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- PDB-4h6q: Structure of oxidized Deinococcus radiodurans proline dehydrogena... -

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Basic information

Entry
Database: PDB / ID: 4h6q
TitleStructure of oxidized Deinococcus radiodurans proline dehydrogenase complexed with L-tetrahydrofuroic acid
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
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-ADENINE DINUCLEOTIDE / TETRAHYDROFURAN-2-CARBOXYLIC ACID / Proline dehydrogenase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.359 Å
AuthorsMin, L. / Tanner, J.J.
CitationJournal: Biochemistry / Year: 2012
Title: Crystal structures and kinetics of monofunctional proline dehydrogenase provide insight into substrate recognition and conformational changes associated with flavin reduction and product release.
Authors: Luo, M. / Arentson, B.W. / Srivastava, D. / Becker, D.F. / Tanner, J.J.
History
DepositionSep 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 28, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Sep 20, 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Proline dehydrogenase
C: Proline dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2337
Polymers70,3382
Non-polymers1,8955
Water8,557475
1
A: Proline dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1634
Polymers35,1691
Non-polymers9943
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Proline dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0713
Polymers35,1691
Non-polymers9022
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.469, 95.462, 136.393
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Proline dehydrogenase


Mass: 35168.961 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: DR_0814, PROLINE DEHYDROGENASE / Plasmid: PKA8H / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q9RW55, 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-TFB / TETRAHYDROFURAN-2-CARBOXYLIC ACID


Mass: 116.115 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H8O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / 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: 2.06 Å3/Da / Density % sol: 40.23 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.2 M magnesium chloride, 25% (w/v) PEG3350, 0.1 mM Bis-tris, 400 mM TETRAHYDROFURAN-2-CARBOXYLIC ACID, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2012
RadiationMonochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.359→78.209 Å / Num. obs: 124194 / % possible obs: 98.9 % / Redundancy: 3.6 % / Rsym value: 0.032 / Net I/σ(I): 17.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.359-1.433.70.4311.865458179180.43198.5
1.43-1.523.60.2423.262177171440.24299.8
1.52-1.623.50.1445.356071160670.14499.3
1.62-1.753.70.0948.156422150670.09499.9
1.75-1.923.60.0612.350601139070.0699.7
1.92-2.153.60.0391845230125110.03999.1
2.15-2.483.70.03121.941339110970.03199.2
2.48-3.043.50.02425.93246992080.02497
3.04-4.33.70.02126.22705873290.02198.3
4.3-78.2093.50.02321.61411040240.02394.2

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2G37

2g37


Resolution: 1.359→78.209 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.9002 / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 17.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1808 11592 5.02 %RANDOM
Rwork0.1482 ---
obs0.1498 124194 95.61 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.83 Å2 / Biso mean: 22.2135 Å2 / Biso min: 6.42 Å2
Refinement stepCycle: LAST / Resolution: 1.359→78.209 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4334 0 128 475 4937
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154726
X-RAY DIFFRACTIONf_angle_d1.7546451
X-RAY DIFFRACTIONf_chiral_restr0.102712
X-RAY DIFFRACTIONf_plane_restr0.008822
X-RAY DIFFRACTIONf_dihedral_angle_d18.9531856
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.359-1.37420.28823900.2596897728791
1.3742-1.39040.30834090.24997619802898
1.3904-1.40740.25344070.22947405781298
1.4074-1.42520.26574120.21997485789798
1.4252-1.44390.24473810.20727508788998
1.4439-1.46370.24123930.19247456784997
1.4637-1.48460.2284050.19347500790597
1.4846-1.50680.23983690.18367343771297
1.5068-1.53030.22083220.16777512783497
1.5303-1.55540.23850.15987234761995
1.5554-1.58230.18753670.15417006737391
1.5823-1.6110.18894210.13547317773896
1.611-1.6420.16433660.12987653801998
1.642-1.67550.17293500.12927530788098
1.6755-1.7120.17833690.13277568793798
1.712-1.75180.17143980.13017480787898
1.7518-1.79560.17524290.13037433786298
1.7956-1.84420.17074620.11977366782897
1.8442-1.89840.17583850.11777353773896
1.8984-1.95970.17353700.12177203757394
1.9597-2.02980.1783890.12317122751193
2.0298-2.1110.16713970.12727489788698
2.111-2.20710.16483520.12647417776997
2.2071-2.32350.17323820.12817357773996
2.3235-2.46910.18593670.13757331769896
2.4691-2.65970.1744060.14887149755594
2.6597-2.92740.1834110.15546697710888
2.9274-3.3510.1943680.16117197756594
3.351-4.22190.16424160.14517050746693
4.2219-78.2090.16033140.16576805711988

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