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- PDB-2ekg: Structure of Thermus thermophilus Proline Dehydrogenase inactivat... -

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Basic information

Entry
Database: PDB / ID: 2ekg
TitleStructure of Thermus thermophilus Proline Dehydrogenase inactivated by N-propargylglycine
ComponentsProline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
KeywordsOXIDOREDUCTASE / proline dehydrogenase / flavoenzyme / PRODH / beta-alpha-barrel / suicide inhibitor / inactivation / flavocyanine
Function / homology
Function and homology information


L-proline catabolic process / proline dehydrogenase / proline dehydrogenase activity / L-proline catabolic process to L-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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsWhite, T.A. / Tanner, J.J.
CitationJournal: Biochemistry / Year: 2008
Title: Structural basis for the inactivation of Thermus thermophilus proline dehydrogenase by N-propargylglycine
Authors: White, T.A. / Johnson, W.H. / Whitman, C.P. / Tanner, J.J.
History
DepositionMar 23, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)79,7778
Polymers77,7332
Non-polymers2,0446
Water6,017334
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8884
Polymers38,8661
Non-polymers1,0223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8884
Polymers38,8661
Non-polymers1,0223
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.383, 90.104, 94.830
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsAUTHORS 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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Components

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


Mass: 38866.418 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: UniProt: Q72IB8, 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.: 334 / 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: 2.26 Å3/Da / Density % sol: 45.65 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 100MM MGCL2, 100MM IMIDAZOLE PH=7.0, 14% 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: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Feb 12, 2007 / Details: beamline optics
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→41.96 Å / Num. obs: 55959 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.82 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.059 / Χ2: 1 / Net I/σ(I): 12.5 / Scaling rejects: 2462
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.78 % / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 3.3 / Num. measured all: 32520 / Num. unique all: 5556 / Χ2: 1.34 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
d*TREK9.7Ldata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
Blu-Icedata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2G37

2g37


Resolution: 1.9→41.1 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.47 / SU ML: 0.086 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2817 5 %RANDOM
Rwork0.195 ---
obs0.196 55878 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.299 Å2
Baniso -1Baniso -2Baniso -3
1-0.18 Å20 Å20 Å2
2---1.28 Å20 Å2
3---1.1 Å2
Refinement stepCycle: LAST / Resolution: 1.9→41.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4750 0 138 334 5222
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224997
X-RAY DIFFRACTIONr_angle_refined_deg1.3142.0296779
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9135586
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.82921.681232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.15815835
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8391562
X-RAY DIFFRACTIONr_chiral_restr0.0870.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023761
X-RAY DIFFRACTIONr_nbd_refined0.1950.22345
X-RAY DIFFRACTIONr_nbtor_refined0.3040.23429
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2371
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.217
X-RAY DIFFRACTIONr_mcbond_it0.641.53010
X-RAY DIFFRACTIONr_mcangle_it1.03124664
X-RAY DIFFRACTIONr_scbond_it1.90932275
X-RAY DIFFRACTIONr_scangle_it3.0934.52115
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 203 -
Rwork0.239 3893 -
obs-4096 99.95 %
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)
18.97233.9998-9.60971.8255-3.648919.81590.0302-1.09350.4194-1.16230.4065-0.0649-0.24060.6856-0.43670.09240.10430.07730.20560.00020.05135.177.340528.939
23.9631-0.27530.31461.9836-0.64432.2667-0.0425-0.2648-0.38790.16740.09890.31430.1826-0.3337-0.0564-0.0196-0.0452-0.0484-0.0602-0.00980.03858.1684-1.34139.0823
32.3161-0.37531.44481.6516-0.10842.97410.0750.015-0.32670.0056-0.06520.04570.22710.0122-0.0097-0.0636-0.0015-0.0361-0.1418-0.0275-0.033328.0645-4.37110.5571
41.1383-0.25950.29831.90240.06090.7912-0.00990.0760.0335-0.1171-0.01220.06770.01730.01620.0221-0.1135-0.011-0.0388-0.1217-0.003-0.133524.186815.26196.9649
57.8106-11.1822-3.489129.06455.67388.9586-0.6969-1.67110.73820.26831.4128-0.7107-0.82570.6978-0.71590.03-0.0201-0.02130.2754-0.0896-0.041310.22363.951719.9031
610.10041.88661.01811.1273-1.21242.6414-0.39420.14740.95990.14990.2850.22560.2752-0.80740.10920.03310.04620.030.3383-0.13580.09387.357958.654516.4618
71.6319-0.54791.29972.3808-0.79624.0964-0.1770.01460.4403-0.0324-0.0662-0.2227-0.65220.0210.24320.0174-0.011-0.0568-0.1476-0.01150.089632.134863.746910.3175
81.15030.03950.12962.3926-0.36031.43520.03510.15650.127-0.3992-0.03560.0361-0.0593-0.03240.0004-0.04320.0292-0.0203-0.10990.0002-0.086928.605847.07730.8916
91.85110.02490.54714.30030.30081.12130.0356-0.06530.02340.17250.0041-0.13880.0473-0.0326-0.0397-0.1345-0.0028-0.0346-0.1248-0.021-0.124631.895840.527918.2294
102.4113-1.31910.99732.9731-0.94121.8678-0.0601-0.21240.19310.03140.09530.2838-0.1289-0.3403-0.0353-0.08730.0078-0.0379-0.0647-0.05530.004425.785454.573218.5589
Refinement TLS group

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

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA5 - 1925 - 39
22AA20 - 6340 - 83
33AA64 - 12184 - 141
44AA122 - 280142 - 300
55AA281 - 293301 - 313
66BB-5 - 3515 - 55
77BB36 - 9956 - 119
88BB100 - 225120 - 245
99BB226 - 259246 - 279
1010BB260 - 293280 - 313

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