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- PDB-6hl9: Crystal Structure of the CsiD Glutarate Hydroxylase in complex wi... -

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Basic information

Entry
Database: PDB / ID: 6hl9
TitleCrystal Structure of the CsiD Glutarate Hydroxylase in complex with Succinate
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
: / SUCCINIC ACID / Glutarate 2-hydroxylase / Glutarate 2-hydroxylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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
DepositionSep 10, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 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)81,6416
Polymers81,2942
Non-polymers3484
Water9,494527
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)163,28312
Polymers162,5874
Non-polymers6968
Water724
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
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)163,28312
Polymers162,5874
Non-polymers6968
Water724
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)123.034, 123.034, 138.327
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 17 through 65 or resid 67...
21(chain B and ((resid 17 and (name N or name...

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
11ASPASPPHEPHE(chain A and (resid 17 through 65 or resid 67...AA17 - 6537 - 85
12VALVALASNASN(chain A and (resid 17 through 65 or resid 67...AA67 - 14287 - 162
13HISHISHISHIS(chain A and (resid 17 through 65 or resid 67...AA154174
14GLNGLNHISHIS(chain A and (resid 17 through 65 or resid 67...AA16 - 32436 - 344
15GLNGLNHISHIS(chain A and (resid 17 through 65 or resid 67...AA16 - 32436 - 344
16GLNGLNHISHIS(chain A and (resid 17 through 65 or resid 67...AA16 - 32436 - 344
17GLNGLNHISHIS(chain A and (resid 17 through 65 or resid 67...AA16 - 32436 - 344
21ASPASPASPASP(chain B and ((resid 17 and (name N or name...BB1737
22GLNGLNHISHIS(chain B and ((resid 17 and (name N or name...BB16 - 32436 - 344
23GLNGLNHISHIS(chain B and ((resid 17 and (name N or name...BB16 - 32436 - 344
24GLNGLNHISHIS(chain B and ((resid 17 and (name N or name...BB16 - 32436 - 344
25GLNGLNHISHIS(chain B and ((resid 17 and (name N or name...BB16 - 32436 - 344

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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 / Production host: Escherichia coli (E. coli)
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-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 3.22 Å3/Da / Density % sol: 61.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Succinic acid pH 7.0, 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: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→46.109 Å / Num. obs: 47789 / % possible obs: 98.3 % / Redundancy: 26.7 % / Biso Wilson estimate: 39.58 Å2 / Rsym value: 0.145 / Net I/σ(I): 22.43
Reflection shellResolution: 2.3→2.35 Å / Rsym value: 1.211

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Processing

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

6gpe


Resolution: 2.3→46.109 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2103 1916 4.01 %
Rwork0.1859 45873 -
obs0.1869 47789 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 129.03 Å2 / Biso mean: 46.1385 Å2 / Biso min: 26.07 Å2
Refinement stepCycle: final / Resolution: 2.3→46.109 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4831 0 18 527 5376
Biso mean--75.02 53.06 -
Num. residues----593
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1736X-RAY DIFFRACTION5.053TORSIONAL
12B1736X-RAY DIFFRACTION5.053TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.3-2.35750.26921450.227432183363
2.3575-2.42130.24621430.223332093352
2.4213-2.49250.25891160.222932293345
2.4925-2.5730.27451350.219532413376
2.573-2.66490.26421050.218732583363
2.6649-2.77160.22491180.20932603378
2.7716-2.89770.24911530.216932153368
2.8977-3.05050.21531330.217532543387
3.0505-3.24150.23811310.206932753406
3.2415-3.49170.20871440.185932593403
3.4917-3.8430.18091490.170832853434
3.843-4.39870.17631390.151833093448
4.3987-5.54040.18341460.146233373483
5.5404-46.11820.21261590.193335243683
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)
10.8885-0.1572-0.06710.666-0.10780.5772-0.0021-0.0634-0.04480.0532-0.00320.00960.00850.02190.00010.2552-0.02010.01860.23690.00490.233145.1921-26.130755.7995
20.5255-0.02810.09621.3808-0.1490.6017-0.03520.07660.0093-0.22730.02750.0495-0.04060.011600.3446-0.0105-0.04170.3342-0.03810.270731.8329-8.95278.6505
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 16 through 324)A16 - 324
2X-RAY DIFFRACTION2(chain 'B' and resid 16 through 324)B16 - 324

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