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

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Basic information

Entry
Database: PDB / ID: 2rgo
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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Assembly

Deposited unit
A: Alpha-Glycerophosphate Oxidase
B: Alpha-Glycerophosphate Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8814
Polymers135,3102
Non-polymers1,5712
Water4,179232
1
A: Alpha-Glycerophosphate Oxidase
hetero molecules

B: Alpha-Glycerophosphate Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,8814
Polymers135,3102
Non-polymers1,5712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y+1/2,-z-11
Buried area4340 Å2
ΔGint-33 kcal/mol
Surface area44100 Å2
MethodPISA
2
A: Alpha-Glycerophosphate Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4412
Polymers67,6551
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Alpha-Glycerophosphate Oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4412
Polymers67,6551
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)128.363, 106.785, 58.887
Angle α, β, γ (deg.)90.00, 99.18, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe asymmetric unit contains 2 monomers. The biological dimer can be generated using the 2-fold symmetry operator -x, y+1/2, -z.

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Components

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


Mass: 67655.148 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus sp. (bacteria) / Gene: glpO / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): B834
References: UniProt: D0VWP7*PLUS, glycerol-3-phosphate oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.94 Å3/Da / Density % sol: 58.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 1000, Tris, magnesium chloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9296 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9296 Å / Relative weight: 1
ReflectionResolution: 2.4→28.89 Å / Num. obs: 54822 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.064 / Net I/σ(I): 9.9
Reflection shellResolution: 2.4→2.53 Å / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 2.8 / Num. unique all: 8692

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2RGH

2rgh


Resolution: 2.4→12 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.732 / SU ML: 0.185 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.4 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24708 2938 5.1 %RANDOM
Rwork0.23759 ---
all0.23808 ---
obs0.23808 54822 94.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.886 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.04 Å2
2---0.02 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.4→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8524 0 106 232 8862
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0228782
X-RAY DIFFRACTIONr_angle_refined_deg1.6752.00211879
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.10151076
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.12524.7400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.517151561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6341557
X-RAY DIFFRACTIONr_chiral_restr0.1110.21329
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026575
X-RAY DIFFRACTIONr_nbd_refined0.2760.23667
X-RAY DIFFRACTIONr_nbtor_refined0.3280.26017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2288
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2910.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2010.23
X-RAY DIFFRACTIONr_mcbond_it1.4571.55381
X-RAY DIFFRACTIONr_mcangle_it2.53928657
X-RAY DIFFRACTIONr_scbond_it2.17333401
X-RAY DIFFRACTIONr_scangle_it3.2374.53222
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 200 -
Rwork0.352 4063 -
obs-4063 97.11 %
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)
10.5846-0.19510.19840.39590.3550.6038-0.0077-0.0421-0.17710.1103-0.01760.11030.06860.05540.02540.08430.02380.07080.11290.03570.0848-8.333-40.8993-19.8359
21.5464-0.71830.29421.1584-0.1680.1853-0.0005-0.0632-0.05630.0238-0.01850.2316-0.0239-0.02230.01910.0670.06980.07530.16670.01480.0169-23.3488-18.7666-21.2372
31.38880.07060.18693.912-0.55850.833-0.1818-0.12820.18610.13820.14860.3897-0.1418-0.00210.03320.04110.0930.08240.17960.0123-0.0136-23.5797-3.6174-20.2577
44.5412.1927-0.47469.8273-4.97313.9827-0.1505-0.1680.59290.57280.0319-0.1608-0.16660.10010.11870.05510.0640.06280.0924-0.0666-0.0252-13.75372.7621-18.1576
50.6729-0.7069-0.07541.69570.41830.66070.0365-0.0404-0.2293-0.0230.01690.16930.05430.011-0.05340.08160.00160.02580.08090.01260.0681-7.057-42.6624-25.5024
60.9305-0.24140.37532.28320.3420.23830.01440.10.0243-0.11840.003-0.0317-0.04240.1055-0.01740.09880.00810.05050.14850.0328-0.0395-3.4922-14.9549-28.9944
70.9893-0.7237-0.67891.82140.48690.48110.04430.0957-0.3054-0.0832-0.08490.5818-0.1102-0.20830.04060.00910.00020.02410.1390.01170.1175-21.5049-35.406-24.5756
84.7663-2.14761.47511.15110.1994.5231-0.3569-0.348-0.0790.36820.25520.1920.1031-0.0450.10170.23760.05920.11930.27160.0611-0.19-7.0063-25.92772.718
91.61940.2052-0.23221.28390.09050.8229-0.1489-0.2814-0.07680.1820.0756-0.0737-0.05320.13410.07330.12170.0633-0.00470.20620.0386-0.05825.8018-28.2507-8.3811
101.1011-0.94940.813910.2268-5.72613.28480.07390.010.0502-0.1967-0.2715-0.560.06580.38930.19760.02250.06050.05710.17720.03140.045113.6874-29.9442-18.8117
110.82871.35050.4662.84581.70531.6493-0.40850.410.0324-0.21890.5990.2937-0.35020.3837-0.19050.0429-0.2295-0.23480.01370.07580.3459-64.3202-28.8028-16.8728
122.48291.74212.33033.04271.37972.2230.00870.5301-0.4740.20280.3972-0.4682-0.03090.2259-0.4059-0.1199-0.07510.00020.1497-0.16580.1996-73.3863-60.4314-26.6481
131.77881.76871.21423.49141.47571.4264-0.28820.29110.11360.06520.3779-0.4372-0.19260.2974-0.0897-0.1171-0.1051-0.1072-0.04510.0060.2375-65.887-35.8535-14.4585
141.44031.51360.91322.49510.58320.7357-0.0742-0.20290.0957-0.00370.04540.3425-0.24540.08180.02870.06080.002-0.1648-0.0653-0.0110.2764-72.8674-37.8207-7.6081
152.4083-0.48161.40274.28930.72211.88990.21560.007-0.43940.56010.1392-0.38240.1581-0.0772-0.35470.0128-0.0371-0.2548-0.07950.01890.3032-68.1327-56.6805-6.0431
163.6099-4.02763.34274.4936-3.72953.09531.2261-2.0042-0.5708-2.0006-0.01742.21022.064-1.103-1.20870.4515-0.00070.00680.45540.00120.4503-81.762-48.4718-12.8404
171.24481.38611.30424.28361.03054.0481-0.79560.25140.384-0.29320.40710.5244-0.25810.0250.38850.0381-0.1603-0.3155-0.0230.09330.3843-79.6249-30.2657-21.209
182.07070.86431.69382.72271.19442.8018-0.44391.1634-0.1388-0.67240.6014-0.7726-0.51780.993-0.1575-0.1712-0.43260.12830.2842-0.02660.2624-53.7972-37.1426-26.0491
191.8634-0.50080.30477.863-4.84993.6131-0.25060.4317-0.33670.24560.454-1.0302-0.21860.4969-0.2034-0.2351-0.1747-0.27910.096-0.21470.6296-49.7-41.6971-10.5481
209.314812.5958-2.737617.1457-3.27882.38660.5206-0.0219-1.12481.28090.0739-1.4616-0.04820.5264-0.5946-0.1223-0.0516-0.54690.0416-0.20630.7825-49.9498-39.16190.6723
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 661 - 66
2X-RAY DIFFRACTION2AA67 - 9967 - 99
3X-RAY DIFFRACTION3AA100 - 145100 - 145
4X-RAY DIFFRACTION4AA146 - 168146 - 168
5X-RAY DIFFRACTION5AA169 - 241169 - 241
6X-RAY DIFFRACTION6AA242 - 351242 - 351
7X-RAY DIFFRACTION7AA352 - 475352 - 475
8X-RAY DIFFRACTION8AA476 - 517476 - 517
9X-RAY DIFFRACTION9AA519 - 572519 - 572
10X-RAY DIFFRACTION10AA573 - 605573 - 605
11X-RAY DIFFRACTION11BB1 - 671 - 67
12X-RAY DIFFRACTION12BB68 - 15268 - 152
13X-RAY DIFFRACTION13BB153 - 223153 - 223
14X-RAY DIFFRACTION14BB224 - 269224 - 269
15X-RAY DIFFRACTION15BB270 - 349270 - 349
16X-RAY DIFFRACTION16BB350 - 360350 - 360
17X-RAY DIFFRACTION17BB409 - 450409 - 450
18X-RAY DIFFRACTION18BB451 - 533451 - 533
19X-RAY DIFFRACTION19BB534 - 569534 - 569
20X-RAY DIFFRACTION20BB570 - 607570 - 607

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