[English] 日本語
Yorodumi
- PDB-8e8t: Structure of the short LOR domain of human AASS -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8e8t
TitleStructure of the short LOR domain of human AASS
ComponentsAlpha-aminoadipic semialdehyde synthase, mitochondrial
KeywordsOXIDOREDUCTASE / lysine metabolism / ketoglutarate / mitochondrial / reductase
Function / homology
Function and homology information


saccharopine dehydrogenase (NADP+, L-lysine-forming) / saccharopine dehydrogenase (NAD+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-lysine-forming) activity / saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity / saccharopine dehydrogenase activity / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / lysine catabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / lysine biosynthetic process via aminoadipic acid / Lysine catabolism ...saccharopine dehydrogenase (NADP+, L-lysine-forming) / saccharopine dehydrogenase (NAD+, L-glutamate-forming) / saccharopine dehydrogenase (NADP+, L-lysine-forming) activity / saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity / saccharopine dehydrogenase activity / saccharopine dehydrogenase (NAD+, L-lysine-forming) activity / lysine catabolic process / L-lysine catabolic process to acetyl-CoA via saccharopine / lysine biosynthetic process via aminoadipic acid / Lysine catabolism / transcription corepressor activity / histone binding / mitochondrial matrix / intracellular membrane-bounded organelle / negative regulation of transcription by RNA polymerase II / mitochondrion / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Saccharopine dehydrogenase, NADP binding domain / Saccharopine dehydrogenase-like, C-terminal / Saccharopine dehydrogenase NADP binding domain / Saccharopine dehydrogenase C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, N-terminal / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/PNT, N-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
Alpha-aminoadipic semialdehyde synthase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsKhamrui, S. / Lazarus, M.B.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM124838 United States
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)R21HD102745 United States
CitationJournal: Open Biology / Year: 2022
Title: Characterization and structure of the human lysine-2-oxoglutarate reductase domain, a novel therapeutic target for treatment of glutaric aciduria type 1.
Authors: Leandro, J. / Khamrui, S. / Suebsuwong, C. / Chen, P.J. / Secor, C. / Dodatko, T. / Yu, C. / Sanchez, R. / DeVita, R.J. / Houten, S.M. / Lazarus, M.B.
History
DepositionAug 25, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-aminoadipic semialdehyde synthase, mitochondrial
B: Alpha-aminoadipic semialdehyde synthase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)96,6942
Polymers96,6942
Non-polymers00
Water4,486249
1
A: Alpha-aminoadipic semialdehyde synthase, mitochondrial

A: Alpha-aminoadipic semialdehyde synthase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)96,6942
Polymers96,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3720 Å2
ΔGint-8 kcal/mol
Surface area32450 Å2
2
B: Alpha-aminoadipic semialdehyde synthase, mitochondrial

B: Alpha-aminoadipic semialdehyde synthase, mitochondrial


Theoretical massNumber of molelcules
Total (without water)96,6942
Polymers96,6942
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area3590 Å2
ΔGint-7 kcal/mol
Surface area33420 Å2
Unit cell
Length a, b, c (Å)77.356, 154.715, 70.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Alpha-aminoadipic semialdehyde synthase, mitochondrial / LKR/SDH


Mass: 48347.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AASS / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q9UDR5, saccharopine dehydrogenase (NADP+, L-lysine-forming), saccharopine dehydrogenase (NAD+, L-glutamate-forming)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 249 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.2M NaCl, 0.1M HEPES, 25% PEG 4000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9201 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jun 26, 2019
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9201 Å / Relative weight: 1
ReflectionResolution: 2.18→42.91 Å / Num. obs: 43284 / % possible obs: 96.7 % / Redundancy: 3.1 % / CC1/2: 0.981 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.11 / Rrim(I) all: 0.206 / Net I/σ(I): 4.4 / Num. measured all: 132605 / Scaling rejects: 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.18-2.252.91.0891095137570.3670.7241.319198
8.99-42.913.10.07919766450.9840.0520.09611.890.4

-
Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QRJ

2qrj


Resolution: 2.18→42.91 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2449 2278 5.27 %
Rwork0.2136 40969 -
obs0.2152 43247 95.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.22 Å2 / Biso mean: 43.6696 Å2 / Biso min: 16.59 Å2
Refinement stepCycle: final / Resolution: 2.18→42.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6326 0 0 249 6575
Biso mean---38.18 -
Num. residues----806
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036464
X-RAY DIFFRACTIONf_angle_d0.568762
X-RAY DIFFRACTIONf_chiral_restr0.044979
X-RAY DIFFRACTIONf_plane_restr0.0041137
X-RAY DIFFRACTIONf_dihedral_angle_d15.0223898
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1801-2.22750.34471370.3136256698
2.2275-2.27930.36071450.3011256996
2.2793-2.33630.31811660.2875250598
2.3363-2.39940.31151360.2691258098
2.3994-2.470.28091060.2595255296
2.47-2.54980.28761600.2547258398
2.5498-2.64090.29611680.2525258298
2.6409-2.74660.30791300.2382261898
2.7466-2.87160.23761510.2159256598
2.8716-3.02290.2411450.2236258198
3.0229-3.21230.26931320.2303260597
3.2123-3.46020.23531440.2141257097
3.4602-3.80820.22881340.1782251394
3.8082-4.35880.19441490.1724248092
4.3588-5.48980.20551480.1704248992
5.4898-42.910.20441270.1934261191
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)
13.59091.5736-1.36076.6198-3.42484.0140.26440.1569-0.30180.32760.1290.06210.2581-0.2172-0.22690.34880.0099-0.05280.2219-0.01170.379143.2245.83143.596
24.21162.3088-1.42737.60141.43232.41260.01290.9901-0.9897-0.70580.0909-0.29420.5314-0.26930.28810.6109-0.01380.04870.423-0.04920.488241.11559.97836.358
31.83380.87980.53252.36410.10291.11150.2488-0.233-0.45320.2025-0.149-0.43090.29690.0221-0.03680.3716-0.0209-0.03780.26260.03820.398644.1848.30549.359
43.7939-0.4686-1.64353.56971.02052.92810.31731.013-0.4951-1.1326-0.09080.2280.38390.0356-0.06480.51770.0325-0.01740.3978-0.08320.389738.94744.07434.88
53.65311.8253-3.72414.24895.43392-0.09981.2615-1.5662-1.1699-0.3631-0.34340.9257-0.31010.27020.6596-0.21440.22471.1642-0.32960.899237.89632.30631.334
64.5976-0.2326-0.30672.5797-0.12251.63380.26340.3381-0.117-0.1469-0.32590.6127-0.1366-0.3814-0.03890.3822-0.06510.00350.3258-0.04130.469624.66843.96941.9
70.76220.2542-0.1561.37180.04510.6047-0.0660.0516-0.00810.0080.07010.14990.0523-0.06650.050.2278-0.0405-0.01240.2093-0.01150.210426.61476.22348.872
85.4918-1.1572.30242.7993-1.02823.2240.0312-0.8882-0.22290.60440.17020.2369-0.2187-0.68940.06080.3552-0.0436-0.0040.35690.00660.2857.44979.73550.496
91.94531.37581.34011.57021.0281.25890.0107-0.0322-0.070.1292-0.06540.20770.2977-0.05840.060.2983-0.05820.02260.2901-0.0260.33096.73370.60941.622
102.4976-1.73542.84862.29590.11567.3840.3944-0.3654-0.94140.01360.18390.24160.58410.4588-0.0680.6502-0.06170.04130.5959-0.22940.65099.55657.13733.332
113.65881.7410.07846.1816-1.2473.8437-0.43551.1521-0.0209-1.02510.12210.0672-0.39640.42630.05340.3735-0.0994-0.01530.53320.00490.348711.94176.15928.997
125.04483.40762.61862.92052.75452.87520.40980.56490.2682-0.4936-0.39260.4355-0.9419-0.57050.09160.4067-0.0906-0.05010.3332-0.0320.369219.20891.69537.928
131.6023-0.14430.26091.1760.02520.795-0.02810.56-0.3735-0.11790.0959-0.08170.13620.12180.03440.3216-0.03080.00640.3403-0.05390.312624.38571.61433.468
143.697-4.2682-2.06195.7611.96017.8854-0.08730.71680.6041-0.78380.14820.634-0.3185-0.81140.03120.77270.0401-0.05880.95760.09540.48120.6479.83522.414
151.1086-0.45190.61552.43870.01770.5363-0.04060.0362-0.0906-0.19730.07640.12260.254-0.11840.01970.2567-0.06730.06550.2314-0.03260.218430.69860.49243.071
161.9075-1.269-0.0412.31310.39310.1650.19160.2888-1.01580.1545-0.22610.03710.6384-0.4672-0.04220.5083-0.10180.0180.31440.01830.65927.98233.64341.66
172.76410.4984-1.05824.123-0.09431.5177-0.06250.03070.0425-0.40240.17241.1012-0.0076-0.28910.00140.3246-0.0517-0.07650.27480.06240.49312.26170.74173.075
182.09751.0223-0.61133.8191-1.00830.3136-0.0811-0.13160.29660.28210.0071.18080.1317-0.3801-0.14110.17110.12680.09260.39910.0821.67573.72975.4878.41
192.58830.175-0.6253.15390.57062.76240.0528-0.86170.23070.4494-0.34550.68890.3423-0.43170.00690.4222-0.04830.09150.5083-0.03050.68628.36263.9586.17
209.0712-1.38591.90445.5841-0.31424.7240.0308-1.4374-0.62630.6699-0.57070.82850.407-0.55630.04520.8630.02060.26320.80540.0850.75774.69459.45894.014
212.993-0.4317-0.18963.60590.73783.4976-0.4933-0.1861-0.7360.6772-0.00380.87231.09260.39370.09810.52190.01830.22730.37550.1030.695414.24850.87280.013
222.1420.1583-0.48291.65450.01820.1038-0.0223-0.1655-0.05420.141-0.07070.0947-0.0112-0.0295-0.00650.3078-0.02050.0270.22470.00920.187839.08168.06475.31
232.20810.3429-0.44572.3996-0.21991.322-0.1299-0.0003-0.1651-0.02780.0476-0.13030.14950.04860.00870.2939-0.0118-0.02370.22210.0020.227146.63763.1469.75
243.99590.6908-0.00655.335-0.30671.93190.11640.1196-1.0114-0.22280.1405-0.85730.73070.7852-0.00680.57310.08470.00750.44970.04970.472654.63250.79471.676
252.13540.7072-0.18312.39030.16241.6651-0.3371-0.0165-0.95350.54980.1624-1.18810.8051-0.18870.11120.71830.032-0.05010.27190.04580.490146.83443.72676.581
264.89790.1258-2.33353.8278-0.58842.5299-0.18190.2097-0.9841-0.0053-0.02780.41681.2654-1.1751-0.03491.3913-0.31030.08120.63430.1270.751636.98534.27485.439
273.27470.5959-0.05062.6362-0.42081.641-0.0175-0.443-0.57210.06490.20820.21270.5946-0.01950.07010.5276-0.0554-0.05120.31040.12190.361445.22950.03882.577
286.16613.02160.77145.5510.93432.46580.0668-0.7201-0.46710.1593-0.14970.08660.3038-0.02150.04940.6655-0.0469-0.10040.52270.15260.551945.41649.44491.487
292.1547-0.1410.29012.5852-0.58381.6130.0497-0.71570.01620.6312-0.0510.07480.1528-0.02740.02690.5761-0.03660.02880.36490.00480.324845.30959.51986.473
303.438-0.21510.76922.7677-0.00912.5177-0.1487-0.85890.52790.61070.0229-0.4588-0.35470.2747-0.00190.5233-0.0657-0.0120.45340.00330.304441.52666.592.473
312.86030.25070.68452.2633-0.76660.85930.1018-0.0899-0.03050.0676-0.11940.27940.16880.01350.0170.3924-0.040.05540.2741-0.03490.242626.962.90477.242
320.93790.0079-0.55143.30191.27320.8398-0.8631-0.2562-0.54720.92030.00881.82220.9009-0.2757-0.11880.5624-0.08750.22970.35350.01071.31753.31150.79379.863
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 24:31 )A24 - 31
2X-RAY DIFFRACTION2( CHAIN A AND RESID 32:36 )A32 - 36
3X-RAY DIFFRACTION3( CHAIN A AND RESID 37:92 )A37 - 92
4X-RAY DIFFRACTION4( CHAIN A AND RESID 93:110 )A93 - 110
5X-RAY DIFFRACTION5( CHAIN A AND RESID 130:130 )A130
6X-RAY DIFFRACTION6( CHAIN A AND RESID 131:144 )A131 - 144
7X-RAY DIFFRACTION7( CHAIN A AND RESID 145:240 )A145 - 240
8X-RAY DIFFRACTION8( CHAIN A AND RESID 241:250 )A241 - 250
9X-RAY DIFFRACTION9( CHAIN A AND RESID 251:312 )A251 - 312
10X-RAY DIFFRACTION10( CHAIN A AND RESID 313:316 )A313 - 316
11X-RAY DIFFRACTION11( CHAIN A AND RESID 318:330 )A318 - 330
12X-RAY DIFFRACTION12( CHAIN A AND RESID 341:348 )A341 - 348
13X-RAY DIFFRACTION13( CHAIN A AND RESID 349:379 )A349 - 379
14X-RAY DIFFRACTION14( CHAIN A AND RESID 380:384 )A380 - 384
15X-RAY DIFFRACTION15( CHAIN A AND RESID 385:428 )A385 - 428
16X-RAY DIFFRACTION16( CHAIN A AND RESID 429:450 )A429 - 450
17X-RAY DIFFRACTION17( CHAIN B AND RESID 24:78 )B24 - 78
18X-RAY DIFFRACTION18( CHAIN B AND RESID 79:83 )B79 - 83
19X-RAY DIFFRACTION19( CHAIN B AND RESID 84:122 )B84 - 122
20X-RAY DIFFRACTION20( CHAIN B AND RESID 123:130 )B123 - 130
21X-RAY DIFFRACTION21( CHAIN B AND RESID 131:144 )B131 - 144
22X-RAY DIFFRACTION22( CHAIN B AND RESID 145:195 )B145 - 195
23X-RAY DIFFRACTION23( CHAIN B AND RESID 196:240 )B196 - 240
24X-RAY DIFFRACTION24( CHAIN B AND RESID 241:253 )B241 - 253
25X-RAY DIFFRACTION25( CHAIN B AND RESID 254:284 )B254 - 284
26X-RAY DIFFRACTION26( CHAIN B AND RESID 285:292 )B285 - 292
27X-RAY DIFFRACTION27( CHAIN B AND RESID 293:313 )B293 - 313
28X-RAY DIFFRACTION28( CHAIN B AND RESID 314:330 )B314 - 330
29X-RAY DIFFRACTION29( CHAIN B AND RESID 341:369 )B341 - 369
30X-RAY DIFFRACTION30( CHAIN B AND RESID 370:388 )B370 - 388
31X-RAY DIFFRACTION31( CHAIN B AND RESID 389:425 )B389 - 425
32X-RAY DIFFRACTION32( CHAIN B AND RESID 426:450 )B426 - 450

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more