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- PDB-4zvw: Structure of apo human ALDH7A1 in space group C2 -

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Basic information

Entry
Database: PDB / ID: 4zvw
TitleStructure of apo human ALDH7A1 in space group C2
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 / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / Lysine catabolism / cellular aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity ...L-aminoadipate-semialdehyde dehydrogenase / L-aminoadipate-semialdehyde dehydrogenase activity / Choline catabolism / choline catabolic process / betaine-aldehyde dehydrogenase / betaine-aldehyde dehydrogenase activity / glycine betaine biosynthetic process from choline / Lysine catabolism / cellular aldehyde metabolic process / glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / 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; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal ...Aldehyde dehydrogenase family 7 member A1-like / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Alpha-aminoadipic semialdehyde dehydrogenase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsTanner, J.J.
CitationJournal: Biochemistry / Year: 2015
Title: Structural Basis of Substrate Recognition by Aldehyde Dehydrogenase 7A1.
Authors: Luo, M. / Tanner, J.J.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Sep 27, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)444,9638
Polymers444,9638
Non-polymers00
Water10,034557
1
A: Alpha-aminoadipic semialdehyde dehydrogenase
B: Alpha-aminoadipic semialdehyde dehydrogenase
C: Alpha-aminoadipic semialdehyde dehydrogenase
D: Alpha-aminoadipic semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)222,4814
Polymers222,4814
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19880 Å2
ΔGint-86 kcal/mol
Surface area62250 Å2
MethodPISA
2
E: Alpha-aminoadipic semialdehyde dehydrogenase
F: Alpha-aminoadipic semialdehyde dehydrogenase
G: Alpha-aminoadipic semialdehyde dehydrogenase
H: Alpha-aminoadipic semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)222,4814
Polymers222,4814
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19960 Å2
ΔGint-94 kcal/mol
Surface area62350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.016, 162.520, 160.045
Angle α, β, γ (deg.)90.000, 94.100, 90.000
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D
51chain E
61chain F
71chain G
81chain H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1

Dom-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1THRTHRGLNGLNchain AAA3 - 5115 - 513
2THRTHRLEULEUchain BBB3 - 5045 - 506
3THRTHRPHEPHEchain CCC3 - 5105 - 512
4LEULEUGLNGLNchain DDD4 - 5116 - 513
5THRTHRGLNGLNchain EEE3 - 5115 - 513
6LEULEUPHEPHEchain FFF4 - 5106 - 512
7THRTHRILEILEchain GGG3 - 5085 - 510
8LEULEUPHEPHEchain HHH4 - 5106 - 512

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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: 55620.367 Da / Num. of mol.: 8
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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 557 / 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: 2.29 Å3/Da / Density % sol: 46.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: The reservoir contained 0.2 M ammonium sulfate, 20% (w/v) polyethylene glycol (PEG) 3350, and 0.1 mM Bis-Tris pH 6.5.
PH range: 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.4→159.64 Å / Num. obs: 153212 / % possible obs: 98.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 28.9 Å2 / CC1/2: 0.967 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.092 / Net I/σ(I): 6.3 / Num. measured all: 559499 / Scaling rejects: 7
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.4-2.443.50.3133.12662676630.8740.19599.7
13.15-159.643.60.0588.833059300.9930.03693.9

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Processing

Software
NameVersionClassification
PHENIXrefinement
Aimless0.3.6data scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J6L

2j6l


Resolution: 2.4→159.636 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 2.04 / Phase error: 26.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2747 7644 4.99 %
Rwork0.2261 145566 -
obs0.2285 153210 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 95.45 Å2 / Biso mean: 37.2518 Å2 / Biso min: 4.09 Å2
Refinement stepCycle: final / Resolution: 2.4→159.636 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms29450 0 0 557 30007
Biso mean---28.44 -
Num. residues----4056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00330063
X-RAY DIFFRACTIONf_angle_d0.73840980
X-RAY DIFFRACTIONf_chiral_restr0.0284663
X-RAY DIFFRACTIONf_plane_restr0.0035365
X-RAY DIFFRACTIONf_dihedral_angle_d10.97310327
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A18006X-RAY DIFFRACTION6.139TORSIONAL
12B18006X-RAY DIFFRACTION6.139TORSIONAL
13C18006X-RAY DIFFRACTION6.139TORSIONAL
14D18006X-RAY DIFFRACTION6.139TORSIONAL
15E18006X-RAY DIFFRACTION6.139TORSIONAL
16F18006X-RAY DIFFRACTION6.139TORSIONAL
17G18006X-RAY DIFFRACTION6.139TORSIONAL
18H18006X-RAY DIFFRACTION6.139TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.42730.31232590.242748805139100
2.4273-2.45580.33782870.24494934522199
2.4558-2.48580.31392710.247948335104100
2.4858-2.51730.29612380.242449295167100
2.5173-2.55040.32062970.241348895186100
2.5504-2.58530.31422870.237748905177100
2.5853-2.62230.29082910.227249335224100
2.6223-2.66140.31472600.229748335093100
2.6614-2.7030.30922770.24849585235100
2.703-2.74730.29912810.242848845165100
2.7473-2.79470.31122470.2448825129100
2.7947-2.84550.30912740.236549335207100
2.8455-2.90030.30922360.24044952518899
2.9003-2.95950.30532360.23594887512399
2.9595-3.02380.30212380.23554855509399
3.0238-3.09420.31642440.23734854509899
3.0942-3.17150.27152390.24364896513598
3.1715-3.25730.30362750.23734804507998
3.2573-3.35320.27162530.23214806505997
3.3532-3.46140.26342250.22974794501996
3.4614-3.58510.24492210.22764745496696
3.5851-3.72870.28532320.23344808504097
3.7287-3.89840.28622530.23724765501896
3.8984-4.10390.27582210.23294729495096
4.1039-4.36110.27042490.22294790503996
4.3611-4.69780.23422450.21584752499796
4.6978-5.17060.24162430.20724798504197
5.1706-5.91880.22952640.2154784504897
5.9188-7.45710.25292830.20364813509697
7.4571-159.98980.17892180.16824956517497
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)
10.67260.1490.17620.68190.44130.85980.0446-0.22460.08530.09120.072-0.1568-0.03030.0919-0.10750.18160.0233-0.01270.2571-0.1080.284857.02858.448234.4753
20.4734-0.23210.38920.88380.20020.67840.0114-0.13210.03140.1674-0.02170.1749-0.0055-0.06490.01630.2212-0.02830.03520.3724-0.13730.322121.709858.409843.4123
31.4083-0.4357-0.36810.6736-0.00920.5261-0.01560.1362-0.1845-0.0044-0.03640.03470.0572-0.1010.04890.195-0.0313-0.02090.2018-0.10140.32245.559818.392723.7396
41.0956-0.02160.20840.6935-0.13790.26710.0155-0.4445-0.10140.3023-0.0265-0.1632-0.03480.02530.01360.3475-0.0918-0.05180.4836-0.0540.327935.985520.203557.8859
50.7230.3957-0.22410.5176-0.25520.3926-0.0043-0.0262-0.0077-0.00620.06660.0761-0.0017-0.1369-0.05680.2327-0.03070.01570.4312-0.22440.364123.840898.892233.3099
60.3719-0.2105-0.17930.5111-0.17830.13350.0288-0.21250.08250.081-0.0048-0.0546-0.0002-0.0092-0.02430.2695-0.08980.00130.4181-0.19560.335257.712299.591543.7273
70.6838-0.0198-0.24520.8117-0.22480.6376-0.0367-0.09560.170.0068-0.02850.0514-0.1389-0.22510.06360.21830.0643-0.05630.3253-0.14810.302635.9225138.708521.4159
81.07350.1843-0.11551.06160.36480.51990.0924-0.41970.08380.2445-0.05460.0605-0.1625-0.0739-0.03430.3543-0.00010.00940.4539-0.12980.279144.488137.999356.4805
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA3 - 511
2X-RAY DIFFRACTION2Chain BB3 - 504
3X-RAY DIFFRACTION3Chain CC3 - 510
4X-RAY DIFFRACTION4Chain DD4 - 511
5X-RAY DIFFRACTION5Chain EE3 - 511
6X-RAY DIFFRACTION6Chain FF4 - 510
7X-RAY DIFFRACTION7Chain GG3 - 508
8X-RAY DIFFRACTION8Chain HH4 - 510

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