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- PDB-4npi: 1.94 Angstroms X-ray crystal structure of NAD- and intermediate- ... -

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Basic information

Entry
Database: PDB / ID: 4npi
Title1.94 Angstroms X-ray crystal structure of NAD- and intermediate- bound alpha-aminomuconate-epsilon-semialdehyde dehydrogenase from Pseudomonas fluorescens
Components2-aminomuconate 6-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / ALDH / Dehydrogenase / NAD+
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / 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, C-terminal / Aldehyde dehydrogenase, N-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: 1.94 Å
AuthorsHuo, L. / Davis, I. / Liu, F. / Iwaki, H. / Hasegawa, Y. / 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
DepositionNov 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Sep 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)211,79616
Polymers208,4824
Non-polymers3,31412
Water30,6621702
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22270 Å2
ΔGint-126 kcal/mol
Surface area58440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.355, 141.747, 174.372
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: 52120.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: nbaE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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.: 1702 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: 20% PEG3350, 0.2 M sodium phosphate dibasic, pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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: Jun 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→34.73 Å / Num. all: 161090 / Num. obs: 152910 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Rmerge(I) obs: 0.1
Reflection shellResolution: 1.95→1.98 Å / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 4I2R

4i2r


Resolution: 1.94→109.99 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / Occupancy max: 1 / Occupancy min: 1 / SU B: 3.62 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21607 7649 5 %RANDOM
Rwork0.17172 ---
obs0.17394 145080 94.26 %-
all-161876 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.391 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20 Å2
2---0.94 Å20 Å2
3---1.72 Å2
Refinement stepCycle: LAST / Resolution: 1.94→109.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14684 0 220 1702 16606
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.01915215
X-RAY DIFFRACTIONr_bond_other_d8.530.0265
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.95920707
X-RAY DIFFRACTIONr_angle_other_deg21.7133129
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.04851928
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.45424.036664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.996152356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6471592
X-RAY DIFFRACTIONr_chiral_restr0.1960.22346
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02111600
X-RAY DIFFRACTIONr_gen_planes_other0.0220.0224
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: 1.94→1.991 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 503 -
Rwork0.242 9013 -
obs--82.95 %

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