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

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Basic information

Entry
Database: PDB / ID: 6vxe
TitleCrystal structure of hydroxyproline dehydratase (HypD) from Clostridioides difficile with substrate trans-4-hydroxy-L-proline bound
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 / 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
4-HYDROXYPROLINE / Trans-4-hydroxy-L-proline dehydratase
Similarity search - Component
Biological speciesClostridioides difficile 70-100-2010 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.464 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)732,70216
Polymers731,6538
Non-polymers1,0498
Water26,2301456
1
A: Trans-4-hydroxy-L-proline dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,5882
Polymers91,4571
Non-polymers1311
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)91,5882
Polymers91,4571
Non-polymers1311
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)91,5882
Polymers91,4571
Non-polymers1311
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)91,5882
Polymers91,4571
Non-polymers1311
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)91,5882
Polymers91,4571
Non-polymers1311
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)91,5882
Polymers91,4571
Non-polymers1311
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)91,5882
Polymers91,4571
Non-polymers1311
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)91,5882
Polymers91,4571
Non-polymers1311
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, trans-4-hydroxy-L-proline dehydratase
#2: Chemical
ChemComp-HYP / 4-HYDROXYPROLINE / HYDROXYPROLINE


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1456 / 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: 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, 100 mM HEPES pH 7.5, 4 mM trans-4-hydroxy-L-proline. Cryoprotectant contained 25% (v/v) dimethyl sulfoxide (DMSO)

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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: Apr 8, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.464→50 Å / Num. obs: 278476 / % possible obs: 99.7 % / Redundancy: 6.98 % / CC1/2: 0.994 / Rsym value: 0.204 / Net I/σ(I): 10.75
Reflection shellResolution: 2.52→2.59 Å / Mean I/σ(I) obs: 2.12 / Num. unique obs: 44812 / CC1/2: 0.721 / Rsym value: 0.975 / % possible all: 99.4

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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: 2.464→49.295 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2296 13593 5 %
Rwork0.1945 258211 -
obs0.1962 271804 96.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.02 Å2 / Biso mean: 36.2598 Å2 / Biso min: 15.67 Å2
Refinement stepCycle: final / Resolution: 2.464→49.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms50072 0 72 1456 51600
Biso mean--28.57 35.94 -
Num. residues----6312
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01251208
X-RAY DIFFRACTIONf_angle_d1.24369168
X-RAY DIFFRACTIONf_dihedral_angle_d22.04919392
X-RAY DIFFRACTIONf_chiral_restr0.0767512
X-RAY DIFFRACTIONf_plane_restr0.0089088
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4641-2.49210.33421380.292265630
2.4921-2.52140.32623550.2849658174
2.5214-2.55210.29364490.2736864997
2.5521-2.58440.32924510.2659890999
2.5844-2.61840.30274840.2612884099
2.6184-2.65430.29534490.2504882799
2.6543-2.69220.28344700.2678915100
2.6922-2.73240.33174670.2688965100
2.7324-2.77510.32224810.25218908100
2.7751-2.82060.2914720.24498876100
2.8206-2.86920.28454610.23788933100
2.8692-2.92140.28154630.23348903100
2.9214-2.97760.27124570.23378951100
2.9776-3.03830.27684710.23398931100
3.0383-3.10440.25144790.22978884100
3.1044-3.17660.26365030.22668858100
3.1766-3.2560.26374970.2228907100
3.256-3.3440.2544620.217893999
3.344-3.44240.25274630.2091869198
3.4424-3.55350.22774470.19888923100
3.5535-3.68050.21984800.18728922100
3.6805-3.82780.21574820.18178973100
3.8278-4.00190.20364720.17418879100
4.0019-4.21280.1964770.16368931100
4.2128-4.47660.17524620.15338905100
4.4766-4.82190.18924560.1469893299
4.8219-5.30670.18624520.1568880598
5.3067-6.07340.19514910.16658924100
6.0734-7.64720.19474300.16159027100
7.6472-49.2950.14634720.1291886798

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