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- PDB-7e01: Trans-3/4-proline-hydroxylase H11 in the sixth reaction state -

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Basic information

Entry
Database: PDB / ID: 70
TitleTrans-3/4-proline-hydroxylase H11 in the sixth reaction state
ComponentsPhytanoyl-CoA dioxygenase
KeywordsHYDROLASE / L-proline / Trans / Hydroxylase / AKG
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / 2-oxoglutarate-dependent dioxygenase activity / iron ion binding / OXYGEN ATOM / PROLINE / Phytanoyl-CoA dioxygenase
Function and homology information
Biological speciesuncultured bacterium esnapd13 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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 3-Hydroxyl-proline
Authors: Gong, W.G. / Yang, L.Y.
History
DepositionJan 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 2, 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
Revision 1.2Apr 17, 2024Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.pdbx_details

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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)30,0154
Polymers29,8681
Non-polymers1473
Water3,423190
1
A: Phytanoyl-CoA dioxygenase
hetero molecules

A: Phytanoyl-CoA dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0298
Polymers59,7352
Non-polymers2946
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_455-x-1,y,-z1
Buried area2410 Å2
ΔGint-20 kcal/mol
Surface area21560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.367, 75.367, 144.753
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-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 3.44 Å3/Da / Density % sol: 64.26 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.7 M Sodium citrate tribasic dihydrate, 0.1 M 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: 1.72→75.37 Å / Num. obs: 44839 / % possible obs: 99.8 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 184.5
Reflection shellResolution: 1.72→1.75 Å / Redundancy: 13.3 % / Rmerge(I) obs: 0.588 / Num. unique obs: 2214 / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNS

6lns
PDB Unreleased entry


Resolution: 1.72→75.37 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.047 / SU ML: 0.067 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.095 / ESU R Free: 0.096 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2363 2204 4.9 %RANDOM
Rwork0.2075 ---
obs0.2089 42635 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.86 Å2 / Biso mean: 36.45 Å2 / Biso min: 13.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.2 Å2-0 Å2-0 Å2
2--0.2 Å2-0 Å2
3----0.41 Å2
Refinement stepCycle: final / Resolution: 1.72→75.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2069 0 10 190 2269
Biso mean--42.25 44.15 -
Num. residues----264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0192152
X-RAY DIFFRACTIONr_bond_other_d0.0020.021988
X-RAY DIFFRACTIONr_angle_refined_deg2.4581.942929
X-RAY DIFFRACTIONr_angle_other_deg1.22134554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1275266
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.79222.952105
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50515328
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.1311519
X-RAY DIFFRACTIONr_chiral_restr0.1690.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0212474
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02529
LS refinement shellResolution: 1.722→1.767 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 159 -
Rwork0.251 3008 -
all-3167 -
obs--97.45 %

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