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- PDB-1e5r: Proline 3-hydroxylase (type II) -apo form -

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Basic information

Entry
Database: PDB / ID: 1e5r
TitleProline 3-hydroxylase (type II) -apo form
ComponentsPROLINE OXIDASE
KeywordsOXIDOREDUCTASE / OXYGENASE / 2-OXOGLUTARATE DEPENDENT OXYGENASE
Function / homology
Function and homology information


proline 3-hydroxylase / proline 3-hydroxylase activity / metal ion binding
Similarity search - Function
Proline Oxidase; Chain: A, Domain 2 / L-proline 3-hydroxylase, C-terminal domain / L-proline 3-hydroxylase, C-terminal / L-proline 3-hydroxylase, C-terminal domain superfamily / L-proline 3-hydroxylase, C-terminal / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Jelly Rolls ...Proline Oxidase; Chain: A, Domain 2 / L-proline 3-hydroxylase, C-terminal domain / L-proline 3-hydroxylase, C-terminal / L-proline 3-hydroxylase, C-terminal domain superfamily / L-proline 3-hydroxylase, C-terminal / Aspartyl/asparaginy/proline hydroxylase / Aspartyl/Asparaginyl beta-hydroxylase / B-lactam Antibiotic, Isopenicillin N Synthase; Chain / Isopenicillin N synthase-like superfamily / Jelly Rolls / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
L-proline cis-3-hydroxylase 2
Similarity search - Component
Biological speciesSTREPTOMYCES SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.3 Å
AuthorsClifton, I.J. / Hsueh, L.C. / Baldwin, J.E. / Schofield, C.J. / Harlos, K.
CitationJournal: Eur.J.Biochem. / Year: 2001
Title: Structure of proline 3-hydroxylase. Evolution of the family of 2-oxoglutarate dependent oxygenases.
Authors: Clifton, I.J. / Hsueh, L.C. / Baldwin, J.E. / Harlos, K. / Schofield, C.J.
History
DepositionJul 28, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 2, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details
Revision 1.4May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROLINE OXIDASE
B: PROLINE OXIDASE


Theoretical massNumber of molelcules
Total (without water)67,2382
Polymers67,2382
Non-polymers00
Water4,648258
1
A: PROLINE OXIDASE

B: PROLINE OXIDASE


Theoretical massNumber of molelcules
Total (without water)67,2382
Polymers67,2382
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_664-x+y+1,-x+1,z-1/31
Unit cell
Length a, b, c (Å)72.540, 72.540, 223.920
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.543931, 0.818673, -0.184157), (0.833083, -0.500548, 0.235422), (0.100554, -0.281472, -0.954286)
Vector: 2.3383, 42.1777, 75.6284)

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Components

#1: Protein PROLINE OXIDASE


Mass: 33618.773 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) STREPTOMYCES SP. (bacteria) / Strain: TH1 / References: UniProt: O09345
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / 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: 2.67 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 2M AMMONIUM SULFATE, 50MM MES BUFFER, PH6, pH 6.00
Crystal grow
*PLUS
Temperature: 21 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
250 mMMES1droppH6.0
350 mMHEPES1reservoirpH7.5
42 %PEG4001reservoir
52.0 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9535
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 2.29→28.51 Å / Num. obs: 31836 / % possible obs: 98.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 12.6
Reflection shellResolution: 2.29→2.37 Å / Redundancy: 2.94 % / Rmerge(I) obs: 0.275 / % possible all: 95.4
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / Num. obs: 31128 / Num. measured all: 357708
Reflection shell
*PLUS
Highest resolution: 2.3 Å

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→28.53 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.275 1252 4 %RANDOM
Rwork0.225 ---
obs0.225 31128 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 78.5125 Å2 / ksol: 0.377423 e/Å3
Displacement parametersBiso mean: 51.1 Å2
Baniso -1Baniso -2Baniso -3
1-2.46 Å23.16 Å20 Å2
2--2.46 Å20 Å2
3----4.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.3→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4216 0 0 258 4474
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.381.5
X-RAY DIFFRACTIONc_mcangle_it4.772
X-RAY DIFFRACTIONc_scbond_it4.862
X-RAY DIFFRACTIONc_scangle_it6.352.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 210 4.3 %
Rwork0.267 4721 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.202 / Rfactor Rfree: 0.253
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.044
X-RAY DIFFRACTIONc_angle_deg2.7
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.32

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