[English] 日本語
Yorodumi
- PDB-9n7c: Glutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-TTTT DNA conjuga... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9n7c
TitleGlutarate L-2-hydroxylase Q184C mutant-5'-Mal-C6-TTTT DNA conjugate at 2.02 Angstrom resolution
ComponentsGlutarate 2-hydroxylase
KeywordsMETAL BINDING PROTEIN / Oxygenase / Hydroxylase / Metal binding
Function / homology
Function and homology information


glutarate dioxygenase / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, with 2-oxoglutarate as one donor, and the other dehydrogenated / glutarate dioxygenase activity / L-lysine catabolic process / ferrous iron binding
Similarity search - Function
Glutarate 2-hydroxylase GlaH / CsiD / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
: / : / Glutarate 2-hydroxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.023 Å
AuthorsHan, Z. / Mirkin, C.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2428112 United States
Other governmentAir Force Office of Scientific Research FA9550-22-1-0300
CitationJournal: Sci Adv / Year: 2026
Title: Diffraction-quality, ultraflexible protein single crystals engineered with DNA.
Authors: Han, Z. / Mirkin, C.A.
History
DepositionFeb 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2026Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutarate 2-hydroxylase
B: Glutarate 2-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9245
Polymers74,5752
Non-polymers3503
Water5,531307
1
A: Glutarate 2-hydroxylase
B: Glutarate 2-hydroxylase
hetero molecules

A: Glutarate 2-hydroxylase
B: Glutarate 2-hydroxylase
hetero molecules

A: Glutarate 2-hydroxylase
B: Glutarate 2-hydroxylase
hetero molecules

A: Glutarate 2-hydroxylase
B: Glutarate 2-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,69820
Polymers298,2988
Non-polymers1,40012
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Unit cell
Length a, b, c (Å)124.211, 124.211, 127.025
Angle α, β, γ (deg.)90, 90, 90
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-581-

HOH

21B-644-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 17 - 316 / Label seq-ID: 17 - 316

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

-
Components

#1: Protein Glutarate 2-hydroxylase / G-2-H


Mass: 37287.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: glaH, EcolC_1047 / Production host: Escherichia coli (E. coli) / References: UniProt: B1IVJ9, glutarate dioxygenase
#2: Chemical ChemComp-A1BVO / (1r,4r)-4-[(2,5-dioxopyrrolidin-1-yl)methyl]cyclohexane-1-carboxamide


Mass: 238.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N2O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 307 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 10 % v/v Glycerol, 0.05 M MES pH 5.5, 1.5 M Ammonium sulfate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.920105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 16, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.920105 Å / Relative weight: 1
ReflectionResolution: 2.02→88.81 Å / Num. obs: 65331 / % possible obs: 100 % / Redundancy: 16.5 % / CC1/2: 1 / Rmerge(I) obs: 0.22 / Rpim(I) all: 0.06 / Rrim(I) all: 0.23 / Net I/σ(I): 9.4
Reflection shellResolution: 2.02→2.07 Å / Redundancy: 14.1 % / Rmerge(I) obs: 3.593 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 63726 / CC1/2: 0.36 / Rpim(I) all: 1.04 / Rrim(I) all: 3.96 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDS20220820data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
Coot0.9.8.92model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.023→88.809 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.942 / Cross valid method: FREE R-VALUE / ESU R: 0.15 / ESU R Free: 0.14 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2405 3143 4.814 %
Rwork0.212 62151 -
all0.213 --
obs-65294 99.988 %
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: 44.209 Å2
Baniso -1Baniso -2Baniso -3
1--1.031 Å20 Å20 Å2
2---1.031 Å20 Å2
3---2.062 Å2
Refinement stepCycle: LAST / Resolution: 2.023→88.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4650 0 9 307 4966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0124806
X-RAY DIFFRACTIONr_angle_refined_deg1.581.8356508
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1955570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.904539
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.0710814
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.81510248
X-RAY DIFFRACTIONr_chiral_restr0.0760.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023716
X-RAY DIFFRACTIONr_nbd_refined0.1980.22050
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23254
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2317
X-RAY DIFFRACTIONr_metal_ion_refined0.0070.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2140.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1620.223
X-RAY DIFFRACTIONr_mcbond_it3.7064.0652289
X-RAY DIFFRACTIONr_mcangle_it5.2157.2692856
X-RAY DIFFRACTIONr_scbond_it5.0344.5922517
X-RAY DIFFRACTIONr_scangle_it7.3248.2253652
X-RAY DIFFRACTIONr_lrange_it9.1445.7127242
X-RAY DIFFRACTIONr_ncsr_local_group_10.0660.059461
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.066070.05009
12BX-RAY DIFFRACTIONLocal ncs0.066070.05009
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.023-2.0760.3541780.33445550.33547330.8940.9031000.333
2.076-2.1320.3172080.30744170.30746260.9260.92699.97840.302
2.132-2.1940.3442410.28843050.29145460.9180.9381000.278
2.194-2.2620.3052300.28941410.2943720.9290.93599.97710.272
2.262-2.3360.2781810.26840750.26842560.9460.9481000.247
2.336-2.4180.2961880.23539160.23841040.9450.9621000.212
2.418-2.5090.2882130.22337810.22639940.950.9671000.199
2.509-2.6110.2291880.21936640.2238520.9670.971000.193
2.611-2.7270.2781720.22335110.22536830.9550.971000.196
2.727-2.860.2521640.21633660.21835300.9630.9711000.192
2.86-3.0150.2741910.23831820.2433730.9510.9631000.21
3.015-3.1970.2821680.22730330.2332010.950.9671000.205
3.197-3.4180.2331340.20728680.20830020.9680.9731000.191
3.418-3.6910.2371480.19826630.228110.9620.9761000.187
3.691-4.0430.2271500.17924610.18226110.9710.9811000.171
4.043-4.5190.161210.15122460.15223670.9860.9871000.151
4.519-5.2160.155890.14520260.14521150.9850.9881000.146
5.216-6.3820.211860.19817270.19918130.9780.9791000.198
6.382-9.0030.219700.22313710.22314410.970.9741000.231
9.003-88.8090.194230.2278430.2268710.9810.96699.42590.277

+
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