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- PDB-8h81: Trans-3/4-proline-hydroxylase H11 with 4-Hydroxyl-proline -

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Basic information

Entry
Database: PDB / ID: 8h81
TitleTrans-3/4-proline-hydroxylase H11 with 4-Hydroxyl-proline
ComponentsPhytanoyl-CoA dioxygenase
KeywordsSTRUCTURAL PROTEIN / L-proline / Trans / Hydroxylase / AKG / HYDROLASE
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding / 4-HYDROXYPROLINE / Phytanoyl-CoA dioxygenase
Function and homology information
Biological speciesuncultured bacterium esnapd13 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsGong, W.M. / Hu, X.Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2023
Title: Structures of L-proline trans-hydroxylase reveal the catalytic specificity and provide deeper insight into AKG-dependent hydroxylation.
Authors: Hu, X. / Huang, X. / Liu, J. / Zheng, P. / Gong, W. / Yang, L.
History
DepositionOct 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9992
Polymers29,8681
Non-polymers1311
Water2,954164
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.289, 75.289, 144.544
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-HYP / 4-HYDROXYPROLINE / HYDROXYPROLINE


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.: 164 / 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: 3.43 Å3/Da / Density % sol: 64.13 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.7M Sodium citrate tribasic dihydrate and 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: Oct 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.84→75.29 Å / Num. obs: 36880 / % possible obs: 99.9 % / Redundancy: 24.4 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.012 / Rrim(I) all: 0.059 / Χ2: 0.843 / Net I/σ(I): 152.6
Reflection shellResolution: 1.84→1.87 Å / Redundancy: 25.1 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 7.8 / Num. unique obs: 1801 / CC1/2: 0.97 / CC star: 0.992 / Rpim(I) all: 0.107 / Rrim(I) all: 0.54 / Χ2: 0.46 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
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: 1.84→24.63 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.959 / SU B: 4.308 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.113 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1819 1952 5.3 %RANDOM
Rwork0.1491 ---
obs0.1509 34875 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 130.04 Å2 / Biso mean: 36.834 Å2 / Biso min: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.45 Å2
Refinement stepCycle: final / Resolution: 1.84→24.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 9 164 2267
Biso mean--43.62 44.61 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0122205
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161961
X-RAY DIFFRACTIONr_angle_refined_deg0.9391.6433007
X-RAY DIFFRACTIONr_angle_other_deg0.3441.554567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4935277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg14.5871021
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.50410348
X-RAY DIFFRACTIONr_chiral_restr0.050.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022587
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_rigid_bond_restr4.9134166
LS refinement shellResolution: 1.84→1.888 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 134 -
Rwork0.161 2497 -
all-2631 -
obs--98.8 %

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