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- PDB-4i26: 2.20 Angstroms X-ray crystal structure of 2-aminomuconate 6-semia... -

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Basic information

Entry
Database: PDB / ID: 4i26
Title2.20 Angstroms X-ray crystal structure of 2-aminomuconate 6-semialdehyde dehydrogenase from Pseudomonas fluorescens
Components2-aminomuconate 6-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aldehyde dehydrogenase / Dehydrogenase
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
2-aminomuconate 6-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas fluorescens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.204 Å
AuthorsDavis, I. / Huo, L. / Chen, L. / 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, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 21, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)216,28212
Polymers215,9034
Non-polymers3798
Water12,647702
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17360 Å2
ΔGint-93 kcal/mol
Surface area60470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.266, 141.894, 172.917
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: 53975.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Strain: KU-7 / Gene: nbaE / Plasmid: pET16Bb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83V33
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Sodium formate, 12% w/v polyethylene glycol 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 2.2→45 Å / Num. all: 109943 / Num. obs: 109724 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.08 / Χ2: 1.475 / Net I/σ(I): 10
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.2411.60.53553620.973199.4
2.24-2.2812.30.4854071.012199.4
2.28-2.32130.42654220.992199.5
2.32-2.3713.40.39154410.986199.9
2.37-2.4213.80.3554270.987199.9
2.42-2.48140.30554091.003199.9
2.48-2.5414.10.26454631.0471100
2.54-2.6114.30.2354581.0681100
2.61-2.6914.30.20954371.157199.9
2.69-2.7714.40.18854561.2121100
2.77-2.8714.50.15954651.294199.9
2.87-2.9914.60.13254691.3641100
2.99-3.1214.50.10855041.4451100
3.12-3.2914.60.08754861.5251100
3.29-3.4914.70.07654861.6721100
3.49-3.7614.60.0755092.177199.9
3.76-4.1414.30.06355432.6231100
4.14-4.74140.05255732.477199.7
4.74-5.9714.50.04756172.07199.9
5.97-4513.50.03957902.037198.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2D4E

2d4e


Resolution: 2.204→31.72 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8177 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 25.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2386 5469 4.99 %Random
Rwork0.1861 ---
all0.1887 110015 --
obs0.1887 109619 99.64 %-
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 27.642 Å2 / ksol: 0.324 e/Å3
Displacement parametersBiso max: 89.68 Å2 / Biso mean: 41.1557 Å2 / Biso min: 17.23 Å2
Baniso -1Baniso -2Baniso -3
1-3.24 Å2-0 Å20 Å2
2---5.5699 Å20 Å2
3---2.3299 Å2
Refinement stepCycle: LAST / Resolution: 2.204→31.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14651 0 23 702 15376
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01414997
X-RAY DIFFRACTIONf_angle_d1.36920388
X-RAY DIFFRACTIONf_chiral_restr0.0752303
X-RAY DIFFRACTIONf_plane_restr0.0062666
X-RAY DIFFRACTIONf_dihedral_angle_d13.8075313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2041-2.22910.35091740.24323215338994
2.2291-2.25540.30431620.23093441360399
2.2554-2.28290.32321690.225934423611100
2.2829-2.31170.28061970.215234193616100
2.3117-2.34220.29741970.211333913588100
2.3422-2.37420.30111930.208834463639100
2.3742-2.40810.28351930.194734133606100
2.4081-2.44410.25931780.189534593637100
2.4441-2.48220.25411740.185934343608100
2.4822-2.52290.28641780.188735003678100
2.5229-2.56640.27091860.194434093595100
2.5664-2.61310.26271630.193935103673100
2.6131-2.66330.27531790.194834683647100
2.6633-2.71760.27111890.202734073596100
2.7176-2.77670.27911900.208734833673100
2.7767-2.84120.29841890.207434603649100
2.8412-2.91220.27671740.201334583632100
2.9122-2.99090.2871720.205234843656100
2.9909-3.07890.28161760.203134873663100
3.0789-3.17810.27781890.198634573646100
3.1781-3.29160.23381780.195935233701100
3.2916-3.42330.26751760.204234673643100
3.4233-3.57890.2411650.199335023667100
3.5789-3.76730.24191840.190335073691100
3.7673-4.00290.20091810.168235253706100
4.0029-4.31120.17981600.15835293689100
4.3112-4.74380.19071840.141335203704100
4.7438-5.42730.2151990.158235273726100
5.4273-6.82660.23521970.195735913788100
6.8266-31.72340.1792230.17893676389999

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