9.439.6813430
X-RAY DIFFRACTIONr_scbond_it6.9967.062838
X-RAY DIFFRACTIONr_scbond_other6.9957.0612839
X-RAY DIFFRACTIONr_scangle_it10.13110.2924097
X-RAY DIFFRACTIONr_scangle_other10.1310.2924098
X-RAY DIFFRACTIONr_lrange_it12.85575.2026355
X-RAY DIFFRACTIONr_lrange_other12.84175.1496352
X-RAY DIFFRACTIONr_ncsr_local_group_10.080.055574
X-RAY DIFFRACTIONr_ncsr_local_group_20.0820.055528
X-RAY DIFFRACTIONr_ncsr_local_group_30.0840.055554
X-RAY DIFFRACTIONr_ncsr_local_group_40.0750.055574
X-RAY DIFFRACTIONr_ncsr_local_group_50.0830.055605
X-RAY DIFFRACTIONr_ncsr_local_group_60.0860.055535
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11BBBX-RAY DIFFRACTIONLocal ncs0.079690.05008
12DDDX-RAY DIFFRACTIONLocal ncs0.079690.05008
23BBBX-RAY DIFFRACTIONLocal ncs0.081980.05007
24CCCX-RAY DIFFRACTIONLocal ncs0.081980.05007
35BBBX-RAY DIFFRACTIONLocal ncs0.083620.05008
36AAAX-RAY DIFFRACTIONLocal ncs0.083620.05008
47DDDX-RAY DIFFRACTIONLocal ncs0.075340.05008
48CCCX-RAY DIFFRACTIONLocal ncs0.075340.05008
59DDDX-RAY DIFFRACTIONLocal ncs0.082820.05008
510AAAX-RAY DIFFRACTIONLocal ncs0.082820.05008
611CCCX-RAY DIFFRACTIONLocal ncs0.086270.05008
612AAAX-RAY DIFFRACTIONLocal ncs0.086270.05008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.38-2.4420.3051620.33331080.33132720.6210.60999.93890.336
2.442-2.5090.3031560.30330120.30331680.7190.7361000.301
2.509-2.5810.3431510.29529460.29730970.7310.7671000.293
2.581-2.660.3071390.26529060.26730450.8320.831000.257
2.66-2.7480.3111230.24827650.2528880.8450.871000.235
2.748-2.8440.2861400.23926700.24128100.8580.8871000.224
2.844-2.9510.2371530.23425720.23427250.8850.891000.217
2.951-3.0710.2651480.21425140.21626620.8890.9091000.195
3.071-3.2070.261340.20423740.20825080.8980.9181000.186
3.207-3.3630.2821130.20323070.20624200.8930.9211000.186
3.363-3.5450.2271020.19522030.19723050.9260.9431000.18
3.545-3.7590.2421080.18820600.19121680.9210.9491000.176
3.759-4.0170.206990.17819710.1820700.9530.9511000.166
4.017-4.3380.196920.15218120.15419040.960.9651000.144
4.338-4.7490.18760.12816840.1317620.9620.97699.88650.121
4.749-5.3060.191890.15515200.15716090.9520.9651000.146
5.306-6.1190.284860.19813370.20414230.9250.9461000.189
6.119-7.4760.199690.17511400.17612090.9560.961000.167
7.476-10.4940.12510.1138970.1139480.9870.9841000.113
10.494-61.2780.204210.2335340.2325590.9520.94999.28440.23

+
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