[English] 日本語
Yorodumi
- PDB-4ij5: Crystal Structure of a Novel-type Phosphoserine Phosphatase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ij5
TitleCrystal Structure of a Novel-type Phosphoserine Phosphatase from Hydrogenobacter thermophilus TK-6
ComponentsPhosphoserine phosphatase 1
KeywordsHYDROLASE / phosphatase
Function / homology
Function and homology information


phosphoserine phosphatase / L-phosphoserine phosphatase activity / L-serine biosynthetic process / cytoplasm
Similarity search - Function
: / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoserine phosphatase 1
Similarity search - Component
Biological speciesHydrogenobacter thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsChiba, Y. / Horita, S. / Ohtsuka, J. / Arai, H. / Nagata, K. / Igarashi, Y. / Tanokura, M. / Ishii, M.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural units important for activity of a novel-type phosphoserine phosphatase from Hydrogenobacter thermophilus TK-6 revealed by crystal structure analysis
Authors: Chiba, Y. / Horita, S. / Ohtsuka, J. / Arai, H. / Nagata, K. / Igarashi, Y. / Tanokura, M. / Ishii, M.
History
DepositionDec 21, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphoserine phosphatase 1
B: Phosphoserine phosphatase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4707
Polymers49,1872
Non-polymers2845
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3170 Å2
ΔGint2 kcal/mol
Surface area17400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.810, 73.630, 124.280
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Phosphoserine phosphatase 1 / PSP 1 / PSPase 1 / Metal-independent phosphoserine phosphatase 1 / iPSP1 / O-phosphoserine phosphohydrolase 1


Mass: 24593.346 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hydrogenobacter thermophilus (bacteria)
Strain: DSM 6534 / IAM 12695 / TK-6 / Gene: pspA, pgmA, HTH_0103, Hydth_0104 / Production host: Escherichia coli (E. coli) / References: UniProt: D3DFG8, phosphoserine phosphatase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.32 Å3/Da / Density % sol: 46.91 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES-NaOH, 10%(v/v) 2-propanol, 20%(w/v) polyethylene glycol 4000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: MAR225HE / Detector: CCD / Date: Jul 22, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→36.1 Å / Num. all: 73684 / Num. obs: 73612 / Redundancy: 8.6 %

-
Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H2E

1h2e


Resolution: 1.5→36.1 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.951 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.461 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.073 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 3714 5 %RANDOM
Rwork0.1836 ---
obs0.1843 73608 99.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 41.06 Å2 / Biso mean: 16.45 Å2 / Biso min: 3.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2---0.06 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.5→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3456 0 17 242 3715
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193577
X-RAY DIFFRACTIONr_bond_other_d0.0010.023481
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.9574833
X-RAY DIFFRACTIONr_angle_other_deg0.7723.0018003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9325432
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82423.488172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.97415665
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7171528
X-RAY DIFFRACTIONr_chiral_restr0.0770.2528
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023962
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02830
LS refinement shellResolution: 1.5→1.541 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.239 282 -
Rwork0.228 5007 -
all-5289 -
obs--98.75 %
Refinement TLS params.

S33: -0.0049 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.64740.0970.22990.4976-0.1942.0332-0.01880.03570.0105-0.00670.02370.0024-0.04140.16090.0062-0.005-0.00170.025-0.00010.0683-8.2145-0.64493.8643
20.6330.08270.53250.42540.12953.08580.011-0.06850.02150.0168-0.0061-0.01670.0221-0.25210.0016-0.0039-0.00560.0347-0.00040.0611-17.0784-2.652530.2812
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 211
2X-RAY DIFFRACTION2B1 - 211

+
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