[English] 日本語
Yorodumi
- PDB-1z88: Crystal structure of Lys154Arg mutant of mature AphA of S. typhimurium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z88
TitleCrystal structure of Lys154Arg mutant of mature AphA of S. typhimurium
ComponentsAphA protein
KeywordsHYDROLASE / Class-B bacterial acid phosphatase / Lys154Arg mutant of mature AphA / metalloenzyme
Function / homology
Function and homology information


acid phosphatase / acid phosphatase activity / outer membrane-bounded periplasmic space / metal ion binding
Similarity search - Function
HAD-superfamily phosphatase, subfamily IIIB, AphA / Acid phosphatase, class B-like / HAD superfamily, subfamily IIIB (Acid phosphatase) / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Class B acid phosphatase / Class B acid phosphatase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.1 Å
AuthorsMakde, R.D. / Gupta, G.D. / Kumar, V.
Citation
Journal: Arch.Biochem.Biophys. / Year: 2007
Title: Structural and mutational analyses reveal the functional role of active-site Lys-154 and Asp-173 of Salmonella typhimurium AphA protein.
Authors: Makde, R.D. / Gupta, G.D. / Mahajan, S.K. / Kumar, V.
#1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2003
Title: Expression, purification, crystallization and preliminary X-ray diffraction studies of recombinant class B non-specific acid phosphatase of Salmonella typhimurium
Authors: Makde, R.D. / Kumar, V. / Gupta, G.D. / Jasti, J. / Singh, T.P. / Mahajan, S.K.
History
DepositionMar 30, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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_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.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: AphA protein
B: AphA protein
C: AphA protein
D: AphA protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,6928
Polymers95,5954
Non-polymers974
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11870 Å2
ΔGint-107 kcal/mol
Surface area34230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.650, 84.210, 149.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein
AphA protein


Mass: 23898.717 Da / Num. of mol.: 4 / Mutation: K154R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: aphA / Plasmid: pET21(A) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P58683, UniProt: Q540U1*PLUS, acid phosphatase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.33 Å3/Da / Density % sol: 47.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.7
Details: PEG 6000, magnesium chloride, sodium acetate, glycerol, pH 4.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 24, 2004 / Details: OSMIC mirror
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 47811 / Num. obs: 47808 / % possible obs: 91.3 % / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 25.3 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 18.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.169 / Mean I/σ(I) obs: 5.2 / Num. unique all: 6600 / % possible all: 87.1

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
CNSrefinement
CCP4(SCALAdata scaling
TRUNCATEdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB entry 1Z5G

1z5g


Resolution: 2.1→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.207 2380 5 %RANDOM
Rwork0.167 ---
all-47778 --
obs-47778 90.6 %-
Solvent computationSolvent model: Flat Model / Bsol: 47.9 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6607 0 4 528 7139
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_mcbond_it1.4
X-RAY DIFFRACTIONc_mcangle_it2.14
X-RAY DIFFRACTIONc_scbond_it2.08
X-RAY DIFFRACTIONc_scangle_it3.1
LS refinement shellResolution: 2.1→2.17 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.259 233 5 %
Rwork0.209 4248 -
obs-4481 86.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.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