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- PDB-8h7y: Trans-3/4-proline-hydroxylase H11 with AKG and L-proline -

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Basic information

Entry
Database: PDB / ID: 8h7y
TitleTrans-3/4-proline-hydroxylase H11 with AKG and L-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 / 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.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 1.1May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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
Water5,242291
1
A: Phytanoyl-CoA dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4264
Polymers30,1091
Non-polymers3173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phytanoyl-CoA dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4264
Polymers30,1091
Non-polymers3173
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.437, 106.437, 145.016
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H9NO2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 3.4 Å3/Da / Density % sol: 63.87 %
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: 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: 2.139→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 / 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
REFMAC5.8.0352refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LNS

6lns
PDB Unreleased entry


Resolution: 2.14→39.79 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 9.184 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.75 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21603 2167 4.9 %RANDOM
Rwork0.15234 ---
obs0.15547 41919 94.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.658 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å2-0 Å2-0 Å2
2---0.13 Å2-0 Å2
3---0.26 Å2
Refinement stepCycle: 1 / Resolution: 2.14→39.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 0 38 291 4544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124374
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163864
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.6425940
X-RAY DIFFRACTIONr_angle_other_deg0.4361.558994
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9745532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.5179.73738
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29310678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.2636
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025082
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02910
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.3773.8252143
X-RAY DIFFRACTIONr_mcbond_other6.3763.8252143
X-RAY DIFFRACTIONr_mcangle_it7.7865.7272670
X-RAY DIFFRACTIONr_mcangle_other7.7855.7272671
X-RAY DIFFRACTIONr_scbond_it7.444.1232231
X-RAY DIFFRACTIONr_scbond_other7.4384.1232232
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.1186.0223271
X-RAY DIFFRACTIONr_long_range_B_refined8.49149.1454900
X-RAY DIFFRACTIONr_long_range_B_other8.49149.1444901
X-RAY DIFFRACTIONr_rigid_bond_restr4.48238238
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.14→2.195 Å
RfactorNum. reflection% reflection
Rfree0.287 159 -
Rwork0.157 3075 -
obs--95.37 %

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