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- PDB-9bwu: Glutarate L-2-hydroxylase (CsiD/GlaH) from Escherichia coli at 2.... -

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Basic information

Entry
Database: PDB / ID: 9bwu
TitleGlutarate L-2-hydroxylase (CsiD/GlaH) from Escherichia coli at 2.20 Angstroms 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: 2.2 Å
AuthorsHan, Z.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)DMR-2104353 United States
CitationJournal: To Be Published
Title: Design of Ferroelectric Protein Crystals via DNA-directed Symmetry Breaking
Authors: Han, Z.
History
DepositionMay 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glutarate 2-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3682
Polymers37,3121
Non-polymers561
Water4,324240
1
A: Glutarate 2-hydroxylase
hetero molecules
x 8


Theoretical massNumber of molelcules
Total (without water)298,94516
Polymers298,4988
Non-polymers4478
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)123.830, 123.830, 139.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-609-

HOH

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Components

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


Mass: 37312.242 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-FE2 / FE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 240 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.58 Å3/Da / Density % sol: 65.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium citrate tribasic monohydrate, 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Feb 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.2→61.92 Å / Num. obs: 26092 / % possible obs: 94 % / Redundancy: 7.2 % / Biso Wilson estimate: 20.33 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.064 / Rrim(I) all: 0.127 / Net I/σ(I): 11.3
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.328 / Mean I/σ(I) obs: 5 / Num. unique obs: 1705 / CC1/2: 0.934 / Rpim(I) all: 0.196 / Rrim(I) all: 0.382 / % possible all: 71.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
Aimless0.7.15data scaling
DIALS3.17.0data reduction
PHASER2.8.3phasing
Coot0.9.8.92model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→61.915 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: FREE R-VALUE / ESU R: 0.186 / ESU R Free: 0.168
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 1359 5.209 %Random selection
Rwork0.1904 24730 --
all0.192 ---
obs-26089 94.045 %-
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: 22.962 Å2
Baniso -1Baniso -2Baniso -3
1-0.046 Å2-0 Å20 Å2
2--0.046 Å2-0 Å2
3----0.092 Å2
Refinement stepCycle: LAST / Resolution: 2.2→61.915 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2373 0 1 240 2614
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0122434
X-RAY DIFFRACTIONr_angle_refined_deg1.9791.8423297
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2995287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.702520
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.80910413
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.4610128
X-RAY DIFFRACTIONr_chiral_restr0.0960.2355
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021883
X-RAY DIFFRACTIONr_nbd_refined0.1940.2964
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21651
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2177
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1440.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0950.220
X-RAY DIFFRACTIONr_mcbond_it2.8251.8341157
X-RAY DIFFRACTIONr_mcangle_it4.0333.2651441
X-RAY DIFFRACTIONr_scbond_it4.62.3461277
X-RAY DIFFRACTIONr_scangle_it6.7794.0841856
X-RAY DIFFRACTIONr_lrange_it8.36422.8833621
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
2.2-2.2570.225830.21616200.21720190.9680.96884.34870.193
2.257-2.3190.313610.22514500.22919500.9290.96877.48720.2
2.319-2.3860.26930.20818420.2119350.9590.9721000.186
2.386-2.4590.277980.21417390.21718370.9430.9721000.19
2.459-2.540.266940.21617340.21918280.960.9721000.194
2.54-2.6290.298920.20216480.20617400.9460.9741000.184
2.629-2.7280.246800.20912550.21116960.9660.97378.71460.193
2.728-2.8390.239950.20515180.20716130.9640.9731000.192
2.839-2.9650.217860.20714790.20715650.9710.9731000.197
2.965-3.1090.214900.20314220.20415120.9720.9751000.2
3.109-3.2770.272720.19613480.19914200.9590.9761000.197
3.277-3.4750.25550.19810960.213560.960.97884.8820.201
3.475-3.7140.195630.18710370.18812820.9770.98185.80340.192
3.714-4.0110.191500.17410090.17511980.9770.98388.39730.185
4.011-4.3920.155520.14510460.14610980.9830.9871000.162
4.392-4.9070.188440.149770.14210210.9830.9891000.155
4.907-5.660.206440.168530.1638970.980.9861000.18
5.66-6.9180.194490.2057240.2047730.9790.9791000.223
6.918-9.7230.238380.1825750.1846130.9640.9811000.212
9.723-61.9150.215200.2313580.233850.9520.96598.18180.302

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