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- PDB-2g37: Structure of Thermus thermophilus L-proline dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 2g37
TitleStructure of Thermus thermophilus L-proline dehydrogenase
Componentsproline dehydrogenase/delta-1-pyrroline-5-carboxylate 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
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3270 / Proline dehydrogenase, bacteria and archaea / Proline oxidase family / TIM Barrel - #220 / Proline dehydrogenase domain / Proline dehydrogenase / FAD-linked oxidoreductase-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3270 / Proline dehydrogenase, bacteria and archaea / Proline oxidase family / TIM Barrel - #220 / Proline dehydrogenase domain / Proline dehydrogenase / FAD-linked oxidoreductase-like / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / : / Proline dehydrogenase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsTanner, J.J. / White, T.A.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Structure and Kinetics of Monofunctional Proline Dehydrogenase from Thermus thermophilus.
Authors: White, T.A. / Krishnan, N. / Becker, D.F. / Tanner, J.J.
History
DepositionFeb 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300Authors state that the true biological unit for the protein is not yet known and at this time their ...Authors state that the true biological unit for the protein is not yet known and at this time their data supports both monomer and dimer in solution

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
B: proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,1368
Polymers76,0922
Non-polymers2,0446
Water4,504250
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.067, 89.590, 94.316
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsData suggests monomer or dimer.

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Components

#1: Protein proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase


Mass: 38045.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27
Gene: proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
Plasmid: PKA8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: GenBank: 46199516, UniProt: Q72IB8*PLUS, EC: 1.5.99.8
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100 mM MgCl2, 100 mM imidazole pH 7.0, 16% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 0.97932 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Jan 23, 2005 / Details: beamline optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionRedundancy: 6.24 % / Av σ(I) over netI: 13.6 / Number: 294280 / Rmerge(I) obs: 0.079 / Χ2: 0.96 / D res high: 2 Å / D res low: 47.16 Å / Num. obs: 46775 / % possible obs: 98
Diffraction reflection shell

ID: 1

Highest resolution (Å)Lowest resolution (Å)Num. obs% possible obs (%)Rmerge(I) obsChi squaredRedundancyRejects
4.3147.16503099.90.0430.937.02252
3.424.3148391000.0480.857.35196
2.993.4247901000.0780.97.38319
2.712.9947471000.1190.997.36427
2.522.7147591000.1510.967.41264
2.372.5247201000.2030.987.34253
2.252.3747121000.2660.996.28186
2.152.25468499.40.2880.994.7134
2.072.15444994.20.31813.7852
22.07404586.30.3991.123.12126
ReflectionResolution: 2→47.16 Å / Num. obs: 46775 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.24 % / Rmerge(I) obs: 0.079 / Χ2: 0.96 / Net I/σ(I): 13.6 / Scaling rejects: 2209
Reflection shellResolution: 2→2.07 Å / % possible obs: 86.3 % / Redundancy: 3.12 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3 / Num. measured all: 12732 / Num. unique obs: 4045 / Χ2: 1.12

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Processing

Software
NameVersionClassificationNB
d*TREK9.2LDzdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
Blu-Icedata collection
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→47.16 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.805 / SU ML: 0.116 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.231 2356 5 %RANDOM
Rwork0.19 ---
all0.192 ---
obs0.192 46715 98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.526 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.85 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4796 0 138 250 5184
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0225044
X-RAY DIFFRACTIONr_angle_refined_deg1.5422.0276848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8725590
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.35121.814237
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.33315857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8911562
X-RAY DIFFRACTIONr_chiral_restr0.0950.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023803
X-RAY DIFFRACTIONr_nbd_refined0.20.22327
X-RAY DIFFRACTIONr_nbtor_refined0.3030.23443
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2352
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0880.27
X-RAY DIFFRACTIONr_mcbond_it0.7151.53039
X-RAY DIFFRACTIONr_mcangle_it1.11224707
X-RAY DIFFRACTIONr_scbond_it1.96932457
X-RAY DIFFRACTIONr_scangle_it3.1844.52141
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 151 -
Rwork0.242 2819 -
obs-2970 84.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5209-0.13780.67482.4799-0.09041.0344-0.0081-0.0805-0.10810.0650.00380.16280.1063-0.11210.0043-0.1252-0.0086-0.0305-0.0968-0.015-0.14220.72148.269.7188
21.2417-0.09380.50212.2397-0.25921.7803-0.0143-0.04790.3203-0.0534-0.05570.1132-0.2351-0.19180.07-0.11180.0191-0.0246-0.0893-0.0365-0.043826.314252.09268.9222
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 29625 - 316
22BB-5 - 29415 - 314

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