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- PDB-2rgh: Structure of Alpha-Glycerophosphate Oxidase from Streptococcus sp... -

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Basic information

Entry
Database: PDB / ID: 2rgh
TitleStructure of Alpha-Glycerophosphate Oxidase from Streptococcus sp.: A Template for the Mitochondrial Alpha-Glycerophosphate Dehydrogenase
ComponentsAlpha-Glycerophosphate Oxidase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN OXIDASE
Function / homology
Function and homology information


glycerol-3-phosphate oxidase activity / glycerol-3-phosphate oxidase / glycerol-3-phosphate dehydrogenase (quinone) activity / glycerol-3-phosphate metabolic process / glycerol-3-phosphate dehydrogenase (FAD) complex / glycerol metabolic process / membrane => GO:0016020 / nucleotide binding
Similarity search - Function
Alpha-glycerophosphate oxidase, cap domain / FAD-dependent glycerol-3-phosphate dehydrogenase / Alpha-glycerophosphate oxidase, C-terminal / Alpha-glycerophosphate oxidase, C-terminal domain superfamily / C-terminal domain of alpha-glycerophosphate oxidase / FAD-dependent glycerol-3-phosphate dehydrogenase signature 1. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 ...Alpha-glycerophosphate oxidase, cap domain / FAD-dependent glycerol-3-phosphate dehydrogenase / Alpha-glycerophosphate oxidase, C-terminal / Alpha-glycerophosphate oxidase, C-terminal domain superfamily / C-terminal domain of alpha-glycerophosphate oxidase / FAD-dependent glycerol-3-phosphate dehydrogenase signature 1. / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / Helicase, Ruva Protein; domain 3 / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Alpha-glycerophosphate oxidase
Similarity search - Component
Biological speciesStreptococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsColussi, T. / Boles, W. / Mallett, T.C. / Karplus, P.A. / Claiborne, A.
CitationJournal: Biochemistry / Year: 2008
Title: Structure of alpha-glycerophosphate oxidase from Streptococcus sp.: a template for the mitochondrial alpha-glycerophosphate dehydrogenase.
Authors: Colussi, T. / Parsonage, D. / Boles, W. / Matsuoka, T. / Mallett, T.C. / Karplus, P.A. / Claiborne, A.
History
DepositionOct 1, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-Glycerophosphate Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1333
Polymers64,2521
Non-polymers8822
Water4,882271
1
A: Alpha-Glycerophosphate Oxidase
hetero molecules

A: Alpha-Glycerophosphate Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,2666
Polymers128,5032
Non-polymers1,7634
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area4600 Å2
ΔGint-65 kcal/mol
Surface area42100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.280, 95.550, 77.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe asymmetric unit contains one monomer. The biological dimer can be generated using the 2-fold symmetry operator -x, -y, z

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Components

#1: Protein Alpha-Glycerophosphate Oxidase / E.C.1.1.3.21 / FAD dependent oxidoreductase


Mass: 64251.586 Da / Num. of mol.: 1 / Fragment: deletion of residues 356-405 / Mutation: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. (bacteria)
Description: Construct with residues 356-405 of Streptococcus sp. Alpha-Glycerophosphate Oxidase deleted
Gene: glpO / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: D0VWY7*PLUS, glycerol-3-phosphate oxidase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.49 Å3/Da / Density % sol: 50.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: sodium sulfate, PEG 3350, beta-mercaptoethanol, glycerol, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 0.9783, 0.979, 0.96
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 12, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97831
20.9791
30.961
ReflectionResolution: 2.1→41.79 Å / Num. all: 38278 / Num. obs: 37395 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.49 % / Rsym value: 0.074 / Net I/σ(I): 12.9
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 4.72 % / Mean I/σ(I) obs: 4 / Num. unique all: 3107 / Rsym value: 0.323 / % possible all: 82.4

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Processing

Software
NameVersionClassification
CBASSdata collection
SOLVEphasing
CNS1.1refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→41.76 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1417 -Random
Rwork0.21 ---
all0.211 29218 --
obs0.211 29134 99.7 %-
Displacement parametersBiso mean: 44.5 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å2-1.73 Å20.66 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.24 Å
Refinement stepCycle: LAST / Resolution: 2.3→41.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4288 0 58 271 4617
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.93
X-RAY DIFFRACTIONc_mcbond_it1.2191.5
X-RAY DIFFRACTIONc_mcangle_it1.9392
X-RAY DIFFRACTIONc_scbond_it2.1092
X-RAY DIFFRACTIONc_scangle_it3.0592.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.02
RfactorNum. reflection% reflection
Rfree0.306 --
Rwork0.243 --
obs-4492 99.2 %

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