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- PDB-4oub: A 2.20 angstroms X-ray crystal structure of E268A 2-aminomucaonat... -

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Basic information

Entry
Database: PDB / ID: 4oub
TitleA 2.20 angstroms X-ray crystal structure of E268A 2-aminomucaonate 6-semialdehyde dehydrogenase catalytic intermediate from Pseudomonas fluorescens
Components2-aminomuconate 6-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aldehyde dehydrogenase / Dehydrogenase / NAD
Function / homology
Function and homology information


polyamine catabolic process / aldehyde dehydrogenase (NAD+) activity / retinal dehydrogenase activity / retinoic acid metabolic process / nucleotide binding
Similarity search - Function
2-hydroxymuconic semialdehyde 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 ...2-hydroxymuconic semialdehyde 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
(2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoic acid / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2-aminomuconate 6-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsHuo, L. / Liu, A.
CitationJournal: Nat Commun / Year: 2015
Title: Crystallographic and spectroscopic snapshots reveal a dehydrogenase in action.
Authors: Huo, L. / Davis, I. / Liu, F. / Andi, B. / Esaki, S. / Iwaki, H. / Hasegawa, Y. / Orville, A.M. / Liu, A.
History
DepositionFeb 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
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_conn_type / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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: 2-aminomuconate 6-semialdehyde dehydrogenase
B: 2-aminomuconate 6-semialdehyde dehydrogenase
C: 2-aminomuconate 6-semialdehyde dehydrogenase
D: 2-aminomuconate 6-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)211,56416
Polymers208,2504
Non-polymers3,31412
Water15,889882
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20890 Å2
ΔGint-152 kcal/mol
Surface area59040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.329, 141.345, 173.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
2-aminomuconate 6-semialdehyde dehydrogenase


Mass: 52062.555 Da / Num. of mol.: 4 / Mutation: E268A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: nbaE / Plasmid: pET16Bb / Production host: Escherichia coli (E. coli) / Strain (production host): KU-7 / References: UniProt: Q83V33
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-2VS / (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoic acid


Mass: 142.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 2.6 Å3/Da / Density % sol: 52.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: 0.2 M sodium phosphate dibasic dihydrate, 20% w/v polyethylene glycol 3350, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 110998 / Num. obs: 110554 / % possible obs: 99.6 % / Redundancy: 11.4 % / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.2-2.2410.30.717199.2
2.24-2.2810.50.635198.9
2.28-2.3210.70.568199.3
2.32-2.3710.80.509199.3
2.37-2.4210.80.468199.4
2.42-2.4810.80.399199.4
2.48-2.5410.80.367199.5
2.54-2.6110.80.3199.7
2.61-2.6910.80.271199.7
2.69-2.7710.90.247199.7
2.77-2.87110.208199.8
2.87-2.9911.20.168199.8
2.99-3.1211.30.14199.9
3.12-3.2911.50.115199.7
3.29-3.4911.80.104199.9
3.49-3.7611.80.091199.8
3.76-4.1411.90.08199.9
4.14-4.7412.60.0661100
4.74-5.9714.10.0571100
5.97-5014.10.041199.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0029refinement
PHENIXrefinement
PDB_EXTRACT3.14data extraction
MAR345data collection
DENZOdata reduction
PHENIXphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4I1W

4i1w


Resolution: 2.19→41 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.655 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.248 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22517 5043 5 %RANDOM
Rwork0.18019 ---
obs0.18242 104815 98.68 %-
all-111788 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.97 Å20 Å20 Å2
2---0.97 Å2-0 Å2
3---1.95 Å2
Refinement stepCycle: LAST / Resolution: 2.19→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14668 0 220 882 15770
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.01915189
X-RAY DIFFRACTIONr_bond_other_d1.3840.0214301
X-RAY DIFFRACTIONr_angle_refined_deg1.6661.95820678
X-RAY DIFFRACTIONr_angle_other_deg2.976332809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.18551928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21324660
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.575152348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.381592
X-RAY DIFFRACTIONr_chiral_restr0.1460.22345
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117400
X-RAY DIFFRACTIONr_gen_planes_other0.0080.023532
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.193→2.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 387 -
Rwork0.228 6757 -
obs--87.61 %

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