[English] 日本語
Yorodumi
- PDB-8dda: Crystal structure of human aminoadipate semialdehyde synthase (AA... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dda
TitleCrystal structure of human aminoadipate semialdehyde synthase (AASS), lysine ketoglutarate reductase (LKR) domain
ComponentsAlpha-aminoadipic semialdehyde synthase, mitochondrial
KeywordsOXIDOREDUCTASE
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 / cytoplasm / cytosol
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: 2.4 Å
AuthorsMuniz, J.R.C. / Kopec, J. / Rembeza, E. / Burgess-Brown, N. / Bountra, C. / Yue, W.W.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust092809/Z/10/Z United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of human aminoadipate semialdehyde synthase (AASS), lysine ketoglutarate reductase (LKR) domain
Authors: Muniz, J.R.C. / Kopec, J. / Rembeza, E. / Burgess-Brown, N. / Bountra, C. / Yue, W.W.
History
DepositionJun 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 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
C: Alpha-aminoadipic semialdehyde synthase, mitochondrial
D: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)212,7476
Polymers212,5554
Non-polymers1922
Water4,774265
1
A: Alpha-aminoadipic semialdehyde synthase, mitochondrial
C: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3743
Polymers106,2772
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-23 kcal/mol
Surface area32880 Å2
MethodPISA
2
B: Alpha-aminoadipic semialdehyde synthase, mitochondrial
D: Alpha-aminoadipic semialdehyde synthase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,3743
Polymers106,2772
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-22 kcal/mol
Surface area32730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.045, 80.533, 91.508
Angle α, β, γ (deg.)77.160, 67.635, 79.425
Int Tables number1
Space group name H-MP1

-
Components

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


Mass: 53138.730 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Lysine-ketoglutarate reductase (LKR) domain, residues 1-476
Source: (gene. exp.) Homo sapiens (human) / Gene: AASS / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UDR5, saccharopine dehydrogenase (NADP+, L-lysine-forming), saccharopine dehydrogenase (NAD+, L-glutamate-forming)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 20% PEG3350 -- 10% ethylene glycol -- 0.2M sodium malonate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.92819 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92819 Å / Relative weight: 1
ReflectionResolution: 2.4→78.04 Å / Num. obs: 71194 / % possible obs: 90 % / Observed criterion σ(I): 1.2 / Redundancy: 2.4 % / CC1/2: 0.553 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.069 / Rrim(I) all: 0.098 / Net I/σ(I): 9
Reflection shellResolution: 2.4→2.45 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.898 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 4508 / CC1/2: 0.553 / Rpim(I) all: 0.898 / Rrim(I) all: 1.269 / % possible all: 91.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q99

2q99


Resolution: 2.4→78.04 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.916 / SU B: 21.638 / SU ML: 0.241 / Cross valid method: THROUGHOUT / ESU R: 0.488 / ESU R Free: 0.284
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.258 3439 4.852 %
Rwork0.2184 67434 -
all0.22 --
obs-70873 89.614 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 61.811 Å2
Baniso -1Baniso -2Baniso -3
1--0.209 Å2-0.317 Å2-0.745 Å2
2---0.959 Å20.253 Å2
3---0.429 Å2
Refinement stepCycle: LAST / Resolution: 2.4→78.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12484 0 10 265 12759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01312786
X-RAY DIFFRACTIONr_bond_other_d0.0010.01511968
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.64117365
X-RAY DIFFRACTIONr_angle_other_deg1.171.57427566
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75251599
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.70521.963657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.201152104
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6131584
X-RAY DIFFRACTIONr_chiral_restr0.0620.21699
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214458
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022838
X-RAY DIFFRACTIONr_nbd_refined0.1910.22222
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.210585
X-RAY DIFFRACTIONr_nbtor_refined0.150.25904
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.25464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2280
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.28
X-RAY DIFFRACTIONr_nbd_other0.1350.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2170.214
X-RAY DIFFRACTIONr_mcbond_it2.1054.556420
X-RAY DIFFRACTIONr_mcbond_other2.1054.556419
X-RAY DIFFRACTIONr_mcangle_it3.5466.8128005
X-RAY DIFFRACTIONr_mcangle_other3.5466.8138006
X-RAY DIFFRACTIONr_scbond_it1.8154.7126366
X-RAY DIFFRACTIONr_scbond_other1.7524.7096359
X-RAY DIFFRACTIONr_scangle_it2.9897.0089358
X-RAY DIFFRACTIONr_scangle_other2.987.0049347
X-RAY DIFFRACTIONr_lrange_it5.65652.2213192
X-RAY DIFFRACTIONr_lrange_other5.64452.20113164
X-RAY DIFFRACTIONr_ncsr_local_group_10.0910.0511747
X-RAY DIFFRACTIONr_ncsr_local_group_20.0910.0511600
X-RAY DIFFRACTIONr_ncsr_local_group_30.0860.0511798
X-RAY DIFFRACTIONr_ncsr_local_group_40.10.0511532
X-RAY DIFFRACTIONr_ncsr_local_group_50.0850.0511703
X-RAY DIFFRACTIONr_ncsr_local_group_60.0940.0511472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.4620.3272560.3175106X-RAY DIFFRACTION91.6581
2.462-2.530.3022460.314934X-RAY DIFFRACTION90.7021
2.53-2.6030.3422540.34670X-RAY DIFFRACTION88.9612
2.603-2.6830.3222160.2864280X-RAY DIFFRACTION83.0593
2.683-2.7710.2832630.2484611X-RAY DIFFRACTION94.0927
2.771-2.8680.2872340.2394484X-RAY DIFFRACTION93.5925
2.868-2.9760.2832010.2224344X-RAY DIFFRACTION93.1543
2.976-3.0980.2782470.2284079X-RAY DIFFRACTION92.0817
3.098-3.2350.271940.2223896X-RAY DIFFRACTION91.4989
3.235-3.3930.2491910.223688X-RAY DIFFRACTION89.5429
3.393-3.5760.271510.2323270X-RAY DIFFRACTION84.2818
3.576-3.7920.3391520.3192932X-RAY DIFFRACTION79.546
3.792-4.0540.2351560.1963159X-RAY DIFFRACTION91.1215
4.054-4.3780.2081400.1692928X-RAY DIFFRACTION91.0926
4.378-4.7940.191260.1522618X-RAY DIFFRACTION88.1465
4.794-5.3580.21110.1622279X-RAY DIFFRACTION84.0366
5.358-6.1820.2861070.192191X-RAY DIFFRACTION94.0262
6.182-7.5610.233790.1881853X-RAY DIFFRACTION91.6074
7.561-10.650.201800.1811281X-RAY DIFFRACTION84.2724
10.65-78.040.252350.224830X-RAY DIFFRACTION95.0549
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)
11.35070.08-0.15650.15720.02350.57660.0139-0.27050.18940.074-0.0023-0.1747-0.00730.0039-0.01160.0824-0.044-0.10290.1088-0.04210.261796.85949.21750.992
21.44620.33680.14260.4572-0.02540.7954-0.12940.2536-0.2659-0.20020.1423-0.17620.0852-0.1641-0.0130.1568-0.0832-0.00870.1125-0.06740.198592.47395.48116.404
32.04270.48680.05420.2013-0.13830.2836-0.20220.480.402-0.07650.16540.08490.0628-0.05970.03680.0848-0.0648-0.09170.20240.09380.235271.17651.64824.197
40.68460.2890.22091.0692-0.04340.47460.143-0.0133-0.28320.4314-0.1445-0.39730.0846-0.11160.00150.2215-0.1011-0.20750.07040.05780.3185104.41791.82650.802
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA1 - 430
2X-RAY DIFFRACTION2ALLB2 - 428
3X-RAY DIFFRACTION3ALLC2 - 427
4X-RAY DIFFRACTION4ALLD1 - 428

+
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://pdbjlvh1.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