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- PDB-8cdf: Structure of glutarate hydroxylase (GlaH) from Escherichia coli a... -

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Basic information

Entry
Database: PDB / ID: 8cdf
TitleStructure of glutarate hydroxylase (GlaH) from Escherichia coli at a resolution of 1.8 angstrom obtained as a contaminant during routine use of E. coli as an expression host
ComponentsGlutarate 2-hydroxylase
KeywordsMETAL BINDING PROTEIN / Carbon-starvation induced / hydroxylase / non haem Fe (II)-dependent oxygenase
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: 1.77 Å
AuthorsAdeyeye, A.A. / Schubert, W.
Funding support South Africa, 1items
OrganizationGrant numberCountry
Other private South Africa
CitationJournal: To Be Published
Title: Structure of glutarate hydroxylase (GlaH) from Escherichia coli at a resolution of 1.8 angstrom obtained as a contaminant during routine use of E. coli as an expression host
Authors: Adeyeye, A.A. / Schubert, W.
History
DepositionJan 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)36,0312
Polymers35,9751
Non-polymers561
Water3,477193
1
A: Glutarate 2-hydroxylase
hetero molecules

A: Glutarate 2-hydroxylase
hetero molecules

A: Glutarate 2-hydroxylase
hetero molecules

A: Glutarate 2-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,1228
Polymers143,8994
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
Buried area6620 Å2
ΔGint-82 kcal/mol
Surface area53880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.132, 121.132, 136.487
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-665-

HOH

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Components

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


Mass: 35974.762 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli)
Gene: csiD, glaH, ACU57_06710, AM464_04980, BGM66_004646, BJI68_04905, C5N07_05545, CTR35_002510, EIZ93_05365, EL79_1036, FOI11_00325, FOI11_022855, FV293_23215, FWK02_21895, G3V95_09995, GIB53_ ...Gene: csiD, glaH, ACU57_06710, AM464_04980, BGM66_004646, BJI68_04905, C5N07_05545, CTR35_002510, EIZ93_05365, EL79_1036, FOI11_00325, FOI11_022855, FV293_23215, FWK02_21895, G3V95_09995, GIB53_09245, GJO56_18475, GKF89_16305, GNW61_23135, GRW05_29650, GRW24_16590, GRW56_10550, GRW57_12335, HMV95_03335, J0541_002578, JNP96_20920, NCTC9045_01367, NCTC9073_04720, NCTC9117_01751, SAMEA3751407_03408
Production host: Escherichia coli (E. coli) / References: UniProt: A0A090H1G1, 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.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.48 Å3/Da / Density % sol: 64.64 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 47 mM K3PO4, 0.4 M (NH4)2SO4, 200 mM KCl, 1mM EDTA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.77→53.37 Å / Num. obs: 49508 / % possible obs: 99.95 % / Redundancy: 11.9 % / Biso Wilson estimate: 33.99 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.102 / Rrim(I) all: 0.106 / Net I/σ(I): 11.9
Reflection shellResolution: 1.77→1.8 Å / Redundancy: 6 % / Mean I/σ(I) obs: 0.3 / Num. unique obs: 2412 / CC1/2: 0.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.77→50.35 Å / SU ML: 0.316 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.5487
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2302 1983 4.05 %
Rwork0.2006 46981 -
obs0.2017 48964 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.05 Å2
Refinement stepCycle: LAST / Resolution: 1.77→50.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2452 0 1 193 2646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00752512
X-RAY DIFFRACTIONf_angle_d0.8793403
X-RAY DIFFRACTIONf_chiral_restr0.0528366
X-RAY DIFFRACTIONf_plane_restr0.008445
X-RAY DIFFRACTIONf_dihedral_angle_d5.6805328
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.77-1.810.45711280.42492902X-RAY DIFFRACTION87.27
1.81-1.860.3841380.38993280X-RAY DIFFRACTION97.41
1.86-1.920.33731400.33213350X-RAY DIFFRACTION99.8
1.92-1.980.29891410.27783336X-RAY DIFFRACTION99.89
1.98-2.050.28191400.24163337X-RAY DIFFRACTION99.74
2.05-2.130.27681410.22893354X-RAY DIFFRACTION99.86
2.13-2.230.26251420.2163375X-RAY DIFFRACTION99.97
2.23-2.350.22821420.20623373X-RAY DIFFRACTION99.94
2.35-2.490.24671420.2013375X-RAY DIFFRACTION100
2.49-2.690.26371440.20083397X-RAY DIFFRACTION100
2.69-2.960.2191440.21653419X-RAY DIFFRACTION99.97
2.96-3.390.2421430.20823411X-RAY DIFFRACTION100
3.39-4.270.21521450.16053451X-RAY DIFFRACTION100
4.27-50.350.17761530.16993621X-RAY DIFFRACTION99.95

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