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- PDB-3vqr: Structure of a dye-linked L-proline dehydrogenase mutant from the... -

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Basic information

Entry
Database: PDB / ID: 3vqr
TitleStructure of a dye-linked L-proline dehydrogenase mutant 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
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / Oxidoreductase
Similarity search - Component
Biological speciesAeropyrum pernix (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsSakuraba, H. / Ohshima, T. / Satomura, T. / Yoneda, K.
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
DepositionMar 29, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 20, 2012Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Nov 8, 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: Putative oxidoreductase
B: Putative oxidoreductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,62410
Polymers97,6862
Non-polymers1,9378
Water3,837213
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8070 Å2
ΔGint-41 kcal/mol
Surface area32320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.987, 70.570, 73.092
Angle α, β, γ (deg.)71.650, 70.850, 70.150
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Putative oxidoreductase / L-proline dehydrogenase


Mass: 48843.207 Da / Num. of mol.: 2 / Fragment: residues 1-427 / Mutation: delta L428
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aeropyrum pernix (archaea) / Strain: K1 / Plasmid: pET15 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9YCJ0
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 213 / 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: 2.19 Å3/Da / Density % sol: 43.88 %
Crystal growTemperature: 293 K / Method: sitting drop / pH: 6.5
Details: PEG8000, Mg acetate, Mes, pH 6.5, sitting drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 2, 2012 / Details: Rhodium coated silicon single crystal
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. all: 52556 / Num. obs: 52556 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.01→2.04 Å / % possible all: 93.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AXB

3axb


Resolution: 2.01→24.2 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.101 / SU ML: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2551 2654 5 %RANDOM
Rwork0.2103 ---
all0.2126 52556 --
obs0.2126 52556 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 114.59 Å2 / Biso mean: 38.6857 Å2 / Biso min: 14.43 Å2
Baniso -1Baniso -2Baniso -3
1-2.33 Å20.52 Å2-0.18 Å2
2---2.41 Å21.22 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 2.01→24.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6550 0 130 213 6893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196832
X-RAY DIFFRACTIONr_angle_refined_deg2.0231.9939268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9195848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97922.353306
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.156151070
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.5871574
X-RAY DIFFRACTIONr_chiral_restr0.1480.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0215270
LS refinement shellResolution: 2.009→2.062 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 150 -
Rwork0.232 3312 -
all-3462 -
obs--85.88 %
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)
10.94020.17230.10112.8284-1.17551.51730.08780.01050.0774-0.0322-0.352-0.2996-0.16250.2950.26420.0501-0.0265-0.02360.12410.04870.114673.815455.719259.7493
20.4395-0.06590.79981.5190.11982.9434-0.0438-0.04850.0660.2618-0.1368-0.127-0.40390.21720.18060.1421-0.1034-0.06650.14640.02680.128577.58858.56680.101
30.0895-0.2207-0.52375.62811.05153.1313-0.05510.021-0.0318-1.1968-0.06810.5390.3289-0.05520.12330.43130.0567-0.15530.1491-0.04490.130961.593735.715442.9994
40.32750.07560.52832.09950.69212.0187-0.01-0.06570.06280.2746-0.19370.1363-0.2498-0.10590.20370.132-0.0328-0.00480.102-0.02470.105966.263954.7379.0605
50.61950.08070.26233.4698-1.64081.9010.073-0.01140.00880.091-0.5752-0.6253-0.13530.48140.50220.0266-0.0426-0.03890.22690.13360.22276.328346.969863.9863
60.9649-0.3447-0.10122.6689-1.21291.94550.0971-0.0285-0.060.0055-0.3412-0.28910.12780.32040.24410.03920.01610.02420.12360.04610.122173.840213.901575.9394
70.55120.0812-0.84671.36730.15842.9517-0.040.0667-0.0814-0.2531-0.1501-0.12310.3340.19920.19010.12310.10270.07120.12810.03170.126477.81810.97355.356
80.13450.84360.01146.65451.36222.94360.0874-0.02570.01671.0637-0.08230.3626-0.3382-0.0326-0.00510.4633-0.01090.16560.1727-0.01530.13561.422333.734192.4063
90.3395-0.0585-0.48572.16980.73261.9506-0.01360.0674-0.0512-0.292-0.18490.12110.2528-0.0750.19860.13870.03890.01150.0955-0.02750.101366.290714.893556.6246
100.66270.0239-0.25423.458-1.38441.80960.05580.0157-0.0356-0.1011-0.5299-0.59770.10210.42790.47410.01430.0380.03620.21960.1250.221176.342422.65971.7002
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 76
2X-RAY DIFFRACTION2A77 - 185
3X-RAY DIFFRACTION3A186 - 222
4X-RAY DIFFRACTION4A223 - 339
5X-RAY DIFFRACTION5A340 - 424
6X-RAY DIFFRACTION6B2 - 76
7X-RAY DIFFRACTION7B77 - 184
8X-RAY DIFFRACTION8B185 - 222
9X-RAY DIFFRACTION9B223 - 339
10X-RAY DIFFRACTION10B340 - 424

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