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- PDB-7dt0: Proline hydroxylase H11-N101I mutant -

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Basic information

Entry
Database: PDB / ID: 7dt0
TitleProline hydroxylase H11-N101I mutant
ComponentsPhytanoyl-CoA dioxygenase
KeywordsHYDROLASE / L-proline / Trans / Hydroxylase / AKG / mutant
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding / 2-OXOGLUTARIC ACID / : / PROLINE / Phytanoyl-CoA dioxygenase
Function and homology information
Biological speciesuncultured bacterium esnapd13 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsGong, W.G. / Yang, L.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Trans-3/4-proline-hydroxylase H11 with AKG and L-proline
Authors: Gong, W.G. / Yang, L.Y.
History
DepositionJan 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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: Phytanoyl-CoA dioxygenase
B: Phytanoyl-CoA dioxygenase
C: Phytanoyl-CoA dioxygenase
D: Phytanoyl-CoA dioxygenase
E: Phytanoyl-CoA dioxygenase
F: Phytanoyl-CoA dioxygenase
G: Phytanoyl-CoA dioxygenase
H: Phytanoyl-CoA dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,46932
Polymers238,9328
Non-polymers2,53724
Water5,278293
1
A: Phytanoyl-CoA dioxygenase
hetero molecules

H: Phytanoyl-CoA dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3678
Polymers59,7332
Non-polymers6346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445x-1/2,-y-1/2,-z1
Buried area3210 Å2
ΔGint-52 kcal/mol
Surface area22950 Å2
MethodPISA
2
B: Phytanoyl-CoA dioxygenase
E: Phytanoyl-CoA dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3678
Polymers59,7332
Non-polymers6346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-52 kcal/mol
Surface area21660 Å2
MethodPISA
3
C: Phytanoyl-CoA dioxygenase
D: Phytanoyl-CoA dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3678
Polymers59,7332
Non-polymers6346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-55 kcal/mol
Surface area21400 Å2
MethodPISA
4
F: Phytanoyl-CoA dioxygenase
G: Phytanoyl-CoA dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3678
Polymers59,7332
Non-polymers6346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-52 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.910, 138.640, 152.550
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Phytanoyl-CoA dioxygenase


Mass: 29866.559 Da / Num. of mol.: 8 / Mutation: N101I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) uncultured bacterium esnapd13 (environmental samples)
Production host: Escherichia coli (E. coli) / References: UniProt: S5TUM1
#2: Chemical
ChemComp-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2.7 Å3/Da / Density % sol: 54.41 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Potassium sodium tartrate tetrahydrate, 16% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.43→102.6 Å / Num. obs: 97664 / % possible obs: 99.8 % / Redundancy: 13.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.127 / Net I/σ(I): 35.44
Reflection shellResolution: 2.43→2.51 Å / Rmerge(I) obs: 0.721 / Num. unique obs: 8710 / CC1/2: 0.947 / Rrim(I) all: 0.773

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNS

6lns
PDB Unreleased entry


Resolution: 2.43→102.6 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.905 / SU B: 8.14 / SU ML: 0.189 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.363 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 4950 5.1 %RANDOM
Rwork0.201 ---
obs0.2044 92714 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 203.83 Å2 / Biso mean: 49.794 Å2 / Biso min: 17.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20 Å20 Å2
2--1.78 Å2-0 Å2
3----2.64 Å2
Refinement stepCycle: final / Resolution: 2.43→102.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15323 0 152 293 15768
Biso mean--66.82 45.19 -
Num. residues----1958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.01915867
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214720
X-RAY DIFFRACTIONr_angle_refined_deg1.8561.94421553
X-RAY DIFFRACTIONr_angle_other_deg1.134333665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3551931
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87522.838754
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.895152387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.67115134
X-RAY DIFFRACTIONr_chiral_restr0.120.22338
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02118058
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023872
LS refinement shellResolution: 2.43→2.493 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 359 -
Rwork0.25 6793 -
all-7152 -
obs--99.82 %

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