[English] 日本語
Yorodumi
- PDB-8a97: ROOM TEMPERATURE CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-H... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a97
TitleROOM TEMPERATURE CRYSTAL STRUCTURE OF THE COFACTOR-DEVOID 1-H-3-HYDROXY-4- OXOQUINALDINE 2,4-DIOXYGENASE (HOD) UNDER XENON PRESSURE (30 bar)
Components1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
KeywordsOXIDOREDUCTASE / ALPHA-BETA HYDROLASE / DIOXYGENASE / COFACTOR-DEVOID / XENON / PRESSURIZATION
Function / homology
Function and homology information


3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase / 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase activity / oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen / catabolic process
Similarity search - Function
: / alpha/beta hydrolase fold / Alpha/beta hydrolase fold-1 / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
D(-)-TARTARIC ACID / XENON / 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
Similarity search - Component
Biological speciesPaenarthrobacter nitroguajacolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.897 Å
AuthorsBui, S. / Prange, T. / Steiner, R.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/I020411/1 United Kingdom
CitationJournal: Chem Sci / Year: 2023
Title: Evolutionary adaptation from hydrolytic to oxygenolytic catalysis at the alpha / beta-hydrolase fold.
Authors: Bui, S. / Gil-Guerrero, S. / van der Linden, P. / Carpentier, P. / Ceccarelli, M. / Jambrina, P.G. / Steiner, R.A.
History
DepositionJun 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
BBB: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
CCC: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
DDD: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,43313
Polymers133,1584
Non-polymers1,2769
Water88349
1
AAA: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5713
Polymers33,2891
Non-polymers2812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7214
Polymers33,2891
Non-polymers4313
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5713
Polymers33,2891
Non-polymers2812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: 1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5713
Polymers33,2891
Non-polymers2812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.860, 169.460, 169.310
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB
32AAA
42CCC
53AAA
63DDD
74BBB
84CCC
95BBB
105DDD
116CCC
126DDD

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111METMETGLNGLNAAAA1 - 27413 - 286
221METMETGLNGLNBBBB1 - 27413 - 286
332METMETGLYGLYAAAA1 - 27513 - 287
442METMETGLYGLYCCCC1 - 27513 - 287
553THRTHRGLNGLNAAAA2 - 27414 - 286
663THRTHRGLNGLNDDDD2 - 27414 - 286
774METMETGLNGLNBBBB1 - 27413 - 286
884METMETGLNGLNCCCC1 - 27413 - 286
995THRTHRGLNGLNBBBB2 - 27414 - 286
10105THRTHRGLNGLNDDDD2 - 27414 - 286
11116THRTHRGLNGLNCCCC2 - 27414 - 286
12126THRTHRGLNGLNDDDD2 - 27414 - 286

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

-
Components

#1: Protein
1H-3-hydroxy-4-oxoquinaldine 2,4-dioxygenase


Mass: 33289.391 Da / Num. of mol.: 4 / Mutation: C69S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenarthrobacter nitroguajacolicus (bacteria)
Gene: hod, meqE, ARUE_113p00080, pAL1.008 / Plasmid: PQE30 / Production host: Escherichia coli (E. coli)
References: UniProt: O31266, 3-hydroxy-2-methylquinolin-4-one 2,4-dioxygenase
#2: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Xe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O6
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4248.22
248.22
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion7PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0
2932vapor diffusion7PROTEIN AT 150 MG/ML IN STORAGE BUFFER 1.65M NA/K TARTRATE, 0.1M HEPES PH 7.0

-
Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.5241
pseudo-merohedral22-H, -L, -K20.4759
ReflectionResolution: 2.897→53.583 Å / Num. obs: 29421 / % possible obs: 99.2 % / Redundancy: 4.4 % / Biso Wilson estimate: 59.9 Å2 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.061 / Net I/σ(I): 5.4
Reflection shellResolution: 2.897→2.95 Å / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1408 / Rpim(I) all: 0.623 / % possible all: 95.8

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
xia2data reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WJ3

2wj3


Resolution: 2.897→53.583 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.659 / SU ML: 0.178 / Cross valid method: THROUGHOUT / ESU R Free: 0.079
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2203 1483 5.047 %
Rwork0.1918 27898 -
all0.193 --
obs-29381 98.806 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 62.756 Å2
Baniso -1Baniso -2Baniso -3
1-3.482 Å20 Å20 Å2
2--0.271 Å2-0 Å2
3----3.753 Å2
Refinement stepCycle: LAST / Resolution: 2.897→53.583 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8966 0 54 49 9069
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0139329
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158383
X-RAY DIFFRACTIONr_ext_dist_refined_d0.010.0114604
X-RAY DIFFRACTIONr_angle_refined_deg1.3121.64312699
X-RAY DIFFRACTIONr_angle_other_deg1.4481.5819351
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.96451102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00421.699559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.172151476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6071572
X-RAY DIFFRACTIONr_chiral_restr0.0810.21133
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210598
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022222
X-RAY DIFFRACTIONr_nbd_refined0.2020.21856
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1760.27758
X-RAY DIFFRACTIONr_nbtor_refined0.1740.24379
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.24266
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2158
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2080.211
X-RAY DIFFRACTIONr_nbd_other0.2690.259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0590.22
X-RAY DIFFRACTIONr_mcbond_it2.6726.6074411
X-RAY DIFFRACTIONr_mcbond_other2.6726.6064409
X-RAY DIFFRACTIONr_mcangle_it4.3369.9095512
X-RAY DIFFRACTIONr_mcangle_other4.3369.9095512
X-RAY DIFFRACTIONr_scbond_it2.3756.7794918
X-RAY DIFFRACTIONr_scbond_other2.3756.784917
X-RAY DIFFRACTIONr_scangle_it3.9110.0857187
X-RAY DIFFRACTIONr_scangle_other3.9110.0857187
X-RAY DIFFRACTIONr_lrange_it7.364134.09320139
X-RAY DIFFRACTIONr_lrange_other7.364134.0920140
X-RAY DIFFRACTIONr_ncsr_local_group_10.0350.059606
X-RAY DIFFRACTIONr_ncsr_local_group_20.0270.059632
X-RAY DIFFRACTIONr_ncsr_local_group_30.0220.059588
X-RAY DIFFRACTIONr_ncsr_local_group_40.0390.059584
X-RAY DIFFRACTIONr_ncsr_local_group_50.0290.059588
X-RAY DIFFRACTIONr_ncsr_local_group_60.0320.059559
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.035330.05011
12BBBX-RAY DIFFRACTIONLocal ncs0.035330.05011
23AAAX-RAY DIFFRACTIONLocal ncs0.026850.05011
24CCCX-RAY DIFFRACTIONLocal ncs0.026850.05011
35AAAX-RAY DIFFRACTIONLocal ncs0.021590.05011
36DDDX-RAY DIFFRACTIONLocal ncs0.021590.05011
47BBBX-RAY DIFFRACTIONLocal ncs0.039420.05011
48CCCX-RAY DIFFRACTIONLocal ncs0.039420.05011
59BBBX-RAY DIFFRACTIONLocal ncs0.029220.05011
510DDDX-RAY DIFFRACTIONLocal ncs0.029220.05011
611CCCX-RAY DIFFRACTIONLocal ncs0.031920.05011
612DDDX-RAY DIFFRACTIONLocal ncs0.031920.05011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.897-2.9720.273750.2511972X-RAY DIFFRACTION93.4703
2.972-3.0540.3171490.2411917X-RAY DIFFRACTION99.7586
3.054-3.1420.227750.2211952X-RAY DIFFRACTION99.9014
3.142-3.2380.2861330.2311883X-RAY DIFFRACTION100
3.238-3.3440.247900.2331792X-RAY DIFFRACTION99.4189
3.344-3.4610.213760.2071822X-RAY DIFFRACTION99.9473
3.461-3.5910.275760.2041688X-RAY DIFFRACTION99.9433
3.591-3.7370.272750.1871703X-RAY DIFFRACTION99.6078
3.737-3.9020.1981490.1561474X-RAY DIFFRACTION99.4485
3.902-4.0920.156750.1671566X-RAY DIFFRACTION99.3943
4.092-4.3120.21740.1721393X-RAY DIFFRACTION98.9211
4.312-4.5710.174750.171399X-RAY DIFFRACTION99.1258
4.571-4.8840.209760.1691277X-RAY DIFFRACTION99.4853
4.884-5.2720.1651268X-RAY DIFFRACTION99.0625
5.272-5.770.211710.1941102X-RAY DIFFRACTION98.5714
5.77-6.4410.269740.2151010X-RAY DIFFRACTION98.1884
6.441-7.420.269720.218876X-RAY DIFFRACTION97.8328
7.42-9.04400.175826X-RAY DIFFRACTION98.3333
9.044-12.6120.172680.176578X-RAY DIFFRACTION97.4359
12.612-53.5830.252400X-RAY DIFFRACTION92.3788

+
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