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- PDB-8h85: Trans-3/4-proline-hydroxylase H11 with 3-hydroxyl-proline -

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Basic information

Entry
Database: PDB / ID: 8h85
TitleTrans-3/4-proline-hydroxylase H11 with 3-hydroxyl-proline
ComponentsPhytanoyl-CoA dioxygenase
KeywordsSTRUCTURAL PROTEIN / L-proline / Trans / Hydroxylase / AKG / HYDROLASE
Function / homologyPhytanoyl-CoA dioxygenase / Phytanoyl-CoA dioxygenase (PhyH) / dioxygenase activity / 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.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 2.0Nov 15, 2023Group: Atomic model / Data collection
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_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

Downloads & links

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Assembly

Deposited unit
A: Phytanoyl-CoA dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2402
Polymers30,1091
Non-polymers1311
Water1,09961
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)75.390, 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: 30108.789 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 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 3.39 Å3/Da / Density % sol: 63.71 %
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: 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→50 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): 8.2 / Num. measured all: 217057
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.38-2.4213.20.5028560.9690.1410.5210.423100
2.42-2.4713.30.4938050.9680.1390.5130.468100
2.47-2.5113.10.4348680.9670.1230.4520.646100
2.51-2.5613.10.3758210.9790.1060.390.445100
2.56-2.62130.3258520.9830.0930.3380.458100
2.62-2.6812.70.2768320.980.080.2870.471100
2.68-2.7512.40.2458570.9870.0720.2550.45100
2.75-2.8211.60.1988350.9910.060.2070.472100
2.82-2.912.70.1598550.9930.0460.1660.50699.9
2.9-313.50.1298550.9970.0360.1340.50999.9
3-3.1113.40.1118400.9970.0310.1150.524100
3.11-3.2313.20.0918550.9980.0260.0950.546100
3.23-3.38130.0738560.9990.0210.0760.6100
3.38-3.5512.70.0618600.9990.0180.0640.642100
3.55-3.7812.10.0478700.9990.0140.0490.725100
3.78-4.0712.20.048590.9990.0120.0420.83499.8
4.07-4.48130.03687910.010.0370.90199.7
4.48-5.1312.50.03388610.010.0341.0399.9
5.13-6.4611.20.0359030.9990.0110.0370.91100
6.46-5010.60.0329870.9990.0110.0342.96398.8

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNS

6lns
PDB Unreleased entry


Resolution: 2.38→32.82 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.954 / SU B: 9.857 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1881 854 5 %RANDOM
Rwork0.1642 ---
obs0.1654 16341 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 150.23 Å2 / Biso mean: 49.303 Å2 / Biso min: 19.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å2-0 Å2
2---0.49 Å2-0 Å2
3---0.98 Å2
Refinement stepCycle: final / Resolution: 2.38→32.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 9 61 2124
Biso mean--71.3 47.14 -
Num. residues----262
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122141
X-RAY DIFFRACTIONr_bond_other_d0.0050.0161894
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.642913
X-RAY DIFFRACTIONr_angle_other_deg0.5621.5524402
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.85263
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.5331020
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.28510326
X-RAY DIFFRACTIONr_chiral_restr0.0750.2313
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022506
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02458
LS refinement shellResolution: 2.385→2.446 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.224 60 -
Rwork0.189 1159 -
all-1219 -
obs--98.47 %
Refinement TLS params.Method: refined / Origin x: -20.2313 Å / Origin y: 5.4531 Å / Origin z: -9.4102 Å
111213212223313233
T0.0364 Å20.04 Å20.0178 Å2-0.1993 Å2-0.0273 Å2--0.0354 Å2
L1.4082 °20.1521 °2-0.7702 °2-0.2658 °20.0779 °2--2.0121 °2
S0.0985 Å °-0.0259 Å °0.0887 Å °-0.0132 Å °-0.0362 Å °-0.0432 Å °-0.1203 Å °-0.3803 Å °-0.0623 Å °

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