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- PDB-6gpn: Crystal Structure of the CsiD Glutarate Hydroxylase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6gpn
TitleCrystal Structure of the CsiD Glutarate Hydroxylase in complex with N-Oxalylglycine
ComponentsGlutarate 2-hydroxylase
KeywordsHYDROLASE / jelly roll / glutarate hydroxylase / alpha-ketoglutarate-dependent
Function / homology
Function and homology information


response to carbon starvation / glutarate dioxygenase activity / 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 / L-lysine catabolic process / ferrous iron binding / iron ion binding / protein-containing complex / identical protein binding
Similarity search - Function
Glutarate 2-hydroxylase GlaH / CsiD / Clavaminate synthase-like / Double-stranded beta-helix / Taurine dioxygenase TauD-like superfamily / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / N-OXALYLGLYCINE / Glutarate 2-hydroxylase / Glutarate 2-hydroxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsWilliams, R.M. / Mayans, O. / Hartig, J.S.
CitationJournal: Nat Commun / Year: 2018
Title: Widespread bacterial lysine degradation proceeding via glutarate and L-2-hydroxyglutarate.
Authors: Knorr, S. / Sinn, M. / Galetskiy, D. / Williams, R.M. / Wang, C. / Muller, N. / Mayans, O. / Schleheck, D. / Hartig, J.S.
History
DepositionJun 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 30, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Source and taxonomy / Structure summary
Category: database_2 / entity ...database_2 / entity / entity_name_com / entity_src_gen / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.pdbx_seq_db_accession_code
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,5525
Polymers81,2942
Non-polymers2593
Water4,900272
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)162,8118
Polymers162,5874
Non-polymers2234
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
2
B: Glutarate 2-hydroxylase
hetero molecules

B: Glutarate 2-hydroxylase
hetero molecules

B: Glutarate 2-hydroxylase
hetero molecules

B: Glutarate 2-hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)163,39912
Polymers162,5874
Non-polymers8128
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_445-y-1/2,x-1/2,z1
crystal symmetry operation4_545y+1/2,-x-1/2,z1
Unit cell
Length a, b, c (Å)121.380, 121.380, 136.570
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 16 through 167 or (resid 168...
21(chain B and (resid 16 through 42 or (resid 43...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNGLUGLU(chain A and (resid 16 through 167 or (resid 168...AA16 - 16736 - 187
12GLUGLUGLUGLU(chain A and (resid 16 through 167 or (resid 168...AA168188
13GLNGLNGLNGLN(chain A and (resid 16 through 167 or (resid 168...AA16 - 32236 - 342
14GLNGLNGLNGLN(chain A and (resid 16 through 167 or (resid 168...AA16 - 32236 - 342
15GLNGLNGLNGLN(chain A and (resid 16 through 167 or (resid 168...AA16 - 32236 - 342
16GLNGLNGLNGLN(chain A and (resid 16 through 167 or (resid 168...AA16 - 32236 - 342
21GLNGLNTHRTHR(chain B and (resid 16 through 42 or (resid 43...BB16 - 4236 - 62
22LYSLYSLYSLYS(chain B and (resid 16 through 42 or (resid 43...BB4363
23GLNGLNGLNGLN(chain B and (resid 16 through 42 or (resid 43...BB16 - 32236 - 342
24GLNGLNGLNGLN(chain B and (resid 16 through 42 or (resid 43...BB16 - 32236 - 342
25GLNGLNGLNGLN(chain B and (resid 16 through 42 or (resid 43...BB16 - 32236 - 342
26GLNGLNGLNGLN(chain B and (resid 16 through 42 or (resid 43...BB16 - 32236 - 342

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Components

#1: Protein Glutarate 2-hydroxylase / G-2-H / Carbon starvation induced protein D


Mass: 40646.805 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: glaH, csiD, gab, ygaT, b2659, JW5427 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P76621, UniProt: A0A1X3JCQ2*PLUS, glutarate dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-OGA / N-OXALYLGLYCINE


Mass: 147.086 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5NO5 / Comment: inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O

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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: 2.98 Å3/Da / Density % sol: 58.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 3.5 M Sodium formate, 0.1 M BIS-TRIS propane pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→44.31 Å / Num. obs: 91254 / % possible obs: 99.99 % / Redundancy: 26.2 % / Rsym value: 0.182 / Net I/σ(I): 17.7
Reflection shellResolution: 1.8→1.86 Å / Rsym value: 3.355

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6GPE

6gpe


Resolution: 2.2→42.914 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 24.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2114 1532 2.93 %
Rwork0.1866 50793 -
obs0.1873 52325 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 125.69 Å2 / Biso mean: 52.7791 Å2 / Biso min: 28.2 Å2
Refinement stepCycle: final / Resolution: 2.2→42.914 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4691 0 12 272 4975
Biso mean--87.79 56.03 -
Num. residues----581
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1724X-RAY DIFFRACTION3.764TORSIONAL
12B1724X-RAY DIFFRACTION3.764TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.2-2.2710.35421490.312245064655
2.271-2.35220.34171400.281745534693
2.3522-2.44640.33341360.249145584694
2.4464-2.55770.28171310.22645544685
2.5577-2.69250.2591550.212345664721
2.6925-2.86120.23181430.200745534696
2.8612-3.0820.25261470.203345864733
3.082-3.39210.22861450.175446174762
3.3921-3.88260.17671180.168646664784
3.8826-4.89060.15561440.141846934837
4.8906-42.92250.1781240.183749415065
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6465-0.63040.040.93480.32131.0321-0.0769-0.33950.23740.1278-0.03210.019-0.0693-0.09550.1010.3942-0.0348-0.05710.372-0.04550.303212.133-31.810755.8537
20.9305-0.3387-0.27381.17140.08620.7489-0.05530.0058-0.0071-0.09040.0195-0.13140.06070.0610.03230.2668-0.03270.0140.28210.04620.329227.6355-46.703912.4942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 16 through 325)A16 - 325
2X-RAY DIFFRACTION2(chain 'B' and resid 18 through 325)B18 - 325

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