[English] 日本語
Yorodumi
- PDB-1t6d: MIRAS phasing of the Aquifex aeolicus Ppx/GppA phosphatase: cryst... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t6d
TitleMIRAS phasing of the Aquifex aeolicus Ppx/GppA phosphatase: crystal structure of the type II variant
Componentsexopolyphosphatase
KeywordsHYDROLASE / alpha/beta protein / Actin-like fold
Function / homology
Function and homology information


guanosine-5'-triphosphate,3'-diphosphate diphosphatase activity / pyrophosphatase activity / nucleobase-containing small molecule interconversion / regulation of transcription by RNA polymerase II / metal ion binding
Similarity search - Function
Ppx/GppA phosphatase / Ppx/GppA phosphatase family / Exopolyphosphatase. Domain 2 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Partial model produced by MIRAS phasing / Resolution: 2.15 Å
AuthorsKristensen, O. / Laurberg, M. / Liljas, A. / Kastrup, J.S. / Gajhede, M.
Citation
Journal: Biochemistry / Year: 2004
Title: Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family
Authors: Kristensen, O. / Laurberg, M. / Liljas, A. / Kastrup, J.S. / Gajhede, M.
#1: Journal: Science / Year: 2001
Title: Role of inorganic polyphosphate in promoting ribosomal protein degradation by the Lon protease in E. coli
Authors: Kuroda, A. / Nomura, K. / Ohtomo, R. / Kato, J. / Ikeda, T. / Takiguchi, N. / Ohtake, H. / Kornberg, A.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993
Title: Guanosine pentaphosphate phosphohydrolase of Escherichia coli is a long-chain exopolyphosphatase
Authors: Keasling, J.D. / Bertsch, L. / Kornberg, A.
#3: Journal: Trends Biochem.Sci. / Year: 1993
Title: Exopolyphosphate phosphatase and guanosine pentaphosphate phosphatase belong to the sugar kinase/actin/hsp 70 superfamily
Authors: Reizer, J. / Reizer, A. / Saier Jr., M.H. / Bork, P. / Sander, C.
History
DepositionMay 6, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 10, 2021Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: exopolyphosphatase
B: exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4475
Polymers72,2542
Non-polymers1933
Water6,017334
1
A: exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2853
Polymers36,1271
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: exopolyphosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1632
Polymers36,1271
Non-polymers351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.461, 83.565, 69.764
Angle α, β, γ (deg.)90.00, 97.39, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological relevant unit is monomeric.

-
Components

#1: Protein exopolyphosphatase / / Ppx/GppA phosphatase


Mass: 36127.094 Da / Num. of mol.: 2 / Mutation: V82M, C138M, V306M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Strain: VF5 / Gene: ppx / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS
References: UniProt: O67040, exopolyphosphatase, guanosine-5'-triphosphate,3'-diphosphate phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 334 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG4000, PEG400, TRIS, acetic acid, magnesium chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 29, 2001 / Details: Sagitally focusing Ge(220) and a multilayer
RadiationMonochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 66436 / Num. obs: 66436 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 23.3
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 8.8 / Num. unique all: 10090 / Rsym value: 0.287 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
SHARPphasing
ARP/wARPmodel building
CNSphasing
RefinementMethod to determine structure: Partial model produced by MIRAS phasing
Resolution: 2.15→29.06 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 2055074.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Anomalous data was used in refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1348 2 %RANDOM
Rwork0.206 ---
all0.207 66398 --
obs0.206 66398 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.2396 Å2 / ksol: 0.335738 e/Å3
Displacement parametersBiso mean: 35.3 Å2
Baniso -1Baniso -2Baniso -3
1--3.27 Å20 Å21 Å2
2--4.41 Å20 Å2
3----1.14 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.15→29.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4850 0 10 334 5194
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d21.4
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.482
X-RAY DIFFRACTIONc_scbond_it2.252
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.15→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.295 239 2.2 %
Rwork0.237 10870 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4CSX.PARAMCSX.TOP
X-RAY DIFFRACTION5TRS.PARAMTRS.TOP

+
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