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- PDB-6gpe: Crystal Structure of the CsiD Glutarate Hydroxylase -

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Basic information

Entry
Database: PDB / ID: 6gpe
TitleCrystal Structure of the CsiD Glutarate Hydroxylase
ComponentsProtein CsiD
KeywordsHYDROLASE / jelly roll / glutarate hydroxylase / alpha-ketoglutarate-dependent
Function / homology
Function and homology information


response to carbon starvation / 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 / 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
: / 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 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2023Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein CsiD
B: Protein CsiD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4054
Polymers81,2942
Non-polymers1122
Water9,350519
1
A: Protein CsiD
hetero molecules

A: Protein CsiD
hetero molecules

A: Protein CsiD
hetero molecules

A: Protein CsiD
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: Protein CsiD
hetero molecules

B: Protein CsiD
hetero molecules

B: Protein CsiD
hetero molecules

B: Protein CsiD
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
Unit cell
Length a, b, c (Å)121.200, 121.200, 137.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-731-

HOH

21B-787-

HOH

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Components

#1: Protein Protein CsiD


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: csiD, gab, ygaT, b2659, JW5427 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P76621
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 519 / 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: 3.09 Å3/Da / Density % sol: 60.25 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: 0.08 M Sodium chloride, 0.012 M Potassium chloride, 0.02 M Magnesium chloride hexahydrate, 0.04 M Sodium cacodylate trihydrate pH 6.0, 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: 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: 1.49→45.67 Å / Num. obs: 158775 / % possible obs: 96.58 % / Redundancy: 23.3 % / Net I/σ(I): 3.7
Reflection shellResolution: 1.53→1.57 Å

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2r6s

2r6s


Resolution: 2.2→42.505 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1983 1437 3 %
Rwork0.1725 --
obs0.1733 47921 91.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→42.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4775 0 2 519 5296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034927
X-RAY DIFFRACTIONf_angle_d0.7366682
X-RAY DIFFRACTIONf_dihedral_angle_d8.4994121
X-RAY DIFFRACTIONf_chiral_restr0.04720
X-RAY DIFFRACTIONf_plane_restr0.004876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.27870.26861450.22374692X-RAY DIFFRACTION94
2.2787-2.36990.25231460.20734711X-RAY DIFFRACTION94
2.3699-2.47780.29821440.20084672X-RAY DIFFRACTION93
2.4778-2.60840.24491420.19164575X-RAY DIFFRACTION91
2.6084-2.77180.18021450.18154695X-RAY DIFFRACTION93
2.7718-2.98570.22791440.17844641X-RAY DIFFRACTION92
2.9857-3.28610.19781430.17184666X-RAY DIFFRACTION92
3.2861-3.76130.17691410.1574547X-RAY DIFFRACTION89
3.7613-4.73790.15281420.1424620X-RAY DIFFRACTION90
4.7379-42.51310.1941450.17944665X-RAY DIFFRACTION86

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