[English] 日本語
Yorodumi
- PDB-6q6j: Human phosphoserine phosphatase with substrate analogue homo-cyst... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6q6j
TitleHuman phosphoserine phosphatase with substrate analogue homo-cysteic acid
ComponentsPhosphoserine phosphatase
KeywordsHYDROLASE / Human phosphoserine phosphatase
Function / homology
Function and homology information


phosphoserine phosphatase / Serine biosynthesis / L-phosphoserine phosphatase activity / L-serine metabolic process / L-serine biosynthetic process / response to testosterone / response to mechanical stimulus / dephosphorylation / response to nutrient levels / in utero embryonic development ...phosphoserine phosphatase / Serine biosynthesis / L-phosphoserine phosphatase activity / L-serine metabolic process / L-serine biosynthetic process / response to testosterone / response to mechanical stimulus / dephosphorylation / response to nutrient levels / in utero embryonic development / magnesium ion binding / protein homodimerization activity / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Phosphoserine phosphatase; domain 2 / Phosphoserine phosphatase / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Phosphoserine phosphatase; domain 2 / Phosphoserine phosphatase / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(2~{S})-2-azanyl-4-sulfo-butanoic acid / Phosphoserine phosphatase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.985 Å
AuthorsWouters, J. / Haufroid, M. / Mirgaux, M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Crystal structures and snapshots along the reaction pathway of human phosphoserine phosphatase.
Authors: Haufroid, M. / Mirgaux, M. / Leherte, L. / Wouters, J.
History
DepositionDec 11, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 24, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,2477
Polymers48,9082
Non-polymers3395
Water3,513195
1
A: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5343
Polymers24,4541
Non-polymers802
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoserine phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,7134
Polymers24,4541
Non-polymers2593
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.230, 130.490, 157.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-496-

HOH

-
Components

#1: Protein Phosphoserine phosphatase / / PSPase / L-3-phosphoserine phosphatase / O-phosphoserine phosphohydrolase


Mass: 24454.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSPH / Plasmid: pet 28 b / Production host: Escherichia coli BL21(DE3) / References: UniProt: P78330, phosphoserine phosphatase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HJT / (2~{S})-2-azanyl-4-sulfo-butanoic acid / Homocysteic acid


Mass: 183.183 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO5S
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: Sodium cacodylate 0.1M pH6.5; CaCl2 0.3M; PEG 2000 20%; DMSO 4%

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.985→40.943 Å / Num. obs: 35482 / % possible obs: 99.55 % / Redundancy: 2 % / Biso Wilson estimate: 37.51 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01873 / Rpim(I) all: 0.01873 / Rrim(I) all: 0.02649 / Net I/σ(I): 17.4
Reflection shellResolution: 1.985→2.056 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2331 / Mean I/σ(I) obs: 2.29 / Num. unique obs: 3380 / CC1/2: 0.969 / Rpim(I) all: 0.2331 / Rrim(I) all: 0.3296 / % possible all: 96.24

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.59 Å46.06 Å
Translation4.59 Å46.06 Å

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASER2.8.1phasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HYY

6hyy


Resolution: 1.985→40.943 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.39
RfactorNum. reflection% reflection
Rfree0.2468 1774 5 %
Rwork0.1981 --
obs0.2005 35467 99.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 136.27 Å2 / Biso mean: 46.1001 Å2 / Biso min: 21.93 Å2
Refinement stepCycle: final / Resolution: 1.985→40.943 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3406 0 15 195 3616
Biso mean--43.86 46.53 -
Num. residues----437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9847-2.03840.44291270.41012407253494
2.0384-2.09830.38081350.293125572692100
2.0983-2.16610.25381350.249825622697100
2.1661-2.24350.29821370.238426082745100
2.2435-2.33330.26931350.228125592694100
2.3333-2.43950.30041350.224225622697100
2.4395-2.56810.28371370.221726052742100
2.5681-2.72890.26021360.220525892725100
2.7289-2.93960.28291360.224725752711100
2.9396-3.23530.23591380.201726282766100
3.2353-3.70320.22361370.178926102747100
3.7032-4.66460.2221420.161626792821100
4.6646-40.95210.21251440.173127522896100

+
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