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- PDB-3axb: Structure of a dye-linked L-proline dehydrogenase from the aerobi... -

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Basic information

Entry
Database: PDB / ID: 3axb
TitleStructure of a dye-linked L-proline dehydrogenase from the aerobic hyperthermophilic archaeon, Aeropyrum pernix
ComponentsPutative oxidoreductase
KeywordsOXIDOREDUCTASE / dinucleotide-binding fold
Function / homology
Function and homology information


nucleotide binding / membrane / cytoplasm
Similarity search - Function
FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PROLINE / Oxidoreductase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.92 Å
AuthorsSakuraba, H. / Ohshima, T. / Satomura, T. / Yoneda, K. / Hara, Y.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structure of Novel Dye-linked L-Proline Dehydrogenase from Hyperthermophilic Archaeon Aeropyrum pernix
Authors: Sakuraba, H. / Satomura, T. / Kawakami, R. / Kim, K. / Hara, Y. / Yoneda, K. / Ohshima, T.
History
DepositionApr 1, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2Jun 20, 2012Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_leaving_atom_flag / _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: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7459
Polymers49,4721
Non-polymers1,2738
Water3,675204
1
A: Putative oxidoreductase
hetero molecules

A: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,49118
Polymers98,9442
Non-polymers2,54616
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_646y+1,x-1,-z+11
Buried area4060 Å2
ΔGint-28 kcal/mol
Surface area32210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.182, 60.182, 274.096
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Putative oxidoreductase / L-proline dehydrogenase


Mass: 49472.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9YCJ0
#2: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 50.96 %
Description: the number of unique measured reflections for data collection contains Friedel pairs.
Mosaicity: 0.228 °
Crystal growTemperature: 293 K / Method: sitting drop / pH: 5.6
Details: PEG4000, ammonium acetate, tri-sodium citrate dihydrate, pH 5.6, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97884, 0.97910, 0.96388
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 18, 2010 / Details: Rhodium coated silicon single crystal
RadiationMonochromator: Si / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978841
20.97911
30.963881
ReflectionRedundancy: 7.6 % / Number: 556722 / Rmerge(I) obs: 0.053 / Χ2: 1.06 / D res high: 1.92 Å / D res low: 50 Å / Num. obs: 73092 / % possible obs: 99.4
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.145099.410.031.2737.6
3.284.1410010.0391.5937.7
2.873.2899.810.0431.1177.7
2.612.8799.910.0581.0177.7
2.422.6199.810.0740.9767.7
2.282.4299.710.0910.9587.7
2.162.2899.610.1120.9437.7
2.072.1699.510.1490.9067.7
1.992.0799.310.2070.8917.7
1.921.9996.610.2520.8886.9
ReflectionResolution: 1.92→50 Å / Num. obs: 73214 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
RefinementMethod to determine structure: MAD / Resolution: 1.92→30.15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 1 / SU B: 2.718 / SU ML: 0.081 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2047 1952 5 %RANDOM
Rwork0.1877 ---
all0.1886 38788 --
obs0.1886 38788 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 58.59 Å2 / Biso mean: 21.877 Å2 / Biso min: 10.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.77 Å20 Å20 Å2
2--0.77 Å20 Å2
3----1.53 Å2
Refinement stepCycle: LAST / Resolution: 1.92→30.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 85 204 3588
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223457
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9994683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0495427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97922.353153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.74615541
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7441537
X-RAY DIFFRACTIONr_chiral_restr0.1070.2496
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212656
X-RAY DIFFRACTIONr_mcbond_it0.7741.52119
X-RAY DIFFRACTIONr_mcangle_it1.45323381
X-RAY DIFFRACTIONr_scbond_it2.6531338
X-RAY DIFFRACTIONr_scangle_it4.3254.51302
LS refinement shellResolution: 1.92→1.97 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 121 -
Rwork0.201 2474 -
all-2595 -
obs--100 %

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