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- PDB-8hy5: Structure of D-amino acid oxidase mutant R38H -

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Basic information

Entry
Database: PDB / ID: 8hy5
TitleStructure of D-amino acid oxidase mutant R38H
ComponentsD-amino-acid oxidase
KeywordsOXIDOREDUCTASE / ALS / amino acid / d-serine / neurodegeneration / schizophrenia
Function / homology
Function and homology information


L-leucine metabolic process / D-amino-acid dehydrogenase activity / D-amino-acid oxidase / D-amino-acid oxidase activity / D-alanine catabolic process / D-serine metabolic process / glycine oxidase activity / L-proline catabolic process / D-amino acid catabolic process / D-serine catabolic process ...L-leucine metabolic process / D-amino-acid dehydrogenase activity / D-amino-acid oxidase / D-amino-acid oxidase activity / D-alanine catabolic process / D-serine metabolic process / glycine oxidase activity / L-proline catabolic process / D-amino acid catabolic process / D-serine catabolic process / Glyoxylate metabolism and glycine degradation / presynaptic active zone / dopamine biosynthetic process / neutrophil-mediated killing of gram-negative bacterium / peroxisomal matrix / digestion / FAD binding / cell projection / Peroxisomal protein import / extracellular space / identical protein binding / cytoplasm / cytosol
Similarity search - Function
D-amino acid oxidase, conserved site / D-amino acid oxidases signature. / D-amino-acid oxidase / FAD dependent oxidoreductase / FAD dependent oxidoreductase
Similarity search - Domain/homology
BENZOIC ACID / FLAVIN-ADENINE DINUCLEOTIDE / D-amino-acid oxidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKhan, S. / Upadhyay, S. / Dave, U. / Kumar, A. / Gomes, J.
Funding support India, 1items
OrganizationGrant numberCountry
Other government India
CitationJournal: Int.J.Biol.Macromol. / Year: 2023
Title: Structural and mechanistic insights into ALS patient derived mutations in D-amino acid oxidase.
Authors: Khan, S. / Upadhyay, S. / Dave, U. / Kumar, A. / Gomes, J.
History
DepositionJan 5, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: D-amino-acid oxidase
B: D-amino-acid oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8268
Polymers83,9252
Non-polymers1,9006
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-28 kcal/mol
Surface area25630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.756, 74.164, 99.037
Angle α, β, γ (deg.)90.000, 91.460, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein D-amino-acid oxidase / DAAO / DAMOX / DAO


Mass: 41962.555 Da / Num. of mol.: 2 / Mutation: R38H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DAO, DAMOX / Production host: Escherichia coli (E. coli) / References: UniProt: P14920, D-amino-acid oxidase

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Non-polymers , 5 types, 161 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-BEZ / BENZOIC ACID


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 1.91 Å3/Da / Density % sol: 35.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 26% PEG 2000 methyl ether, 0.1M Potassium Thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97989 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 22, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97989 Å / Relative weight: 1
ReflectionResolution: 2.1→49.5 Å / Num. obs: 37081 / % possible obs: 100 % / Redundancy: 7.5 % / Biso Wilson estimate: 32.77 Å2 / CC1/2: 0.999 / Net I/σ(I): 13.4
Reflection shellResolution: 2.1→2.1 Å / Num. unique obs: 2993 / CC1/2: 0.76

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DU8

2du8


Resolution: 2.1→34.96 Å / SU ML: 0.2426 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.711
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.235 1754 4.74 %
Rwork0.2068 35249 -
obs0.2081 37003 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→34.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5333 0 129 155 5617
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00295623
X-RAY DIFFRACTIONf_angle_d0.58077679
X-RAY DIFFRACTIONf_chiral_restr0.0446818
X-RAY DIFFRACTIONf_plane_restr0.005978
X-RAY DIFFRACTIONf_dihedral_angle_d13.2827740
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.160.29331270.26922679X-RAY DIFFRACTION99.93
2.16-2.220.38871060.29072720X-RAY DIFFRACTION99.93
2.22-2.290.41151070.36262715X-RAY DIFFRACTION98.77
2.29-2.370.29321340.26882676X-RAY DIFFRACTION99.96
2.37-2.470.30691690.25632692X-RAY DIFFRACTION100
2.47-2.580.2331640.24022676X-RAY DIFFRACTION99.89
2.58-2.720.30821380.24022698X-RAY DIFFRACTION99.82
2.72-2.890.27331470.2272701X-RAY DIFFRACTION99.93
2.89-3.110.24351310.21312714X-RAY DIFFRACTION99.93
3.11-3.420.2331280.20572726X-RAY DIFFRACTION99.93
3.42-3.920.1941290.17292737X-RAY DIFFRACTION99.93
3.92-4.930.18881590.15862710X-RAY DIFFRACTION99.83
4.93-34.960.18951150.17592805X-RAY DIFFRACTION99.86
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)
15.060858463091.671219238690.1410946694035.055563155340.0002381086782653.45099327471-0.0163343444752-0.3627530368150.3095441270860.241283072687-0.1719060945150.7244125195180.270085545721-1.234971921670.2521039217150.275084493191-0.02845010029610.00548417003610.495633159864-0.06293139639330.270605430954-21.45214752492.25479595448-12.1964459641
27.59119086038-1.94170997702-4.488940885971.758098644520.384425949523.359708461990.07983651220850.46585351340.3992180723010.137943080166-0.155566517473-0.0787886986062-0.916094214739-0.3662100521730.0284784135940.4451172414760.053548582666-0.04066055686730.4131531933660.0002663861944770.331482268921-14.59850068097.82237995005-14.086048857
33.88146223357-0.421132412825-1.800544433652.155312954920.9830119363324.103685729650.0866552226916-0.197668120795-0.009304587951680.221117900502-0.1029256659240.138449059393-0.0261639149305-0.1768377631740.0638420939890.213969564137-0.0526111523987-0.006740615737760.227478523545-0.02103007271420.222587160141-12.3667843649-11.5079380695-28.4595116307
40.927708054373-0.4454474972440.008602720703372.409330304311.290454758183.891956654650.0559924852209-0.0964374989810.0806962196508-0.0612590235001-0.17640621093-0.00678589048006-0.359755632871-0.119043703040.102151459050.184282278147-0.0671829479521-0.008528102700650.2556915169680.05545109513890.260395342779-10.6545359445-3.49856978486-25.5121137025
50.84566087080.463843043292-0.2384475045861.26844986761.440558908565.762765980710.0438856232737-0.1916538600850.05020881185970.27156645744-0.0261180912848-0.09608800743360.2341607287310.295820879510.003502848459880.2028693603140.00412566346642-0.01905013900240.2603186847770.016017108320.260151555873-1.96405920513-4.59112947663-20.6282714432
63.437490932472.769950188121.234650189572.37394262831.745332357438.331936872030.0908000545667-0.3056152385280.1492628303630.245987814451-0.0736871393891-0.02095006800590.04770694841950.2121184442170.01984953264680.2448041394570.0143199100668-0.002609236341050.2367432102460.01348097661030.3013365187553.28298979496-1.25837748401-25.895412194
71.488141262490.507530053531-0.1762247321830.9433492732690.3496370982533.141283230370.004904265832550.02904692620220.114649286905-0.02203007757780.0265730267719-0.164808085314-0.07859388603630.71618038328-0.06336566626990.278891778918-0.0592844665204-0.02925671934840.4757947975330.02573748869240.3823825869847.62339348247-1.3339261294-32.3505632451
82.59356716577-1.37592447194-1.191493488174.339760292742.56795369513.15990062544-0.230881653965-0.252240566522-0.009222632033171.19220745649-0.004889533784990.1146991718910.439464255209-0.2374996575650.1340788531270.516481123247-0.04436639038980.01575341866120.482922479613-0.0213775645920.276208704513-13.6520611392-5.87681364235-3.11018036343
95.26516675678-1.56442425496-2.453388799725.384635433750.226665221475.17131149565-0.0981643055701-0.509326295627-0.1514744955120.223590120119-0.09152642292390.5502855106160.413812729239-0.781352931880.1664999729970.286907786554-0.114890523696-0.01195214235190.465535599666-0.05801285509180.257155212596-20.5394005571-6.3607285489-12.4077347617
102.961312664410.0137515386159-1.378636009762.99934266257-0.5105268988084.39128876766-0.221038705260.191658733657-0.263200849942-0.2773023452050.14602214847-0.064445120780.3393377909260.2308955946950.08536720378950.229926879127-0.026397173007-0.01846209977250.245305169534-0.02987757209490.170269287476-0.0381310117885-6.6740579797-69.2969946175
112.295198791991.04538873805-1.160051794811.75172428326-0.9934428173553.92901712348-0.06385162419590.0609235337956-0.0641686821096-0.11958793211-0.00780262652194-0.02732815963760.0343692922070.1122610055050.02556662560730.1568975519650.019256548169-0.01970590277270.0936250160627-0.04642467729240.194672415329-7.41095021796-6.07652267277-62.359371668
121.07213541832-0.307033361766-0.7703305646721.690308813-2.078311638593.80420684690.04813707584410.140702610547-0.0395682067442-0.08770504422750.2406568797310.3106013384640.104124305186-0.281904489234-0.2438564377940.2329781505530.0206768749128-0.02335070823330.2733475457650.02786842319460.339841771985-19.6055608013-1.52392353045-54.977536349
131.67574384479-0.284125339737-1.237911640680.7864573917420.01124505416742.94070197516-0.12239950860.240559205102-0.028906258491-0.1367588126990.08154200147290.1622347550560.152384618424-0.2506122997820.02335200475790.239919965654-0.0704560850357-0.02419402489140.1961371127330.009338227159970.261963181951-11.7512942866-2.34969449923-67.226171971
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 23 )AA1 - 231 - 23
22chain 'A' and (resid 24 through 47 )AA24 - 4724 - 44
33chain 'A' and (resid 48 through 109 )AA48 - 10945 - 106
44chain 'A' and (resid 110 through 172 )AA110 - 172107 - 169
55chain 'A' and (resid 173 through 227 )AA173 - 227170 - 224
66chain 'A' and (resid 228 through 252 )AA228 - 252225 - 249
77chain 'A' and (resid 253 through 285 )AA253 - 285250 - 282
88chain 'A' and (resid 286 through 311 )AA286 - 311283 - 308
99chain 'A' and (resid 312 through 338 )AA312 - 338309 - 335
1010chain 'B' and (resid 1 through 78 )BE1 - 781 - 75
1111chain 'B' and (resid 79 through 195 )BE79 - 19576 - 192
1212chain 'B' and (resid 196 through 227 )BE196 - 227193 - 224
1313chain 'B' and (resid 228 through 338 )BE228 - 338225 - 335

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