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- PDB-5kll: Crystal structure of 2-hydroxymuconate-6-semialdehyde derived tau... -

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Basic information

Entry
Database: PDB / ID: 5kll
TitleCrystal structure of 2-hydroxymuconate-6-semialdehyde derived tautomeric intermediate in 2-aminomuconate 6-semialdehyde dehydrogenase N169D
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
Chem-6UN / 2-aminomuconate 6-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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_conn_angle / 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_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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
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)225,25312
Polymers224,5924
Non-polymers6608
Water21,4381190
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16090 Å2
ΔGint-127 kcal/mol
Surface area60190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.364, 143.055, 174.076
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-6UN / (3~{E},5~{E})-6-oxidanyl-2-oxidanylidene-hexa-3,5-dienoic acid


Mass: 142.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6O4
#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


Mass: 18.015 Da / Num. of mol.: 1190 / 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: 2.45 Å3/Da / Density % sol: 49.78 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.08 M Na2HPO4 pH 9.1, 13% (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: Nov 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 115719 / % possible obs: 99.6 % / Redundancy: 14.3 % / Biso Wilson estimate: 34.03 Å2 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.036 / Rrim(I) all: 0.136 / Χ2: 1.09 / Net I/av σ(I): 26.548 / Net I/σ(I): 6.9 / Num. measured all: 1651243
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.16-2.24140.929198.9
2.24-2.3314.20.692199.5
2.33-2.4314.30.532199.2
2.43-2.5614.30.389199.5
2.56-2.7214.20.286199.7
2.72-2.9314.30.208199.7
2.93-3.2314.30.142199.8
3.23-3.6914.50.106199.9
3.69-4.6514.50.08199.9
4.65-5014.20.064199.6

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Processing

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

4i26


Resolution: 2.17→35.152 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.33
RfactorNum. reflection% reflection
Rfree0.2178 1999 1.73 %
Rwork0.1695 --
obs0.1703 115617 98.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 38.681 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 84.54 Å2 / Biso mean: 36.5527 Å2 / Biso min: 18.01 Å2
Baniso -1Baniso -2Baniso -3
1--3.2283 Å2-0 Å20 Å2
2---3.7157 Å20 Å2
3---6.944 Å2
Refinement stepCycle: final / Resolution: 2.17→35.152 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14684 0 44 1196 15924
Biso mean--37.95 41.87 -
Num. residues----1932
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00815092
X-RAY DIFFRACTIONf_angle_d1.05820514
X-RAY DIFFRACTIONf_chiral_restr0.072315
X-RAY DIFFRACTIONf_plane_restr0.0042693
X-RAY DIFFRACTIONf_dihedral_angle_d14.215380
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 (%)
2.1699-2.22410.27681240.20977055717987
2.2241-2.28430.27221420.20548066820899
2.2843-2.35150.27761430.18958105824899
2.3515-2.42730.25551420.18588047818999
2.4273-2.51410.25551420.182181208262100
2.5141-2.61470.23921430.184881108253100
2.6147-2.73370.27651430.19381178260100
2.7337-2.87770.27771440.193381778321100
2.8777-3.05790.24981450.192281948339100
3.0579-3.29390.2441430.175481838326100
3.2939-3.6250.21931450.167582298374100
3.625-4.14890.1881460.147682698415100
4.1489-5.22440.15671470.132683508497100
5.2244-35.15650.18531500.172585968746100

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