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- PDB-5klo: Crystal structure of thioacyl intermediate in 2-aminomuconate 6-s... -

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Basic information

Entry
Database: PDB / ID: 5klo
TitleCrystal structure of thioacyl intermediate in 2-aminomuconate 6-semialdehyde dehydrogenase N169A
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
(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: 1.79 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
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)227,73016
Polymers224,4164
Non-polymers3,31412
Water26,4641469
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21070 Å2
ΔGint-148 kcal/mol
Surface area58620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.111, 141.724, 171.505
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 BL21(DE3) (bacteria) / References: UniProt: Q83V33
#2: 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
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1469 / 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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 0.15 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: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→50 Å / Num. obs: 193366 / % possible obs: 95.3 % / Redundancy: 11.7 % / Biso Wilson estimate: 30.4 Å2 / Rmerge(I) obs: 0.076 / Net I/av σ(I): 34.641 / Net I/σ(I): 8.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.79-1.8511.80.813186.8
1.85-1.93120.564192.2
1.93-2.02120.344194.1
2.02-2.1211.90.245195.6
2.12-2.2611.90.171196.7
2.26-2.4311.90.128197.6
2.43-2.6711.90.1198.1
2.67-3.0611.80.08198.4
3.06-3.8611.50.063198.2
3.86-5010.70.051194.9

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Processing

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

4i26


Resolution: 1.79→34.896 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.13
RfactorNum. reflection% reflection
Rfree0.2032 2000 1.03 %
Rwork0.1789 --
obs0.1791 193288 95.05 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Bsol: 58.753 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 73.65 Å2 / Biso mean: 34.07 Å2 / Biso min: 18.16 Å2
Baniso -1Baniso -2Baniso -3
1--5.5599 Å2-0 Å20 Å2
2---1.9015 Å20 Å2
3---7.4614 Å2
Refinement stepCycle: final / Resolution: 1.79→34.896 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14679 0 220 1475 16374
Biso mean--38.35 42.04 -
Num. residues----1933
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00715228
X-RAY DIFFRACTIONf_angle_d1.11820719
X-RAY DIFFRACTIONf_chiral_restr0.0762341
X-RAY DIFFRACTIONf_plane_restr0.0042689
X-RAY DIFFRACTIONf_dihedral_angle_d15.1355424
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 (%)
1.7853-1.830.28571210.2328115911171282
1.83-1.87940.27271370.2176130621319992
1.8794-1.93470.24421390.2085132301336993
1.9347-1.99720.24841390.1997134241356394
1.9972-2.06850.2631420.197135371367995
2.0685-2.15140.23361440.1925137641390896
2.1514-2.24920.22181440.1835138221396697
2.2492-2.36780.21261470.1799139681411598
2.3678-2.51610.19951460.1815140531419998
2.5161-2.71030.20131480.1773140591420798
2.7103-2.98290.20051480.1813142161436498
2.9829-3.41430.21041480.1795142411438998
3.4143-4.30040.17071490.1562141861433597
4.3004-34.90250.19381480.1802141351428394

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