[English] 日本語
Yorodumi
- PDB-5yvz: Crystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5yvz
TitleCrystal structure of the Kdo hydroxylase KdoO, a non-heme Fe(II) alphaketoglutarate dependent dioxygenase in complex with alphaketoglutarate and Fe(III)
ComponentsUncharacterized protein KdoO
KeywordsBIOSYNTHETIC PROTEIN / Fe(II)/O2/alphaketoglutarate dependent dioxygenase / KDO2-lipid A dioxygenase / deoxysugar dioxygenase / LPS biosynthesis
Function / homologyKdo hydroxylase / 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase / ACETATE ION / 2-OXOGLUTARIC ACID / : / 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo) hydroxylase
Function and homology information
Biological speciesMethylacidiphilum infernorum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChung, H.S. / Pemble, C.W. / Joo, S.H. / Raetz, C.R.
Funding support United States, 1items
OrganizationGrant numberCountry
NIH United States
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Biochemical and Structural Insights into an Fe(II)/ alpha-Ketoglutarate/O2-Dependent Dioxygenase, Kdo 3-Hydroxylase (KdoO).
Authors: Joo, S.H. / Pemble, C.W. / Yang, E.G. / Raetz, C.R.H. / Chung, H.S.
History
DepositionNov 28, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 24, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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.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.value / _struct_conn.pdbx_dist_value / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Uncharacterized protein KdoO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,52411
Polymers36,2391
Non-polymers1,28510
Water2,990166
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-12 kcal/mol
Surface area13930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.710, 59.204, 116.264
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Uncharacterized protein KdoO / 3-deoxy-D-manno-octulosonic acid hydorxylase / Kdo hydroxylase


Mass: 36239.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylacidiphilum infernorum (isolate V4) (bacteria)
Gene: Minf_1012 / Production host: Escherichia coli (E. coli) / References: UniProt: B3DUR4

-
Non-polymers , 7 types, 176 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-AKG / 2-OXOGLUTARIC ACID / Α-Ketoglutaric acid


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 166 / 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: 2.17 Å3/Da / Density % sol: 43.33 %
Crystal growTemperature: 288 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Sodium acetate (pH=4.5), 200mM Lithium sulfate, 50 % v/v PEG 400

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 41701 / % possible obs: 98.2 % / Redundancy: 10 % / Biso Wilson estimate: 19.12 Å2 / Rmerge(I) obs: 0.104 / Χ2: 1.434 / Net I/σ(I): 11.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.6-1.637.30.46818280.717186.5
1.63-1.667.60.46819120.74192.2
1.66-1.698.10.44419770.721194.5
1.69-1.728.60.38120320.772198.3
1.72-1.769.20.34120520.819197.3
1.76-1.89.80.29920620.894198.8
1.8-1.85100.26920800.979199
1.85-1.910.30.23920771.084199.4
1.9-1.9510.40.20120781.223199.2
1.95-2.0210.40.18121071.321199.2
2.02-2.0910.40.15620941.496199.7
2.09-2.1710.50.14421091.5541100
2.17-2.2710.60.13421271.531199.9
2.27-2.3910.70.12620921.619199.8
2.39-2.5410.70.12121341.7811100
2.54-2.74110.11221271.7031100
2.74-3.0111.20.10321581.8511100
3.01-3.4511.30.09221542.0861100
3.45-4.34110.08121922.21100
4.34-50100.08323092.226199.1

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y7S

5y7s
PDB Unreleased entry


Resolution: 1.6→34.547 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.95
RfactorNum. reflection% reflection
Rfree0.1822 2082 5 %
Rwork0.1595 --
obs0.1607 41632 97.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 104.94 Å2 / Biso mean: 29.4555 Å2 / Biso min: 11.17 Å2
Refinement stepCycle: final / Resolution: 1.6→34.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 73 166 2612
Biso mean--54.93 39.18 -
Num. residues----294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052516
X-RAY DIFFRACTIONf_angle_d0.793387
X-RAY DIFFRACTIONf_chiral_restr0.054361
X-RAY DIFFRACTIONf_plane_restr0.005431
X-RAY DIFFRACTIONf_dihedral_angle_d16.8091525
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5997-1.6370.2661170.20312246236385
1.637-1.67790.18511330.19322486261994
1.6779-1.72330.22731330.17262558269197
1.7233-1.7740.19381390.16522598273798
1.774-1.83120.16851380.15652645278399
1.8312-1.89670.21471400.15692627276799
1.8967-1.97260.17581380.15442667280599
1.9726-2.06240.16571380.152426362774100
2.0624-2.17110.19281410.152626722813100
2.1711-2.30710.16811410.154326772818100
2.3071-2.48520.21371410.1626772818100
2.4852-2.73520.17371420.161927032845100
2.7352-3.13070.19291440.165127352879100
3.1307-3.94350.15841450.144927612906100
3.9435-34.55490.18181520.16582862301499
Refinement TLS params.

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 °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.83030.55360.77442.60320.4872.725-0.0054-0.14360.07770.2024-0.0492-0.1191-0.16850.03040.03050.1155-0.00290.0220.11840.00050.1322-3.13353.3933-6.08
20.35330.73390.46258.08117.31486.760.1277-0.1564-0.29820.1940.804-1.78630.35580.992-0.78130.2978-0.014-0.00450.3974-0.05080.569814.9546-2.2915-17.636
30.4922-0.07820.01091.80830.16670.9180.05030.0416-0.03290.0121-0.0453-0.06920.12760.0509-0.0130.10270.0028-0.00090.1237-0.00270.10271.9383-11.5084-17.0725
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 127 )A11 - 127
2X-RAY DIFFRACTION2chain 'A' and (resid 128 through 145 )A128 - 145
3X-RAY DIFFRACTION3chain 'A' and (resid 146 through 307 )A146 - 307

+
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