[English] 日本語
Yorodumi
- PDB-4hgq: Crystal structure of E56A mutant of 2-keto-3-deoxy-D-glycero-D-ga... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hgq
TitleCrystal structure of E56A mutant of 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase from Bacteroides thetaiotaomicron
ComponentsAcylneuraminate cytidylyltransferase
KeywordsTransferase / Hydrolase / Rossmann Fold / Phosphohydroylase
Function / homology
Function and homology information


3-deoxy-D-glycero-D-galacto-nonulopyranosonate 9-phosphatase / hydrolase activity, acting on ester bonds / metal ion binding
Similarity search - Function
KdsC family / HAD-superfamily hydrolase,subfamily IIIA / haloacid dehalogenase-like hydrolase / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
2-keto-3-deoxy-D-glycero-D-galacto-9-phosphonononic acid phosphatase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.28 Å
AuthorsDaughtry, K.D. / Allen, K.N.
CitationJournal: Biochemistry / Year: 2013
Title: Structural Basis for the Divergence of Substrate Specificity and Biological Function within HAD Phosphatases in Lipopolysaccharide and Sialic Acid Biosynthesis.
Authors: Daughtry, K.D. / Huang, H. / Malashkevich, V. / Patskovsky, Y. / Liu, W. / Ramagopal, U. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / Dunaway-Mariano, D. / Allen, K.N.
History
DepositionOct 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Database references
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations
Category: citation_author / pdbx_struct_conn_angle ...citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Acylneuraminate cytidylyltransferase
B: Acylneuraminate cytidylyltransferase
C: Acylneuraminate cytidylyltransferase
D: Acylneuraminate cytidylyltransferase
E: Acylneuraminate cytidylyltransferase
F: Acylneuraminate cytidylyltransferase
G: Acylneuraminate cytidylyltransferase
H: Acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,62716
Polymers146,4328
Non-polymers1948
Water10,124562
1
A: Acylneuraminate cytidylyltransferase
B: Acylneuraminate cytidylyltransferase
C: Acylneuraminate cytidylyltransferase
D: Acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3138
Polymers73,2164
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9820 Å2
ΔGint-70 kcal/mol
Surface area25620 Å2
MethodPISA
2
E: Acylneuraminate cytidylyltransferase
F: Acylneuraminate cytidylyltransferase
G: Acylneuraminate cytidylyltransferase
H: Acylneuraminate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3138
Polymers73,2164
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9620 Å2
ΔGint-68 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.941, 94.116, 161.497
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221

-
Components

#1: Protein
Acylneuraminate cytidylyltransferase / 2-keto-3-deoxy-D-glycero-D-galactonononate-9-phosphate phosphohydrolase


Mass: 18304.027 Da / Num. of mol.: 8 / Mutation: E56A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_1713 / Plasmid: pET-3A-626 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8A712
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 562 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM Bis-Tris, 200 mM magnesium chloride, 23% polyethylene glycol 3350. The crystal was dragged through paratone prior to flash-cooling, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Jul 28, 2009 / Details: Helios multi-layer optics
RadiationMonochromator: rotating-anode / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.28→37.1 Å / Num. all: 62511 / Num. obs: 62511 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.21 % / Rsym value: 0.0878 / Net I/σ(I): 11.6
Reflection shellResolution: 2.28→2.37 Å / Redundancy: 4.63 % / Mean I/σ(I) obs: 2.2 / Num. unique all: 3877 / Rsym value: 0.4648 / % possible all: 100

-
Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
PROTEUM PLUSPLUSdata reduction
PROTEUM PLUSPLUSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3e8m

3e8m


Resolution: 2.28→37.1 Å / SU ML: 0.33 / σ(F): 0 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2493 3557 3.19 %random
Rwork0.1954 ---
obs0.1971 62511 93.24 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20.641 Å2 / ksol: 0.316 e/Å3
Displacement parametersBiso mean: 25.75 Å2
Baniso -1Baniso -2Baniso -3
1--3.193 Å20 Å20 Å2
2---0.2331 Å2-0 Å2
3---3.4261 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.28→37.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10320 0 8 562 10890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00710527
X-RAY DIFFRACTIONf_angle_d1.01514199
X-RAY DIFFRACTIONf_dihedral_angle_d15.393881
X-RAY DIFFRACTIONf_chiral_restr0.071587
X-RAY DIFFRACTIONf_plane_restr0.0031822
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.28-2.36150.32553210.27879774X-RAY DIFFRACTION85
2.3615-2.4560.32743230.2610080X-RAY DIFFRACTION87
2.456-2.56780.32133320.25110367X-RAY DIFFRACTION90
2.5678-2.70310.29783690.224810639X-RAY DIFFRACTION92
2.7031-2.87240.30093320.224210907X-RAY DIFFRACTION94
2.8724-3.09410.26913690.217110909X-RAY DIFFRACTION95
3.0941-3.40520.26423740.202811140X-RAY DIFFRACTION96
3.4052-3.89750.24013820.176311205X-RAY DIFFRACTION97
3.8975-4.90870.17893700.138211329X-RAY DIFFRACTION98
4.9087-37.10.18773850.157911452X-RAY DIFFRACTION99

+
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