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- PDB-7e07: Trans-3/4-proline-hydroxylase H11 with AKG and L-proline -

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Basic information

Entry
Database: PDB / ID: 70000000
TitleTrans-3/4-proline-hydroxylase H11 with AKG and L-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 / 2-OXOGLUTARIC ACID / : / PROLINE / Phytanoyl-CoA dioxygenase
Function and homology information
Biological speciesuncultured bacterium esnapd13 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.14 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 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,8528
Polymers60,2182
Non-polymers6346
Water7,026390
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2720 Å2
ΔGint-30 kcal/mol
Surface area22630 Å2
Unit cell
Length a, b, c (Å)106.437, 106.437, 145.016
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Phytanoyl-CoA dioxygenase


Mass: 30108.789 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2
#4: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 64.01 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 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: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.14→85.81 Å / Num. obs: 44086 / % possible obs: 94.46 % / Redundancy: 28.6 % / Rmerge(I) obs: 0.132 / Rpim(I) all: 0.025 / Rrim(I) all: 0.135 / Χ2: 3.133 / Net I/σ(I): 8.3
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 28.9 % / Rmerge(I) obs: 0.529 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2262 / CC1/2: 0.981 / CC star: 0.995 / Rpim(I) all: 0.1 / Rrim(I) all: 0.538 / Χ2: 1.419 / % possible all: 99

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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: 2.14→85.81 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.936 / SU B: 4.364 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.188 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 2167 4.9 %RANDOM
Rwork0.1885 ---
obs0.1907 41919 94.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 123.01 Å2 / Biso mean: 39 Å2 / Biso min: 15.86 Å2
Baniso -1Baniso -2Baniso -3
1-1.69 Å2-0 Å2-0 Å2
2--1.69 Å2-0 Å2
3----3.38 Å2
Refinement stepCycle: final / Resolution: 2.14→85.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4218 0 38 390 4646
Biso mean--38.11 47.86 -
Num. residues----535
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194391
X-RAY DIFFRACTIONr_bond_other_d0.0020.024068
X-RAY DIFFRACTIONr_angle_refined_deg1.9631.9425968
X-RAY DIFFRACTIONr_angle_other_deg1.09639335
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5035536
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.03323.394218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00115684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1341536
X-RAY DIFFRACTIONr_chiral_restr0.1180.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0215042
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021066
LS refinement shellResolution: 2.14→2.195 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.317 160 -
Rwork0.204 3082 -
obs--95.38 %

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