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- PDB-4h6r: Structure of reduced Deinococcus radiodurans proline dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 4h6r
TitleStructure of reduced Deinococcus radiodurans proline dehydrogenase
ComponentsProline dehydrogenase
KeywordsOXIDOREDUCTASE / BETA8-ALPHA8-BARREL / FLAVOENZYME
Function / homology
Function and homology information


L-proline catabolic process / proline dehydrogenase / proline dehydrogenase activity / L-proline catabolic process to L-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
ACETATE ION / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE / Proline dehydrogenase
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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)71,9725
Polymers70,3382
Non-polymers1,6343
Water5,350297
1
A: Proline dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9572
Polymers35,1691
Non-polymers7881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: Proline dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0163
Polymers35,1691
Non-polymers8472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.352, 95.688, 135.964
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-FDA / DIHYDROFLAVINE-ADENINE DINUCLEOTIDE


Mass: 787.566 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H35N9O15P2
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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 Å3/Da / Density % sol: 38.64 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.2 M magnesium chloride, 25% (w/v) PEG3350, and 0.1 mM Bis-tris, pH 5.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Aug 11, 2012 / Details: BEAMLINE OPTICS
RadiationMonochromator: BEAMLINE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→47.844 Å / Num. obs: 58089 / % possible obs: 100 % / Redundancy: 7.2 % / Rsym value: 0.065 / Net I/σ(I): 22.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.8470.8370.95835783400.837100
1.84-1.967.20.5031.55705979540.503100
1.96-2.097.30.2672.95392974320.267100
2.09-2.267.30.15655059669540.156100
2.26-2.477.30.11174702264260.111100
2.47-2.777.20.07510.34226958490.075100
2.77-3.27.30.04417.13765851830.044100
3.2-3.917.10.02824.23138244380.028100
3.91-5.5370.02229.12424234770.022100
5.53-47.8446.60.01928.31337620360.01999.8

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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: 1.75→40.959 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.868 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0.95 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 5617 5.1 %RANDOM
Rwork0.1824 ---
obs0.184 55029 99.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.09 Å2 / Biso mean: 28.7038 Å2 / Biso min: 8.79 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40.959 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4150 0 110 297 4557
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134350
X-RAY DIFFRACTIONf_angle_d1.4535925
X-RAY DIFFRACTIONf_chiral_restr0.105659
X-RAY DIFFRACTIONf_plane_restr0.007768
X-RAY DIFFRACTIONf_dihedral_angle_d15.6951583
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 (%)
1.75-1.76990.31451950.30323463365899
1.7699-1.79070.36622100.29334863696100
1.7907-1.81260.34122060.278734903696100
1.8126-1.83550.27072190.229234433662100
1.8355-1.85960.2641710.22434203591100
1.8596-1.88510.25352020.221535543756100
1.8851-1.91210.25631890.239634313620100
1.9121-1.94060.24551720.24383485365799
1.9406-1.97090.251700.207535423712100
1.9709-2.00320.23291770.194134273604100
2.0032-2.03780.22811940.185634793673100
2.0378-2.07480.24741950.188334863681100
2.0748-2.11470.25751720.184134743646100
2.1147-2.15790.18091600.177135573717100
2.1579-2.20480.19351810.17334583639100
2.2048-2.25610.20291790.166434843663100
2.2561-2.31250.2181810.172634933674100
2.3125-2.3750.19551780.170435013679100
2.375-2.44490.20511750.173435003675100
2.4449-2.52380.20651780.177335023680100
2.5238-2.6140.21721900.178534633653100
2.614-2.71860.21352350.181234843719100
2.7186-2.84230.21182050.173134433648100
2.8423-2.99220.23871990.18834453644100
2.9922-3.17960.19411610.178935383699100
3.1796-3.42490.22182110.173734593670100
3.4249-3.76940.15322000.151934723672100
3.7694-4.31430.18631820.154735033685100
4.3143-5.43360.1831760.163734883664100
5.4336-40.9590.21691540.198935043658100

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