[English] 日本語
Yorodumi
- PDB-1aja: THREE-DIMENSIONAL STRUCTURE OF THE D153G MUTANT OF E. COLI ALKALI... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1aja
TitleTHREE-DIMENSIONAL STRUCTURE OF THE D153G MUTANT OF E. COLI ALKALINE PHOSPHATASE: A MUTANT WITH WEAKER MAGNESIUM BINDING AND INCREASED CATALYTIC ACTIVITY
ComponentsALKALINE PHOSPHATASE
KeywordsNON SPECIFIC MONO-ESTERASE
Function / homology
Function and homology information


oxidoreductase activity, acting on phosphorus or arsenic in donors / alkaline phosphatase / alkaline phosphatase activity / hydrogenase (acceptor) activity / phosphoprotein phosphatase activity / protein dephosphorylation / outer membrane-bounded periplasmic space / periplasmic space / magnesium ion binding / zinc ion binding
Similarity search - Function
Alkaline phosphatase, active site / Alkaline phosphatase active site. / Alkaline phosphatase / Alkaline phosphatase / Alkaline phosphatase homologues / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alkaline phosphatase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsDealwis, C.G. / Chen, L. / Abad-Zapatero, C.
Citation
Journal: Biochemistry / Year: 1995
Title: Crystallographic analysis of reversible metal binding observed in a mutant (Asp153-->Gly) of Escherichia coli alkaline phosphatase.
Authors: Dealwis, C.G. / Brennan, C. / Christianson, K. / Mandecki, W. / Abad-Zapatero, C.
#1: Journal: To be Published
Title: Crystallographic Analysis of Reversible Metal Binding Observed in a Mutant (Asp 153--> Gly) of E. Coli Alkaline Phosphatase
Authors: Dealwis, C. / Brennan, C. / Christianson, K. / Mandecki, W. / Abad-Zapatero, A.
#2: Journal: Protein Eng. / Year: 1992
Title: 3-D Structure of the (Asp 101-->Ser) of E.Coli Alkaline Phosphatase with Higher Catalytic Activity
Authors: Chen, L. / Neidhart, D. / Kohlbrenner, M. / Mandecki, W. / Bell, S. / Sowadski, J. / Abad-Zapatero, C.
History
DepositionAug 19, 1995Processing site: BNL
Revision 1.0Nov 14, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Other
Category: database_2 / pdbx_database_status / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification
Remark 700SHEET SHEET DETERMINATION METHOD: KABSCH & SANDER; SHEET_ID: S1A; SAME AS 1ALK. SHEET_ID: S2A; SAME ...SHEET SHEET DETERMINATION METHOD: KABSCH & SANDER; SHEET_ID: S1A; SAME AS 1ALK. SHEET_ID: S2A; SAME AS 1ALK. SHEET_ID: S1B; SAME AS 1ALK. SHEET_ID: S2B; SAME AS 1ALK.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALKALINE PHOSPHATASE
B: ALKALINE PHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)94,0752
Polymers94,0752
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6690 Å2
ΔGint-24 kcal/mol
Surface area28550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)195.020, 166.930, 76.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: SER A 295 - PRO A 297 OMEGA = 293.04 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION

-
Components

#1: Protein ALKALINE PHOSPHATASE


Mass: 47037.348 Da / Num. of mol.: 2 / Mutation: D153G
Source method: isolated from a genetically manipulated source
Details: APO ENZYME / Source: (gene. exp.) Escherichia coli (E. coli)
Description: LAC PROMOTER. FOR MORE INFORMATION ABOUT THE EXPRESSION SYSTEM CONSULT MANDECKI ET AL. GENE 94, 103-107; (1990).
Gene: PHOA / Plasmid: PWM528 AS BAMH1/HINDIII RESTRICTION FRAGMENT / Gene (production host): PHOA / Production host: Escherichia coli (E. coli) / References: UniProt: P00634, alkaline phosphatase
Has protein modificationY
Source detailsFOR MORE INFORMATION ABOUT THE EXPRESSION SYSTEM CONSULT MANDECKI ET AL. GENE 94, 103-107; (1990).

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.78 %
Crystal grow
*PLUS
pH: 9.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 mg/mlprotein1drop
220 %(w/v)ammonium sulfate1drop
3100 mMTris-HCl1drop
410 mM1dropMgSO4
50.01 mM1dropZnCl2
631.6 %ammonium sulfate1reservoir
7100 mMTris-HCl1reservoir
810 mM1reservoirMgSO4

-
Data collection

Diffraction sourceWavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Jan 6, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 40175 / % possible obs: 77 % / Observed criterion σ(I): 0 / Redundancy: 1.65 % / Rmerge(I) obs: 0.08
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 65477 / % possible obs: 76.5 % / Rmerge(I) obs: 0.08

-
Processing

Software
NameClassification
R-AXISdata collection
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
RefinementResolution: 2.5→6 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.162 -
obs0.162 34945
Displacement parametersBiso mean: 11 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.5→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6352 0 0 0 6352
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_angle_deg2.2
X-RAY DIFFRACTIONx_dihedral_angle_deg24.2
X-RAY DIFFRACTIONx_improper_angle_deg1.1

+
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