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- PDB-6v0z: Structure of ALDH7A1 mutant R441C complexed with NAD -

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Basic information

Entry
Database: PDB / ID: 6v0z
TitleStructure of ALDH7A1 mutant R441C complexed with NAD
ComponentsAlpha-aminoadipic semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / NAD / LYSINE CATABOLISM
Function / homology
Function and homology information


L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / betaine-aldehyde dehydrogenase activity / betaine-aldehyde dehydrogenase / glycine betaine biosynthetic process from choline / Lysine catabolism / cellular aldehyde metabolic process / aldehyde dehydrogenase (NAD+) ...L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / betaine-aldehyde dehydrogenase activity / betaine-aldehyde dehydrogenase / glycine betaine biosynthetic process from choline / Lysine catabolism / cellular aldehyde metabolic process / aldehyde dehydrogenase (NAD+) / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) activity / sensory perception of sound / mitochondrial matrix / mitochondrion / extracellular exosome / identical protein binding / nucleus / cytosol
Similarity search - Function
Aldehyde dehydrogenase family 7 member A1-like / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsKorasick, D.A. / Tanner, J.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM093123 United States
CitationJournal: To Be Published
Title: Structure of ALDH7A1 mutant R441C complexed with NAD
Authors: Korasick, D.A. / Tanner, J.J.
History
DepositionNov 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha-aminoadipic semialdehyde dehydrogenase
B: Alpha-aminoadipic semialdehyde dehydrogenase
C: Alpha-aminoadipic semialdehyde dehydrogenase
D: Alpha-aminoadipic semialdehyde dehydrogenase
E: Alpha-aminoadipic semialdehyde dehydrogenase
F: Alpha-aminoadipic semialdehyde dehydrogenase
G: Alpha-aminoadipic semialdehyde dehydrogenase
H: Alpha-aminoadipic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)449,90017
Polymers444,5308
Non-polymers5,3699
Water29,1841620
1
A: Alpha-aminoadipic semialdehyde dehydrogenase
B: Alpha-aminoadipic semialdehyde dehydrogenase
C: Alpha-aminoadipic semialdehyde dehydrogenase
D: Alpha-aminoadipic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,9819
Polymers222,2654
Non-polymers2,7165
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26620 Å2
ΔGint-130 kcal/mol
Surface area59890 Å2
MethodPISA
2
E: Alpha-aminoadipic semialdehyde dehydrogenase
F: Alpha-aminoadipic semialdehyde dehydrogenase
G: Alpha-aminoadipic semialdehyde dehydrogenase
H: Alpha-aminoadipic semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,9198
Polymers222,2654
Non-polymers2,6544
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26220 Å2
ΔGint-132 kcal/mol
Surface area60330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.964, 161.647, 158.542
Angle α, β, γ (deg.)90.000, 94.450, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 3 through 14 or (resid 15...
21(chain B and (resid 3 through 14 or (resid 15...
31(chain C and (resid 3 through 14 or (resid 15...
41(chain D and (resid 3 through 14 or (resid 15...
51(chain E and (resid 3 through 14 or (resid 15...
61(chain F and (resid 3 through 14 or (resid 15...
71(chain G and (resid 3 through 19 or (resid 20...
81(chain H and (resid 3 through 19 or (resid 20...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 3 through 14 or (resid 15...A3 - 14
121(chain A and (resid 3 through 14 or (resid 15...A15
131(chain A and (resid 3 through 14 or (resid 15...A3 - 601
141(chain A and (resid 3 through 14 or (resid 15...A3 - 601
151(chain A and (resid 3 through 14 or (resid 15...A3 - 601
161(chain A and (resid 3 through 14 or (resid 15...A3 - 601
211(chain B and (resid 3 through 14 or (resid 15...B3 - 14
221(chain B and (resid 3 through 14 or (resid 15...B15
231(chain B and (resid 3 through 14 or (resid 15...B3 - 601
241(chain B and (resid 3 through 14 or (resid 15...B3 - 601
251(chain B and (resid 3 through 14 or (resid 15...B3 - 601
261(chain B and (resid 3 through 14 or (resid 15...B3 - 601
311(chain C and (resid 3 through 14 or (resid 15...C3 - 14
321(chain C and (resid 3 through 14 or (resid 15...C15
331(chain C and (resid 3 through 14 or (resid 15...C3 - 601
341(chain C and (resid 3 through 14 or (resid 15...C3 - 601
351(chain C and (resid 3 through 14 or (resid 15...C3 - 601
411(chain D and (resid 3 through 14 or (resid 15...D3 - 14
421(chain D and (resid 3 through 14 or (resid 15...D15
431(chain D and (resid 3 through 14 or (resid 15...D3 - 601
441(chain D and (resid 3 through 14 or (resid 15...D3 - 601
451(chain D and (resid 3 through 14 or (resid 15...D3 - 601
461(chain D and (resid 3 through 14 or (resid 15...D3 - 601
511(chain E and (resid 3 through 14 or (resid 15...E3 - 14
521(chain E and (resid 3 through 14 or (resid 15...E15
531(chain E and (resid 3 through 14 or (resid 15...E3 - 601
541(chain E and (resid 3 through 14 or (resid 15...E3 - 601
551(chain E and (resid 3 through 14 or (resid 15...E3 - 601
611(chain F and (resid 3 through 14 or (resid 15...F3 - 14
621(chain F and (resid 3 through 14 or (resid 15...F15
631(chain F and (resid 3 through 14 or (resid 15...F3 - 601
711(chain G and (resid 3 through 19 or (resid 20...G3 - 19
721(chain G and (resid 3 through 19 or (resid 20...G20 - 21
731(chain G and (resid 3 through 19 or (resid 20...G3 - 601
741(chain G and (resid 3 through 19 or (resid 20...G3 - 601
751(chain G and (resid 3 through 19 or (resid 20...G3 - 601
761(chain G and (resid 3 through 19 or (resid 20...G3 - 601
811(chain H and (resid 3 through 19 or (resid 20...H3 - 19
821(chain H and (resid 3 through 19 or (resid 20...H20 - 21
831(chain H and (resid 3 through 19 or (resid 20...H3 - 601
841(chain H and (resid 3 through 19 or (resid 20...H3 - 601
851(chain H and (resid 3 through 19 or (resid 20...H3 - 601
861(chain H and (resid 3 through 19 or (resid 20...H3 - 601

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Components

#1: Protein
Alpha-aminoadipic semialdehyde dehydrogenase / Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / Betaine ...Alpha-AASA dehydrogenase / Aldehyde dehydrogenase family 7 member A1 / Antiquitin-1 / Betaine aldehyde dehydrogenase / Delta1-piperideine-6-carboxylate dehydrogenase / P6c dehydrogenase


Mass: 55566.312 Da / Num. of mol.: 8 / Mutation: R441C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH7A1, ATQ1 / Production host: Escherichia coli (E. coli)
References: UniProt: P49419, L-aminoadipate-semialdehyde dehydrogenase, aldehyde dehydrogenase (NAD+), betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1620 / Source method: isolated from a natural source / Formula: H2O
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: 2.23 Å3/Da / Density % sol: 44.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 21% PEG 3350, 0.2 M magnesium chloride, Bis-Tris pH 6.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1.00003 Å
DetectorType: RDI CMOS_8M / Detector: CMOS / Date: Oct 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.02→48.073 Å / Num. obs: 252123 / % possible obs: 99.3 % / Redundancy: 3.6 % / CC1/2: 0.987 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.108 / Rrim(I) all: 0.207 / Net I/σ(I): 6.5
Reflection shellResolution: 2.02→2.05 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1.646 / Num. measured all: 41141 / Num. unique obs: 12517 / CC1/2: 0.345 / Rpim(I) all: 1.077 / Rrim(I) all: 1.973 / Net I/σ(I) obs: 0.7 / % possible all: 99.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.14-3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4zuk
Resolution: 2.02→48.073 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 26.33
RfactorNum. reflection% reflection
Rfree0.2488 12316 4.91 %
Rwork0.1937 --
obs0.1964 250997 98.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.31 Å2 / Biso mean: 29.8094 Å2 / Biso min: 9.2 Å2
Refinement stepCycle: final / Resolution: 2.02→48.073 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30792 0 356 1620 32768
Biso mean--31.71 29.81 -
Num. residues----4072
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A18753X-RAY DIFFRACTION8.01TORSIONAL
12B18753X-RAY DIFFRACTION8.01TORSIONAL
13C18753X-RAY DIFFRACTION8.01TORSIONAL
14D18753X-RAY DIFFRACTION8.01TORSIONAL
15E18753X-RAY DIFFRACTION8.01TORSIONAL
16F18753X-RAY DIFFRACTION8.01TORSIONAL
17G18753X-RAY DIFFRACTION8.01TORSIONAL
18H18753X-RAY DIFFRACTION8.01TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.02-2.0430.37554000.3165769696
2.043-2.0670.3764080.3339767396
2.067-2.09220.34744000.298785898
2.0922-2.11870.34914270.2846803099
2.1187-2.14660.34854330.2771793099
2.1466-2.1760.33594060.26747992100
2.176-2.20710.31844040.25317978100
2.2071-2.240.35734110.2985787298
2.24-2.2750.33224260.2762783298
2.275-2.31230.31854510.2399794799
2.3123-2.35220.30414390.2342790299
2.3522-2.39490.30314330.2278056100
2.3949-2.4410.29234440.22258030100
2.441-2.49080.27224470.21148003100
2.4908-2.5450.28463870.20248056100
2.545-2.60420.25544150.19488030100
2.6042-2.66930.26444290.2048795799
2.6693-2.74150.27314310.20657988100
2.7415-2.82210.25243870.1938057100
2.8221-2.91320.2654100.19588028100
2.9132-3.01730.26064030.19068040100
3.0173-3.13810.25053880.18888048100
3.1381-3.28090.22933780.1735806599
3.2809-3.45380.22923730.1741790698
3.4538-3.67010.21884410.1663784998
3.6701-3.95340.214170.1597781497
3.9534-4.3510.20263110.1489800698
4.351-4.980.1614300.1309790598
4.98-6.27210.19363630.1505809299
6.2721-48.0730.16984240.1579804198
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.38190.22980.06980.42940.11010.41360.016-0.0093-0.06180.0030.013-0.08930.01670.1001-0.02420.15440.0126-0.00410.1872-0.0460.268756.88358.682533.8721
20.3589-0.10030.03150.6570.12450.43480.0055-0.04820.03910.0506-0.04150.1463-0.0267-0.09780.03430.1521-0.02120.01920.1938-0.04740.247122.464258.286443.2188
30.4351-0.1498-0.08670.37050.05310.3132-0.01360.0938-0.1706-0.0527-0.03170.03450.0316-0.03610.0390.1592-0.00120.00540.1932-0.04230.306345.504418.747123.6224
40.29330.04170.05390.3345-0.12910.58410.0187-0.1115-0.06950.0998-0.0117-0.04690.01820.0336-0.00980.2084-0.0205-0.01890.2210.00410.245136.077320.393357.9193
50.78680.404-0.13930.3767-0.14090.2354-0.02890.0338-0.0082-0.03260.02550.06030.0271-0.0690.0010.1685-0.00010.00250.2012-0.07940.244823.879898.251733.1999
60.3649-0.1226-0.07640.3467-0.02510.35250.0174-0.0304-0.04980.0324-0.017-0.07340.00960.05310.0060.1775-0.0241-0.00960.2318-0.05770.287158.194498.912143.2838
70.407-0.0522-0.03820.4596-0.1140.3580.0011-0.03060.1257-0.0486-0.0140.0856-0.035-0.07270.00490.17980.0108-0.02510.2181-0.06010.327435.4162137.735321.9811
80.5923-0.0038-0.2550.30950.12190.34860.0298-0.19840.10210.11270.0124-0.0028-0.03840.0167-0.04480.2237-0.02170.02240.2627-0.08130.265444.093137.224556.5494
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 511)A3 - 511
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 511)B3 - 511
3X-RAY DIFFRACTION3(chain 'C' and resid 3 through 511)C3 - 511
4X-RAY DIFFRACTION4(chain 'D' and resid 3 through 511)D3 - 511
5X-RAY DIFFRACTION5(chain 'E' and resid 3 through 511)E3 - 511
6X-RAY DIFFRACTION6(chain 'F' and resid 3 through 511)F3 - 511
7X-RAY DIFFRACTION7(chain 'G' and resid 3 through 511)G3 - 511
8X-RAY DIFFRACTION8(chain 'H' and resid 3 through 511)H3 - 511

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