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- PDB-4oe5: Structure of Human ALDH4A1 Crystallized in Space Group P21 -

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Basic information

Entry
Database: PDB / ID: 4oe5
TitleStructure of Human ALDH4A1 Crystallized in Space Group P21
ComponentsDelta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
KeywordsOXIDOREDUCTASE / ALDEHYDE DEHYDROGENASE / ALDH4A1 / ROSSMANN FOLD / NAD / MITOCHONDRIA
Function / homology
Function and homology information


Proline catabolism / proline metabolic process / 4-hydroxyproline catabolic process / proline catabolic process / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / aldehyde dehydrogenase (NAD+) activity / Glyoxylate metabolism and glycine degradation / electron transfer activity ...Proline catabolism / proline metabolic process / 4-hydroxyproline catabolic process / proline catabolic process / L-glutamate gamma-semialdehyde dehydrogenase / 1-pyrroline-5-carboxylate dehydrogenase activity / proline catabolic process to glutamate / aldehyde dehydrogenase (NAD+) activity / Glyoxylate metabolism and glycine degradation / electron transfer activity / mitochondrial matrix / mitochondrion / identical protein binding / cytosol
Similarity search - Function
Delta-1-pyrroline-5-carboxylate dehydrogenase / 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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain ...Delta-1-pyrroline-5-carboxylate dehydrogenase / 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, cysteine active site / Aldehyde dehydrogenases cysteine 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
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTanner, J.J.
CitationJournal: Biochemistry / Year: 2014
Title: Structural Studies of Yeast Delta (1)-Pyrroline-5-carboxylate Dehydrogenase (ALDH4A1): Active Site Flexibility and Oligomeric State.
Authors: Pemberton, T.A. / Srivastava, D. / Sanyal, N. / Henzl, M.T. / Becker, D.F. / Tanner, J.J.
History
DepositionJan 11, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Mar 18, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 1.4Sep 20, 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 / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
C: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
D: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)241,2608
Polymers240,5204
Non-polymers7394
Water4,342241
1
A: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
B: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,7615
Polymers120,2602
Non-polymers5013
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 Å2
ΔGint-19 kcal/mol
Surface area37100 Å2
MethodPISA
2
C: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
D: Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,4983
Polymers120,2602
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-15 kcal/mol
Surface area37140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.960, 121.335, 93.397
Angle α, β, γ (deg.)90.000, 104.230, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Delta-1-pyrroline-5-carboxylate dehydrogenase, mitochondrial / P5C dehydrogenase / Aldehyde dehydrogenase family 4 member A1 / L-glutamate gamma-semialdehyde dehydrogenase


Mass: 60130.094 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ALDH4, ALDH4A1, P5CDH / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3)pLysS
References: UniProt: P30038, L-glutamate gamma-semialdehyde dehydrogenase
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 - 25 % (w/v) PEG 3350, 0.2 M MgCl2, and 0.1 M HEPES at pH 7.0 - 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 28, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 139296 / % possible obs: 96.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.049 / Χ2: 0.956 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.95-2.023.30.453133560.764193
2.02-2.13.30.333134340.784193.3
2.1-2.23.40.219135860.823194.4
2.2-2.313.40.168137230.866195.4
2.31-2.463.40.123138850.887196.3
2.46-2.653.50.095139940.919197.2
2.65-2.913.60.066141250.987198
2.91-3.333.70.046142981.118198.8
3.33-4.23.70.032143521.273199.2
4.2-503.70.023145431.014199.3

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8_1069refinement
PDB_EXTRACT3.14data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3V9G

3v9g


Resolution: 1.95→42.411 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8145 / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2347 6972 5.01 %random
Rwork0.1938 ---
obs0.1959 139239 96.21 %-
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.47 Å2 / Biso mean: 33.1479 Å2 / Biso min: 10.62 Å2
Refinement stepCycle: LAST / Resolution: 1.95→42.411 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15149 0 46 241 15436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715562
X-RAY DIFFRACTIONf_angle_d1.01221236
X-RAY DIFFRACTIONf_chiral_restr0.0682418
X-RAY DIFFRACTIONf_plane_restr0.0052771
X-RAY DIFFRACTIONf_dihedral_angle_d12.3595348
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9484-2.01810.30116490.2279123291297890
2.0181-2.09880.28056930.2199128191351293
2.0988-2.19440.27966790.2093128971357694
2.1944-2.31010.26197150.2031130741378995
2.3101-2.45480.26456960.2033131951389196
2.4548-2.64430.26247070.204133341404197
2.6443-2.91030.26556880.2107134661415498
2.9103-3.33130.26847100.2247136391434999
3.3313-4.19650.20466810.1799137141439599
4.1965-42.42070.1847540.1632138001455499
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)
11.3616-0.3880.4610.7737-0.21690.6860.01690.23140.0875-0.0878-0.00070.0992-0.0432-0.0578-0.0210.149-0.02150.01510.22070.03240.1306-9.5167-5.182411.4309
21.59020.29070.24871.26740.06670.4165-0.02260.19210.02470.11040.0167-0.1602-0.01670.08630.00020.1714-0.040.02560.193-0.02520.187927.03225.803421.165
31.5011-0.67460.55960.94260.01930.47640.0007-0.1370.0114-0.04770.0247-0.07990.0071-0.0477-0.020.17340.0353-0.00180.1362-0.00560.106818.5915-6.887264.9814
41.09410.47040.17421.04380.35660.44020.0336-0.03450.0233-0.077-0.11880.2040.0112-0.11750.06080.17060.0553-0.01830.1789-0.03360.2345-16.3176.782652.8798
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1Chain AA23 - 551
2X-RAY DIFFRACTION2Chain BB23 - 551
3X-RAY DIFFRACTION3Chain CC23 - 551
4X-RAY DIFFRACTION4Chain DD23 - 551

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