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- PDB-5m42: Structure of Thermus thermophilus L-proline dehydrogenase lacking... -

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Basic information

Entry
Database: PDB / ID: 5m42
TitleStructure of Thermus thermophilus L-proline dehydrogenase lacking alpha helices A, B and C
ComponentsProline dehydrogenase
KeywordsOXIDOREDUCTASE / BETA8-ALPHA8-BARREL / FLAVOENZYME
Function / homology
Function and homology information


proline catabolic process / proline dehydrogenase / proline dehydrogenase activity / proline catabolic process to glutamate / FAD binding / protein homodimerization activity
Similarity search - Function
Proline dehydrogenase, bacteria and archaea / Proline oxidase family / TIM Barrel - #220 / Proline dehydrogenase domain / Proline dehydrogenase / FAD-linked oxidoreductase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Proline dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMartinez-Julvez, M. / Huijbers, M.M.E. / van Berkel, W.J.H. / Medina, M.
Funding support Spain, Netherlands, 2items
OrganizationGrant numberCountry
MINECOBIO2013-42978-P Spain
NWO and the Graduate School VLAGERA-IB-2 Netherlands
CitationJournal: Sci Rep / Year: 2017
Title: Proline dehydrogenase from Thermus thermophilus does not discriminate between FAD and FMN as cofactor.
Authors: Huijbers, M.M. / Martinez-Julvez, M. / Westphal, A.H. / Delgado-Arciniega, E. / Medina, M. / van Berkel, W.J.
History
DepositionOct 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proline dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8832
Polymers32,4271
Non-polymers4561
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area790 Å2
ΔGint-5 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.920, 131.920, 36.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Proline dehydrogenase / PRODH / Proline oxidase / TtPRODH


Mass: 32426.514 Da / Num. of mol.: 1 / Mutation: Delection of alpha helices A,B and C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_C1214 / Production host: Escherichia coli (E. coli) / References: UniProt: Q72IB8, proline dehydrogenase
#2: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 2.84 Å3/Da / Density % sol: 56.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 20 % v/v 2-propanol, 0.2 M calcium chloride dihydrate and 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.2→65.96 Å / Num. obs: 18892 / % possible obs: 100 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.139 / Net I/σ(I): 10.9
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 8.7 % / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G37

2g37


Resolution: 2.2→60.01 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.356 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.171
RfactorNum. reflection% reflectionSelection details
Rfree0.22484 972 5.1 %RANDOM
Rwork0.18227 ---
obs0.18454 17907 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 37.672 Å2
Baniso -1Baniso -2Baniso -3
1--1.03 Å2-0.51 Å2-0 Å2
2---1.03 Å20 Å2
3---3.33 Å2
Refinement stepCycle: 1 / Resolution: 2.2→60.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1976 0 31 64 2071
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0192048
X-RAY DIFFRACTIONr_bond_other_d0.0020.022015
X-RAY DIFFRACTIONr_angle_refined_deg2.0812.0222772
X-RAY DIFFRACTIONr_angle_other_deg1.09634618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7165241
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62422.12199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.43315367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6511526
X-RAY DIFFRACTIONr_chiral_restr0.1150.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0212248
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02466
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_it3.2173.436967
X-RAY DIFFRACTIONr_mcbond_other3.2023.433966
X-RAY DIFFRACTIONr_mcangle_it4.6135.1461207
X-RAY DIFFRACTIONr_mcangle_other4.6125.1481208
X-RAY DIFFRACTIONr_scbond_it4.3834.0291081
X-RAY DIFFRACTIONr_scbond_other4.3694.0311079
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7755.8521565
X-RAY DIFFRACTIONr_long_range_B_refined8.98229.4222398
X-RAY DIFFRACTIONr_long_range_B_other8.9929.4052391
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 61 -
Rwork0.269 1307 -
obs--100 %

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