[English] 日本語
Yorodumi
- PDB-1rlt: Transition State Analogue of ybiV from E. coli K12 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1rlt
TitleTransition State Analogue of ybiV from E. coli K12
ComponentsPhosphatase
KeywordsHYDROLASE / HAD Family / Transition-state analogue / aluminum fluoride / phosphatase
Function / homology
Function and homology information


sorbitol-6-phosphatase activity / sugar-phosphatase / fructose-1-phosphatase activity / sugar-phosphatase activity / phosphatase activity / magnesium ion binding / cytosol
Similarity search - Function
Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical cof family signature 2. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical cof family signature 2. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / ALUMINUM FLUORIDE / Sugar phosphatase YbiV
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsRoberts, A. / Lee, S.Y. / McCullagh, E. / Silversmith, R.E. / Wemmer, D.E.
CitationJournal: Proteins / Year: 2005
Title: Ybiv from Escherichia coli K12 is a HAD phosphatase.
Authors: Roberts, A. / Lee, S.Y. / McCullagh, E. / Silversmith, R.E. / Wemmer, D.E.
History
DepositionNov 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_label_seq_id / _struct_conn_type.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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact ...pdbx_entry_details / pdbx_validate_close_contact / struct_conn / struct_conn_type

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Phosphatase
B: Phosphatase
C: Phosphatase
D: Phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,71215
Polymers122,0364
Non-polymers67611
Water7,152397
1
A: Phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6764
Polymers30,5091
Non-polymers1673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6173
Polymers30,5091
Non-polymers1082
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7094
Polymers30,5091
Non-polymers2003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7094
Polymers30,5091
Non-polymers2003
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.761, 91.166, 183.850
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 4 molecules ABCD

#1: Protein
Phosphatase


Mass: 30508.881 Da / Num. of mol.: 4 / Mutation: S2A, S267Y
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YBIV, B0822 / Plasmid: pet21d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 (pACYC)
References: UniProt: P75792, Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases

-
Non-polymers , 5 types, 408 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: AlF3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 50.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: PEG 8000, sodium acetate, aluminum chloride, sodium fluoride, cacodylic acid, magnesium chloride, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 12, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 61606 / Num. obs: 61606 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Biso Wilson estimate: 20.9 Å2 / Rsym value: 0.08 / Net I/σ(I): 31
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 5 % / Mean I/σ(I) obs: 5 / Num. unique all: 3058 / Rsym value: 0.25 / % possible all: 100

-
Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1RLM

1rlm


Resolution: 2.2→19.93 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 181307.64 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 6051 10.1 %RANDOM
Rwork0.221 ---
all0.242 59839 --
obs0.221 59839 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.1787 Å2 / ksol: 0.340939 e/Å3
Displacement parametersBiso mean: 40.9 Å2
Baniso -1Baniso -2Baniso -3
1--10.02 Å20 Å20 Å2
2---6.63 Å20 Å2
3---16.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8516 0 36 397 8949
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d1.22
X-RAY DIFFRACTIONc_mcbond_it2.071.5
X-RAY DIFFRACTIONc_mcangle_it3.552
X-RAY DIFFRACTIONc_scbond_it3.422
X-RAY DIFFRACTIONc_scangle_it5.322.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 922 10 %
Rwork0.284 8330 -
obs-8330 90.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMCRY.TOP
X-RAY DIFFRACTION3WATER.PARAMALFNEW.TOP
X-RAY DIFFRACTION4ALFNEW.PARAM

+
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