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- PDB-6vxc: Crystal structure of hydroxyproline dehydratase (HypD) from Clost... -

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Basic information

Entry
Database: PDB / ID: 6vxc
TitleCrystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile
ComponentsTrans-4-hydroxy-L-proline dehydratase
KeywordsLYASE / glycyl radical enzyme / hydroxyproline dehydratase
Function / homology
Function and homology information


trans-4-hydroxy-L-proline dehydratase / 4-hydroxyproline metabolic process / proline salvage / formate C-acetyltransferase / formate C-acetyltransferase activity / carbon-oxygen lyase activity / cytosol
Similarity search - Function
: / : / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 ...: / : / Pyruvate formate lyase domain / Pyruvate formate lyase-like / Pyruvate formate-lyase domain profile. / Glycine radical / Glycine radical domain / Glycine radical domain profile. / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain / Anaerobic Ribonucleotide-triphosphate Reductase Large Chain - #20 / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Trans-4-hydroxy-L-proline dehydratase / Pyruvate formate-lyase
Similarity search - Component
Biological speciesClostridioides difficile 70-100-2010 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsBackman, L.R.F. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM069857 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM126982 United States
CitationJournal: Elife / Year: 2020
Title: Molecular basis for catabolism of the abundant metabolitetrans-4-hydroxy-L-proline by a microbial glycyl radical enzyme.
Authors: Backman, L.R. / Huang, Y.Y. / Andorfer, M.C. / Gold, B. / Raines, R.T. / Balskus, E.P. / Drennan, C.L.
History
DepositionFeb 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trans-4-hydroxy-L-proline dehydratase
B: Trans-4-hydroxy-L-proline dehydratase
C: Trans-4-hydroxy-L-proline dehydratase
D: Trans-4-hydroxy-L-proline dehydratase
E: Trans-4-hydroxy-L-proline dehydratase
F: Trans-4-hydroxy-L-proline dehydratase
G: Trans-4-hydroxy-L-proline dehydratase
H: Trans-4-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)732,39016
Polymers731,6538
Non-polymers7378
Water86,7424815
1
A: Trans-4-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5492
Polymers91,4571
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trans-4-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5492
Polymers91,4571
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Trans-4-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5492
Polymers91,4571
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Trans-4-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5492
Polymers91,4571
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Trans-4-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5492
Polymers91,4571
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Trans-4-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5492
Polymers91,4571
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
G: Trans-4-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5492
Polymers91,4571
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
H: Trans-4-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5492
Polymers91,4571
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.346, 341.655, 122.605
Angle α, β, γ (deg.)90.000, 107.140, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Trans-4-hydroxy-L-proline dehydratase / Glycyl radical enzyme / Hyp dehydratase / HypD


Mass: 91456.609 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile 70-100-2010 (bacteria)
Gene: pflD, csdB_2, BGU81_07860, BN1095_640054, BN1096_740112, BN1097_360077, SAMEA3375004_02654
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A031WDE4, UniProt: Q180C6*PLUS, trans-4-hydroxy-L-proline dehydratase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4815 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.74 Å3/Da / Density % sol: 55.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 14% (w/v) polyethylene glycol (PEG) 3350, 100 mM potassium chloride, and 100 mM HEPES pH 7.5. Cryoprotectant contained 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.048→50 Å / Num. obs: 486251 / % possible obs: 99 % / Redundancy: 7.07 % / CC1/2: 0.99 / Rsym value: 0.168 / Net I/σ(I): 8.4
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 7.01 % / Mean I/σ(I) obs: 1.82 / Num. unique obs: 24062 / CC1/2: 0.588 / Rsym value: 0.757 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FAU

5fau


Resolution: 2.05→49.817 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.45
RfactorNum. reflection% reflection
Rfree0.1949 24248 4.99 %
Rwork0.1672 --
obs0.1685 486153 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 85.55 Å2 / Biso mean: 21.0358 Å2 / Biso min: 6.2 Å2
Refinement stepCycle: final / Resolution: 2.05→49.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50048 0 48 4815 54911
Biso mean--24.98 27.81 -
Num. residues----6312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00751104
X-RAY DIFFRACTIONf_angle_d0.95669008
X-RAY DIFFRACTIONf_dihedral_angle_d21.81219360
X-RAY DIFFRACTIONf_chiral_restr0.0827488
X-RAY DIFFRACTIONf_plane_restr0.0069064
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.05-2.0710.2717590.22631402091
2.071-2.09530.25688030.224215598100
2.0953-2.12090.24898000.214515512100
2.1209-2.14770.25078720.21215445100
2.1477-2.1760.25137870.210515494100
2.176-2.20580.23948170.20011540399
2.2058-2.23730.25378240.20081550799
2.2373-2.27070.24447990.19931551999
2.2707-2.30620.2357960.1891538599
2.3062-2.3440.22328230.19071540899
2.344-2.38440.21637780.18561544299
2.3844-2.42780.21748010.1831530699
2.4278-2.47450.2127780.18611531498
2.4745-2.5250.22137750.18091519098
2.525-2.57990.22558030.179815524100
2.5799-2.63990.21418110.17315553100
2.6399-2.70590.20568160.171915477100
2.7059-2.7790.20048280.170215536100
2.779-2.86080.20658090.17261548599
2.8608-2.95310.20987940.16981545999
2.9531-3.05870.19938150.16981539899
3.0587-3.18110.19468530.16421519398
3.1811-3.32590.18468270.15541523298
3.3259-3.50120.1728010.149715574100
3.5012-3.72050.16678380.142115581100
3.7205-4.00760.15218190.136215501100
4.0076-4.41070.15218250.13681545199
4.4107-5.04840.15037750.1351527498
5.0484-6.35840.18558360.167715587100
6.3584-49.8170.16547860.15821553799

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