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- PDB-7e05: Trans-3/4-proline-hydroxylase H11 apo structure -

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Basic information

Entry
Database: PDB / ID: 700000
TitleTrans-3/4-proline-hydroxylase H11 apo structure
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 / Phytanoyl-CoA dioxygenase
Function and homology information
Biological speciesuncultured bacterium esnapd13 (environmental samples)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.88 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


Theoretical massNumber of molelcules
Total (without water)60,2182
Polymers60,2182
Non-polymers00
Water9,962553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint1 kcal/mol
Surface area22860 Å2
Unit cell
Length a, b, c (Å)106.500, 106.500, 143.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11B-560-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O

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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: 63.68 %
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: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.88→50 Å / Num. obs: 64234 / % possible obs: 99.7 % / Redundancy: 15.2 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 25.3
Reflection shellResolution: 1.88→1.93 Å / Mean I/σ(I) obs: 5.48 / Num. unique obs: 4933 / CC1/2: 0.951 / % possible all: 99.8

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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: 5NCI

5nci


Resolution: 1.88→42.78 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.538 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.107 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.211 3381 5 %RANDOM
Rwork0.171 ---
obs0.173 64234 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 145.31 Å2 / Biso mean: 31.72 Å2 / Biso min: 12 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.88→42.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4170 0 0 553 4723
Biso mean---38.19 -
Num. residues----526
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0194328
X-RAY DIFFRACTIONr_bond_other_d0.0020.024032
X-RAY DIFFRACTIONr_angle_refined_deg2.0861.9395883
X-RAY DIFFRACTIONr_angle_other_deg1.11239248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3735530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.43623.088217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80915685
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0351539
X-RAY DIFFRACTIONr_chiral_restr0.1420.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0214959
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021064
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_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.88→1.93 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 244 -
Rwork0.26 4601 -
all-4845 -
obs--98.58 %

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