[English] 日本語
Yorodumi
- PDB-5m86: Crystal Structure of the Thermoplasma acidophilum Protein Ta1207 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m86
TitleCrystal Structure of the Thermoplasma acidophilum Protein Ta1207
ComponentsTa1207
KeywordsUNKNOWN FUNCTION / pentamer
Function / homologyTa1207 family / Ta1207 family / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsPathare, G.R. / Nagy, I. / Bracher, A.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2017
Title: Crystal structure of the Thermoplasma acidophilum protein Ta1207.
Authors: Pathare, G.R. / Nagy, I. / Hubert, A. / Thomas, D.R. / Bracher, A.
History
DepositionOct 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 2017Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2017Group: Database references / Structure summary / Category: citation / entity
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_description
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim
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_asym_id / _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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ta1207
B: Ta1207
C: Ta1207
D: Ta1207
E: Ta1207
F: Ta1207
G: Ta1207
H: Ta1207
I: Ta1207
J: Ta1207
hetero molecules


Theoretical massNumber of molelcules
Total (without water)395,68940
Polymers394,01210
Non-polymers1,67630
Water13,565753
1
A: Ta1207
B: Ta1207
C: Ta1207
D: Ta1207
F: Ta1207
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,84420
Polymers197,0065
Non-polymers83815
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: Ta1207
G: Ta1207
H: Ta1207
I: Ta1207
J: Ta1207
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,84420
Polymers197,0065
Non-polymers83815
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)228.639, 112.821, 221.328
Angle α, β, γ (deg.)90.000, 118.700, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H
91chain I
101chain J

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: HOH / End label comp-ID: HOH / Auth seq-ID: 5 - 501 / Label seq-ID: 5

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA - OA
2chain BBB - PA
3chain CCC - QA
4chain DDD - RA
5chain EEE - SA
6chain FFF - TA
7chain GGG - UA
8chain HHH - VA
9chain III - WA
10chain JJJ - XA

-
Components

#1: Protein
Ta1207


Mass: 39401.246 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Gene: Ta1207 / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9HIW9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 753 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.29 % / Mosaicity: 0.08 °
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6
Details: 50 mM MES pH 6.0, 200 mM Ca-diacetate and 20%(w/v) PEG3350

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97901,0.97916,0.97670
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979011
20.979161
30.97671
ReflectionResolution: 2.39→49.17 Å / Num. obs: 191535 / % possible obs: 98.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 46.17 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.048 / Rrim(I) all: 0.09 / Net I/σ(I): 13.6 / Num. measured all: 663454
Reflection shellResolution: 2.39→2.43 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.703 / Mean I/σ(I) obs: 2.1 / Num. unique all: 8492 / CC1/2: 0.621 / % possible all: 88.4

-
Phasing

PhasingMethod: MAD
Phasing dmFOM : 0.85 / FOM acentric: 0.85 / FOM centric: 0.77 / Reflection: 81633 / Reflection acentric: 78313 / Reflection centric: 4283
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
8-49.1650.970.980.9353564827529
5-80.940.950.91630415462842
4-50.930.930.872034919562787
3.5-40.850.850.792050519867638
3-3.50.690.690.653643835478960
2.8-30.480.480.462249221965527

-
Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
RESOLVE2.13phasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
XSCALEdata scaling
SHELXDphasing
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.4→29.658 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 20.79
RfactorNum. reflection% reflection
Rfree0.2026 9569 5.02 %
Rwork0.1765 --
obs0.1778 190646 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 240.53 Å2 / Biso mean: 62.5588 Å2 / Biso min: 25.48 Å2
Refinement stepCycle: final / Resolution: 2.4→29.658 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26350 0 160 753 27263
Biso mean--87.18 53.85 -
Num. residues----3210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00627098
X-RAY DIFFRACTIONf_angle_d0.91536570
X-RAY DIFFRACTIONf_chiral_restr0.0343980
X-RAY DIFFRACTIONf_plane_restr0.0054630
X-RAY DIFFRACTIONf_dihedral_angle_d12.4629970
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A19833X-RAY DIFFRACTION9.032TORSIONAL
12B19833X-RAY DIFFRACTION9.032TORSIONAL
13C19833X-RAY DIFFRACTION9.032TORSIONAL
14D19833X-RAY DIFFRACTION9.032TORSIONAL
15E19833X-RAY DIFFRACTION9.032TORSIONAL
16F19833X-RAY DIFFRACTION9.032TORSIONAL
17G19833X-RAY DIFFRACTION9.032TORSIONAL
18H19833X-RAY DIFFRACTION9.032TORSIONAL
19I19833X-RAY DIFFRACTION9.032TORSIONAL
110J19833X-RAY DIFFRACTION9.032TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3999-2.42720.3013330.28165885621898
2.4272-2.45570.31273220.26566066638899
2.4557-2.48570.28212800.2595998627899
2.4857-2.51710.28393300.25446014634499
2.5171-2.55020.29263090.25326069637899
2.5502-2.58510.29493230.25045949627299
2.5851-2.62210.25183410.24056027636899
2.6221-2.66120.26873170.23626041635899
2.6612-2.70270.27633160.23376008632499
2.7027-2.7470.24373390.22485991633099
2.747-2.79430.27873440.22686008635299
2.7943-2.84510.23153250.21856059638499
2.8451-2.89980.25632920.21376066635899
2.8998-2.95890.23552960.21325913620998
2.9589-3.02320.24313030.21866071637499
3.0232-3.09350.23053020.21246058636099
3.0935-3.17070.22533170.2046058637599
3.1707-3.25640.25183420.20895997633999
3.2564-3.35210.22313180.19486061637999
3.3521-3.46010.21013740.18925996637099
3.4601-3.58360.21823230.18356041636499
3.5836-3.72680.20493230.17986048637199
3.7268-3.8960.18792790.16766051633098
3.896-4.1010.16852960.14656079637599
4.101-4.35710.16343300.13596066639699
4.3571-4.69240.15033200.12186092641299
4.6924-5.16230.13843430.11896036637999
5.1623-5.90420.17492990.14396053635298
5.9042-7.41940.19263210.16186125644699
7.4194-29.66050.15033120.14326151646398
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)
11.2569-0.0907-0.26172.20880.13411.07790.0071-0.2697-0.060.1989-0.0605-0.15810.12390.11990.03490.35690.00420.03610.64120.07250.2479-22.578972.736690.57
21.59850.1815-0.48212.0744-0.84511.82670.0853-0.3820.12910.32560.03040.008-0.30110.1274-0.08170.4356-0.05990.06760.6229-0.09770.2818-23.6289115.045988.5738
31.3507-0.387-1.0261.54610.39632.72620.0812-0.29390.18880.0980.0927-0.1424-0.3680.4611-0.11260.3976-0.12080.07060.4461-0.06050.30080.0617127.13155.5698
40.82370.2847-0.25242.3447-0.24781.62340.0235-0.1868-0.04060.2992-0.0557-0.0788-0.01970.40240.05180.20880.0111-0.00450.57080.00690.256615.911692.474537.1095
51.8191-0.0528-0.26591.5629-0.26051.453-0.06330.129-0.146-0.1818-0.0110.11440.2313-0.13090.04790.4673-0.07530.04560.4602-0.09750.332-44.053955.17725.5123
61.95070.3708-0.83141.18840.05592.0683-0.0428-0.2411-0.15410.1577-0.0274-0.09890.15960.25250.03350.38010.11940.04840.44080.07640.32212.28758.691558.9308
71.5063-0.2352-0.55752.5588-0.00341.2984-0.09020.29380.0037-0.0161-0.00150.220.115-0.28360.07230.3394-0.0546-0.06830.5766-0.01190.166-30.303188.72393.4494
81.5890.0032-0.75061.29980.35922.05220.07030.28970.3238-0.12150.0340.1746-0.3017-0.3698-0.05120.43760.1199-0.04960.4590.08680.4274-46.0479123.614221.5525
90.81780.4907-0.23112.5848-0.48851.30980.0613-0.00330.14040.0633-0.00540.3752-0.1777-0.27-0.03740.30750.13770.02880.5946-0.03880.4255-69.776111.843654.803
101.099-0.3523-0.12711.3340.27941.6133-0.10940.0155-0.07610.00830.10430.06010.168-0.29910.01270.3187-0.11610.04280.6289-0.0020.2908-68.475169.440956.9854
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 325 )A5 - 325
2X-RAY DIFFRACTION2chain 'B' and (resid 5 through 325 )B5 - 325
3X-RAY DIFFRACTION3chain 'C' and (resid 5 through 325 )C5 - 325
4X-RAY DIFFRACTION4chain 'D' and (resid 5 through 325 )D5 - 325
5X-RAY DIFFRACTION5chain 'E' and (resid 5 through 325 )E5 - 325
6X-RAY DIFFRACTION6chain 'F' and (resid 5 through 325 )F5 - 325
7X-RAY DIFFRACTION7chain 'G' and (resid 5 through 325 )G5 - 325
8X-RAY DIFFRACTION8chain 'H' and (resid 5 through 325 )H5 - 325
9X-RAY DIFFRACTION9chain 'I' and (resid 5 through 325 )I5 - 325
10X-RAY DIFFRACTION10chain 'J' and (resid 5 through 325 )J5 - 325

+
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