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

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Basic information

Entry
Database: PDB / ID: 5kln
TitleCrystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase N169A in complex with NAD+
Components2-aminomuconate 6-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / 2-aminomuconate 6-semialdehyde dehydrogenase / kynurenine pathway
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 2-aminomuconate 6-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.992 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 24, 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 ...citation / citation_author / pdbx_struct_oper_list / struct_conn
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 / _struct_conn.pdbx_dist_value / _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
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)227,16212
Polymers224,4164
Non-polymers2,7468
Water21,2401179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21190 Å2
ΔGint-155 kcal/mol
Surface area59930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.698, 140.991, 173.272
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: 56104.020 Da / Num. of mol.: 4 / Mutation: N169A
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 / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1179 / 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: 2.41 Å3/Da / Density % sol: 49.05 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.16 M Na2HPO4 pH 9.1, 15% (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: Jul 31, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 148478 / % possible obs: 99.8 % / Redundancy: 12.1 % / Biso Wilson estimate: 34.4 Å2 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.031 / Rrim(I) all: 0.105 / Χ2: 1.078 / Net I/av σ(I): 29.24 / Net I/σ(I): 8.4 / Num. measured all: 1803057
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.99-2.069.70.692146800.8520.2340.7330.71399.6
2.06-2.1412.50.536147170.9470.160.5590.748100
2.14-2.2412.60.373147250.9710.110.3890.793100
2.24-2.3612.60.274147470.9820.0810.2860.855100
2.36-2.5112.60.203147760.9880.060.2120.915100
2.51-2.712.60.156148120.9920.0460.1631.019100
2.7-2.9712.50.123148520.9940.0370.1291.142100
2.97-3.412.40.093148740.9960.0280.0971.27499.8
3.4-4.2912.30.081149780.9960.0250.0851.68699.8
4.29-5011.60.069153170.9960.0220.0731.57899

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Processing

Software
NameVersionClassification
PHENIXphenix.refine: 1.7.3_928refinement
SCALEPACKdata scaling
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4I26

4i26


Resolution: 1.992→34.54 Å / FOM work R set: 0.8417 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 2000 1.35 %
Rwork0.187 146365 -
obs0.1874 148365 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 62.766 Å2 / ksol: 0.358 e/Å3
Displacement parametersBiso max: 80.31 Å2 / Biso mean: 38.18 Å2 / Biso min: 19.82 Å2
Baniso -1Baniso -2Baniso -3
1--1.0918 Å2-0 Å20 Å2
2---6.1023 Å20 Å2
3---7.1941 Å2
Refinement stepCycle: final / Resolution: 1.992→34.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14679 0 180 1179 16038
Biso mean--34.09 46.2 -
Num. residues----1933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815212
X-RAY DIFFRACTIONf_angle_d1.1420713
X-RAY DIFFRACTIONf_chiral_restr0.0732343
X-RAY DIFFRACTIONf_plane_restr0.0042687
X-RAY DIFFRACTIONf_dihedral_angle_d13.9335402
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 (%)
1.9919-2.04170.30271400.2373103021044299
2.0417-2.09690.27321420.21561036410506100
2.0969-2.15860.24151420.20621039710539100
2.1586-2.22830.25511420.20221035510497100
2.2283-2.30790.24971410.20071037510516100
2.3079-2.40030.25491430.19311042910572100
2.4003-2.50950.20211420.19231038610528100
2.5095-2.64180.25121430.18781043010573100
2.6418-2.80720.27411420.20051042710569100
2.8072-3.02380.21651440.19171048310627100
3.0238-3.32790.18881420.1721046210604100
3.3279-3.80890.19661440.1681052810672100
3.8089-4.79680.20041440.16771056810712100
4.7968-34.54550.22421490.2022108591100899

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