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- PDB-9n57: Glutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-AAATTT DNA conju... -

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Basic information

Entry
Database: PDB / ID: 9n57
TitleGlutarate L-2-hydroxylase K270C mutant-5'-Mal-C2-AAATTT DNA conjugate in I422 space group
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
: / 1-ETHYL-PYRROLIDINE-2,5-DIONE / Glutarate 2-hydroxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 United States
CitationJournal: Sci Adv / Year: 2026
Title: Diffraction-quality, ultraflexible protein single crystals engineered with DNA.
Authors: Han, Z. / Mirkin, C.A.
History
DepositionFeb 3, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glutarate 2-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4693
Polymers37,2861
Non-polymers1832
Water3,027168
1
A: Glutarate 2-hydroxylase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)299,75424
Polymers298,2908
Non-polymers1,46416
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
Unit cell
Length a, b, c (Å)120.996, 120.996, 137.384
Angle α, β, γ (deg.)90, 90, 90
Int Tables number97
Space group name H-MI422

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Components

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


Mass: 37286.203 Da / Num. of mol.: 1
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-NEN / 1-ETHYL-PYRROLIDINE-2,5-DIONE


Mass: 127.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.37 Å3/Da / Density % sol: 63.52 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Sodium chloride, 0.04 M Sodium cacodylate trihydrate pH 7.0, 30 % v/v (+/-)-2-Methyl-2,4-pentanediol, 0.012 M Spermine tetrahydrochloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.979338 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979338 Å / Relative weight: 1
ReflectionResolution: 1.64→33.43 Å / Num. obs: 62305 / % possible obs: 100 % / Redundancy: 16.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.181 / Rpim(I) all: 0.066 / Rrim(I) all: 0.193 / Χ2: 1 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
8.98-33.4313.60.06432.94420.9980.0230.0690.7298.1
1.64-1.6715.64.5840.830310.261.7294.9020.99100

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDS20230630data reduction
Aimless0.7.15data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.64→33.427 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: FREE R-VALUE / ESU R: 0.071 / ESU R Free: 0.069 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.203 3057 4.907 %
Rwork0.1646 59247 -
all0.167 --
obs-62304 99.974 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.3 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 34.226 Å2
Baniso -1Baniso -2Baniso -3
1-3.033 Å2-0 Å20 Å2
2--3.033 Å2-0 Å2
3----6.066 Å2
Refinement stepCycle: LAST / Resolution: 1.64→33.427 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2298 0 8 168 2474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0122373
X-RAY DIFFRACTIONr_angle_refined_deg1.4361.833213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8525281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.914518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62810399
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.88410123
X-RAY DIFFRACTIONr_chiral_restr0.0710.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021841
X-RAY DIFFRACTIONr_nbd_refined0.2030.2925
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21617
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2135
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.234
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1050.214
X-RAY DIFFRACTIONr_mcbond_it13.9372.861130
X-RAY DIFFRACTIONr_mcangle_it17.4555.1371409
X-RAY DIFFRACTIONr_scbond_it21.9283.611243
X-RAY DIFFRACTIONr_scangle_it28.2526.3321804
X-RAY DIFFRACTIONr_lrange_it30.1433.943456
X-RAY DIFFRACTIONr_rigid_bond_restr3.88532373
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
1.64-1.6830.3742100.32443120.32745220.8740.921000.321
1.683-1.7280.3462340.30441910.30644250.9050.9331000.298
1.728-1.7780.2982030.27541120.27643150.9260.9441000.264
1.778-1.8330.2922190.24339780.24641970.9310.9551000.227
1.833-1.8930.2641850.2138880.21340730.9490.9721000.189
1.893-1.9590.2262080.18237140.18439220.970.981000.162
1.959-2.0330.21820.16936300.17138120.9760.9831000.15
2.033-2.1160.1941730.16434820.16536550.9690.9841000.145
2.116-2.2090.2141660.15333620.15635280.9690.9871000.136
2.209-2.3170.1941550.1531960.15233510.9740.9871000.134
2.317-2.4410.1951530.15330780.15532310.9720.9871000.138
2.441-2.5880.1811600.15428810.15630410.9820.9881000.142
2.588-2.7660.2111510.16527140.16728660.9750.98699.96510.156
2.766-2.9860.2181170.16325700.16626870.9760.9841000.16
2.986-3.2680.1721090.15323720.15424810.9840.9851000.156
3.268-3.650.1751200.14321380.14522580.980.9881000.154
3.65-4.2060.161960.12119170.12320130.9860.9921000.135
4.206-5.1310.1461020.12816080.12917100.9890.9911000.15
5.131-7.1720.231660.17413080.17613740.9690.9811000.202
7.172-33.4270.238480.1747960.1788450.9710.97699.88170.2

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