[English] 日本語
Yorodumi
- PDB-1o51: Crystal structure of a putative PII-like signaling protein (TM002... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1o51
TitleCrystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.50 A resolution
ComponentsHypothetical protein TM0021
KeywordsSIGNALING PROTEIN / Ferredoxin-like fold / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


UPF0166 / Uncharacterized ACR, COG1993 / Alpha-Beta Plaits - #120 / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / UPF0166 protein TM_0021
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a putative PII-like signaling protein (TM0021) from Thermotoga maritima at 2.5 A resolution
Authors: Schwarzenbacher, R. / von Delft, F. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. ...Authors: Schwarzenbacher, R. / von Delft, F. / Abdubek, P. / Ambing, E. / Biorac, T. / Brinen, L.S. / Canaves, J.M. / Cambell, J. / Chiu, H.J. / Dai, X. / Deacon, A.M. / DiDonato, M. / Elsliger, M.A. / Eshagi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Hampton, E. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / Levin, I. / McMullan, D. / McPhillips, T.M. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Quijano, K. / Robb, A. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Xu, Q. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionAug 1, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionAug 19, 2003ID: 1O2C
Revision 1.0Aug 19, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Jul 18, 2018Group: Data collection / Database references / Derived calculations
Category: pdbx_database_related / pdbx_struct_special_symmetry
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hypothetical protein TM0021
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0444
Polymers13,4251
Non-polymers6193
Water70339
1
A: Hypothetical protein TM0021
hetero molecules

A: Hypothetical protein TM0021
hetero molecules

A: Hypothetical protein TM0021
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,13312
Polymers40,2753
Non-polymers1,8589
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z+1/2,-x+1/2,-y1
crystal symmetry operation12_554-y+1/2,-z,x-1/21
Buried area8630 Å2
ΔGint-187 kcal/mol
Surface area12380 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)100.110, 100.110, 100.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11A-302-

SO4

21A-304-

HOH

31A-328-

HOH

-
Components

#1: Protein Hypothetical protein TM0021


Mass: 13425.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0021 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WXM9
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 3.8 Å3/Da / Density % sol: 67.37 %
Crystal growTemperature: 293 K / pH: 5.6
Details: 2M ammonium sulfate, 0.1M tri-sodium citrate dihydrate pH 5.6, 0.2M potassium sodium tartrate tetrahydrate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K, pH 5.60
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1droppH7.9
2150 mM1dropNaCl
30.25 mMTCEP1drop
417 mg/mlprotein1drop
52.0 Mammonium sulfate1reservoir
60.2 Msodium potassium tartrate1reservoir
70.1 Mcitrate1reservoirpH5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97914, 0.97934
DetectorType: APS-1 / Detector: CCD / Date: Oct 27, 2002
Details: WATER COOLED FOCUSING 2ND CRYSTAL, ROSENBAUM-ROCK VERTICAL FOCUSING MIRROR
RadiationMonochromator: ROSENBAUM-ROCK DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979141
20.979341
ReflectionResolution: 2.5→50 Å / Num. obs: 6359 / % possible obs: 100 % / Redundancy: 43.83 % / Biso Wilson estimate: 51.99 Å2 / Rsym value: 0.109 / Net I/σ(I): 70.05
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 0.57 % / Mean I/σ(I) obs: 10.64 / Rsym value: 0.588 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 70.71 Å / Num. obs: 6360 / Num. measured all: 126573 / Rmerge(I) obs: 0.085
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 4.6

-
Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
RESOLVEmodel building
SOLVEphasing
REFMAC5.1.9999refinement
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→44.77 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.923 / SU B: 11.317 / SU ML: 0.129 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.276 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1, PROMINENT DIFFERENCE DENSITY ON THE CRYSTALLOGRAPHIC (AND BIOLOGICAL) THREE-FOLD AXIS WAS INTERPRETED AS TWO SULFATE IONS, EVEN THOUGH BOTH ARE REFINED TO HIGH B-FACTORS.2, THERE IS WEAK ...Details: 1, PROMINENT DIFFERENCE DENSITY ON THE CRYSTALLOGRAPHIC (AND BIOLOGICAL) THREE-FOLD AXIS WAS INTERPRETED AS TWO SULFATE IONS, EVEN THOUGH BOTH ARE REFINED TO HIGH B-FACTORS.2, THERE IS WEAK AND AMBIGUOUS DENSITY INDICATING THE GENERAL LOCATION OF THE LAST RESIDUE OMITTED IN THE CHAIN BREAK, SER59A.3, HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.229 787 12.4 %RANDOM
Rwork0.184 ---
obs0.19 5544 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→44.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms703 0 37 39 779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.022761
X-RAY DIFFRACTIONr_bond_other_d0.0010.02698
X-RAY DIFFRACTIONr_angle_refined_deg1.7842.0261033
X-RAY DIFFRACTIONr_angle_other_deg0.87331613
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.913589
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.25724.06232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15215129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.487153
X-RAY DIFFRACTIONr_chiral_restr0.0920.2115
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02799
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02150
X-RAY DIFFRACTIONr_nbd_refined0.2410.2113
X-RAY DIFFRACTIONr_nbd_other0.190.2633
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.2506
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.224
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2220.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.220
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.8581.5441
X-RAY DIFFRACTIONr_mcangle_it1.6852708
X-RAY DIFFRACTIONr_scbond_it2.5863320
X-RAY DIFFRACTIONr_scangle_it4.2314.5324
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.57 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.247 76
Rwork0.171 371
Refinement TLS params.Method: refined / Origin x: 48.212 Å / Origin y: 12.387 Å / Origin z: 4.348 Å
111213212223313233
T-0.0264 Å2-0.0201 Å20.0034 Å2--0.2146 Å2-0.0658 Å2---0.1646 Å2
L5.7424 °2-0.0523 °22.4899 °2-3.7382 °2-1.3634 °2--4.8187 °2
S-0.2259 Å °-0.3676 Å °0.4388 Å °0.5771 Å °0.0022 Å °0.1537 Å °-0.7102 Å °-0.1453 Å °0.2237 Å °
Refinement
*PLUS
Lowest resolution: 70.71 Å / Num. reflection obs: 6331 / % reflection Rfree: 12.4 % / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.78

+
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