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- PDB-7e09: Trans-3/4-proline-hydroxylase H11 with 3-hydroxyl-proline -

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Basic information

Entry
Database: PDB / ID: 7000000000
TitleTrans-3/4-proline-hydroxylase H11 with 3-hydroxyl-proline
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 / 3-HYDROXYPROLINE / Phytanoyl-CoA dioxygenase
Function and homology information
Biological speciesuncultured bacterium esnapd13 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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 27, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond / Item: _atom_site.auth_atom_id / _atom_site.label_atom_id
Revision 2.1Nov 29, 2023Group: Refinement description / Category: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9992
Polymers29,8681
Non-polymers1311
Water43224
1
A: Phytanoyl-CoA dioxygenase
hetero molecules

A: Phytanoyl-CoA dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9974
Polymers59,7352
Non-polymers2622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area2650 Å2
ΔGint-16 kcal/mol
Surface area21440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.390, 75.390, 143.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122

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Components

#1: Protein Phytanoyl-CoA dioxygenase


Mass: 29867.504 Da / Num. of mol.: 1
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-HY3 / 3-HYDROXYPROLINE / (2S,3S)-3-hydroxypyrrolidine-2-carboxylic acid


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 3.42 Å3/Da / Density % sol: 64 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 0.7
Details: 0.7M Sodium citrate tribasic dihydrate, 0.1M Bis-Tris propane (pH 7.0)

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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: Dec 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.38→75.39 Å / Num. obs: 17231 / % possible obs: 99.9 % / Redundancy: 12.6 % / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.02 / Rrim(I) all: 0.07 / Χ2: 0.72 / Net I/σ(I): 86.4
Reflection shellResolution: 2.38→2.42 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.502 / Mean I/σ(I) obs: 10.3 / Num. unique obs: 856 / CC1/2: 0.969 / CC star: 0.992 / Rpim(I) all: 0.141 / Rrim(I) all: 0.521 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNS

6lns
PDB Unreleased entry


Resolution: 2.38→75.39 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.933 / SU B: 5.772 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.197
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2255 854 5 %RANDOM
Rwork0.1916 ---
obs0.1933 16341 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 140.05 Å2 / Biso mean: 50.263 Å2 / Biso min: 18.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.38→75.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2059 0 9 24 2092
Biso mean--65.5 45.94 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192140
X-RAY DIFFRACTIONr_bond_other_d0.0020.021987
X-RAY DIFFRACTIONr_angle_refined_deg1.8981.9422909
X-RAY DIFFRACTIONr_angle_other_deg1.09934557
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8145262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59822.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79915332
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3661519
X-RAY DIFFRACTIONr_chiral_restr0.1180.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212449
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02526
LS refinement shellResolution: 2.385→2.446 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 60 -
Rwork0.238 1165 -
all-1225 -
obs--98.47 %

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