[English] 日本語
Yorodumi
- PDB-5too: Crystal structure of alkaline phosphatase PafA T79S, N100A, K162A... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5too
TitleCrystal structure of alkaline phosphatase PafA T79S, N100A, K162A, R164A mutant
ComponentsAlkaline phosphatase PafA
KeywordsHYDROLASE / Alkaline Phosphatase / Phosphomonoesterase / PafA / Weak phosphate binder / Zinc bimetallo core
Function / homology
Function and homology information


carbohydrate phosphatase activity / glucose-1-phosphatase activity / glucose-6-phosphatase activity / sugar-phosphatase activity / alkaline phosphatase / alkaline phosphatase activity / periplasmic space / zinc ion binding / metal ion binding
Similarity search - Function
Gyrase A; domain 2 - #150 / Alkaline phosphatase, prokaryotic / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Alkaline-phosphatase-like, core domain superfamily / Gyrase A; domain 2 / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alkaline phosphatase PafA
Similarity search - Component
Biological speciesElizabethkingia meningoseptica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.031 Å
AuthorsLyubimov, A.Y. / Sunden, F. / AlSadhan, I. / Herschlag, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM64798 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Differential catalytic promiscuity of the alkaline phosphatase superfamily bimetallo core reveals mechanistic features underlying enzyme evolution.
Authors: Sunden, F. / AlSadhan, I. / Lyubimov, A. / Doukov, T. / Swan, J. / Herschlag, D.
History
DepositionOct 18, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alkaline phosphatase PafA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4176
Polymers61,1201
Non-polymers2975
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)113.329, 113.329, 69.790
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

-
Components

#1: Protein Alkaline phosphatase PafA / AP PafA


Mass: 61120.406 Da / Num. of mol.: 1 / Fragment: UNP residues 21-546
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia meningoseptica (bacteria)
Gene: pafA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9KJX5, alkaline phosphatase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 1.95 Å3/Da / Density % sol: 32.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 22% PEG3350, 0.1 M sodium acetate, pH 4.4, 0.2 M ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 31, 2016
RadiationMonochromator: Si(111) Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.03→41.01 Å / Num. obs: 28568 / % possible obs: 99.9 % / Redundancy: 8.5 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Net I/σ(I): 9.6
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 8.8 % / Rmerge(I) obs: 1.518 / CC1/2: 0.66 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation6.96 Å41.01 Å
Translation6.96 Å41.01 Å

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
Aimless0.5.27data scaling
PHASER2.6.0phasing
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.2data extraction
MOSFLMdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TJ3

5tj3


Resolution: 2.031→41.009 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.01
RfactorNum. reflection% reflection
Rfree0.2086 1493 5.23 %
Rwork0.1704 --
obs0.1724 28561 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 99.1 Å2 / Biso mean: 40.6973 Å2 / Biso min: 16.98 Å2
Refinement stepCycle: final / Resolution: 2.031→41.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4019 0 5 217 4241
Biso mean--48.25 37.66 -
Num. residues----517
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134120
X-RAY DIFFRACTIONf_angle_d1.1845611
X-RAY DIFFRACTIONf_chiral_restr0.069622
X-RAY DIFFRACTIONf_plane_restr0.009721
X-RAY DIFFRACTIONf_dihedral_angle_d19.6381457
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.0312-2.09670.32251020.254624592561
2.0967-2.17170.26491800.236924062586
2.1717-2.25860.29341210.222224672588
2.2586-2.36140.27931490.210824492598
2.3614-2.48590.2241500.198724082558
2.4859-2.64160.22461470.181224482595
2.6416-2.84550.24161200.179524702590
2.8455-3.13180.24611290.177124762605
3.1318-3.58470.2061260.162124712597
3.5847-4.51540.1761280.136724882616
4.5154-41.01760.15021410.145825262667

+
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