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- PDB-5kj5: Crystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase... -

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Basic information

Entry
Database: PDB / ID: 5kj5
TitleCrystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase N169D in complex with NAD+
Components2-aminomuconate 6-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / 2-aminomuconate 6-semialdehyde dehydrogenase / kynurenine pathway
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2-aminomuconate 6-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.113 Å
AuthorsYang, Y. / Davis, I. / Ha, U. / Wang, Y. / Shin, I. / Liu, A.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: A Pitcher-and-Catcher Mechanism Drives Endogenous Substrate Isomerization by a Dehydrogenase in Kynurenine Metabolism.
Authors: Yang, Y. / Davis, I. / Ha, U. / Wang, Y. / Shin, I. / Liu, A.
History
DepositionJun 17, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1May 26, 2021Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
D: 2-aminomuconate 6-semialdehyde dehydrogenase
B: 2-aminomuconate 6-semialdehyde dehydrogenase
C: 2-aminomuconate 6-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,2468
Polymers224,5924
Non-polymers2,6544
Water15,187843
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20430 Å2
ΔGint-112 kcal/mol
Surface area60050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.684, 142.389, 173.383
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
2-aminomuconate 6-semialdehyde dehydrogenase


Mass: 56148.027 Da / Num. of mol.: 4 / Mutation: N169D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: nbaE / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 843 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.08 M Na2HPO4 pH 9.1, 14% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→50 Å / Num. obs: 125557 / % possible obs: 99.8 % / Redundancy: 14.2 % / Biso Wilson estimate: 41.56 Å2 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.033 / Rrim(I) all: 0.121 / Χ2: 1.03 / Net I/av σ(I): 27.75 / Net I/σ(I): 5.9 / Num. measured all: 1782869
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.11-2.1914.10.925124190.8850.2560.9610.505100
2.19-2.2714.60.693124600.9280.1880.7190.57100
2.27-2.3814.70.517124610.9530.140.5360.645100
2.38-2.514.70.384124610.9710.1040.3980.755100
2.5-2.6614.60.287124910.9780.0780.2980.883100
2.66-2.8614.50.211125340.9860.0580.2191.026100
2.86-3.1514.40.149125930.9920.0410.1541.211100
3.15-3.6114.20.111125880.9950.0310.1161.54399.9
3.61-4.5413.30.084126350.9960.0240.0871.7799.4
4.54-5013.10.063129150.9970.0190.0661.47798.3

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Processing

Software
NameVersionClassification
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I26

4i26


Resolution: 2.113→31.85 Å / FOM work R set: 0.8196 / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2365 2000 1.59 %
Rwork0.1895 123462 -
obs0.1903 125462 99.59 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.244 Å2 / ksol: 0.332 e/Å3
Displacement parametersBiso max: 87.34 Å2 / Biso mean: 44.81 Å2 / Biso min: 23.53 Å2
Baniso -1Baniso -2Baniso -3
1--3.6525 Å2-0 Å20 Å2
2---5.1827 Å20 Å2
3---8.8352 Å2
Refinement stepCycle: final / Resolution: 2.113→31.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14691 0 176 843 15710
Biso mean--47.57 48.27 -
Num. residues----1933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815200
X-RAY DIFFRACTIONf_angle_d1.10220695
X-RAY DIFFRACTIONf_chiral_restr0.0732341
X-RAY DIFFRACTIONf_plane_restr0.0042685
X-RAY DIFFRACTIONf_dihedral_angle_d14.2995396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1135-2.16630.28881380.24978549868797
2.1663-2.22490.30881420.240587318873100
2.2249-2.29030.30021420.234387658907100
2.2903-2.36420.28321420.228787798921100
2.3642-2.44870.30621420.225387458887100
2.4487-2.54670.29361430.223288218964100
2.5467-2.66260.29741410.222887798920100
2.6626-2.80290.27181440.217288368980100
2.8029-2.97830.27031430.21888138956100
2.9783-3.20810.26431440.200488518995100
3.2081-3.53060.22641420.188788599001100
3.5306-4.04060.21921450.169188949039100
4.0406-5.08740.17541430.15028896903999
5.0874-31.85390.21421490.17869144929399

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