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- PDB-4i1w: 2.00 Angstroms X-ray crystal structure of NAD- bound 2-aminomucon... -

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Basic information

Entry
Database: PDB / ID: 4i1w
Title2.00 Angstroms X-ray crystal structure of NAD- bound 2-aminomuconate 6-semialdehyde dehydrogenase from Pseudomonas fluorescens
Components2-aminomuconate 6-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aldehyde dehydrogenase / Dehydrogenase / NAD
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: 1.992 Å
AuthorsHuo, L. / Davis, I. / 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 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)218,74110
Polymers215,9034
Non-polymers2,8386
Water30,3011682
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20840 Å2
ΔGint-110 kcal/mol
Surface area60200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.584, 141.999, 174.382
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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) / Gene: nbaE / Plasmid: pET16Bb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1682 / 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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 9.1
Details: 0.2 M Sodium phosphate dibasic dihydrate, 20% w/v Polyethylene glycol 3,350 , pH 9.1, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→35 Å / Num. all: 149904 / Num. obs: 149605 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rmerge(I) obs: 0.112 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2-2.079.10.891198.9
2.07-2.1511.90.7741100
2.15-2.2513.50.581100
2.25-2.3714.10.4431100
2.37-2.5214.40.3211100
2.52-2.7114.70.2241100
2.71-2.99150.151100
2.99-3.4215.10.0871100
3.42-4.3114.90.0641100
4.31-3514.60.04199.2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
REFMAC5.7.0029refinement
PDB_EXTRACT3.11data extraction
SERGUIdata collection
HKL-2000data reduction
PHENIXphasing
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2D4E

2d4e


Resolution: 1.992→22.257 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.25 / σ(F): 1.33 / Phase error: 22.2 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflection
Rfree0.2183 7485 5.01 %
Rwork0.1697 --
obs0.1721 149298 99.31 %
all-150484 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.522 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.384 Å2-0 Å20 Å2
2---3.9388 Å20 Å2
3---5.3228 Å2
Refinement stepCycle: LAST / Resolution: 1.992→22.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14684 0 188 1682 16554
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01215235
X-RAY DIFFRACTIONf_angle_d1.42620744
X-RAY DIFFRACTIONf_dihedral_angle_d13.8755380
X-RAY DIFFRACTIONf_chiral_restr0.1332346
X-RAY DIFFRACTIONf_plane_restr0.0062686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9921-2.01470.34482160.26984048X-RAY DIFFRACTION86
2.0147-2.03840.32852480.25334649X-RAY DIFFRACTION99
2.0384-2.06320.28952560.22494678X-RAY DIFFRACTION100
2.0632-2.08930.29672540.2214699X-RAY DIFFRACTION100
2.0893-2.11680.27892450.20874695X-RAY DIFFRACTION100
2.1168-2.14580.27862600.19734700X-RAY DIFFRACTION100
2.1458-2.17640.24482590.19224717X-RAY DIFFRACTION100
2.1764-2.20890.24842290.18864725X-RAY DIFFRACTION100
2.2089-2.24330.25662340.18484707X-RAY DIFFRACTION100
2.2433-2.28010.26922530.1864754X-RAY DIFFRACTION100
2.2801-2.31940.24652490.17484712X-RAY DIFFRACTION100
2.3194-2.36150.24742530.17254719X-RAY DIFFRACTION100
2.3615-2.40690.24242690.16494694X-RAY DIFFRACTION100
2.4069-2.45590.24132680.16494702X-RAY DIFFRACTION100
2.4559-2.50930.22452300.16544762X-RAY DIFFRACTION100
2.5093-2.56750.21612530.15984734X-RAY DIFFRACTION100
2.5675-2.63170.23422310.16274753X-RAY DIFFRACTION100
2.6317-2.70270.21462740.16134728X-RAY DIFFRACTION100
2.7027-2.78210.23212580.16224742X-RAY DIFFRACTION100
2.7821-2.87170.21732370.16594755X-RAY DIFFRACTION100
2.8717-2.97410.20932550.16644742X-RAY DIFFRACTION100
2.9741-3.09290.2562610.17694728X-RAY DIFFRACTION100
3.0929-3.23320.2232650.16994747X-RAY DIFFRACTION100
3.2332-3.40310.2112340.17244807X-RAY DIFFRACTION100
3.4031-3.61550.21652560.17574754X-RAY DIFFRACTION100
3.6155-3.89330.20292580.16484769X-RAY DIFFRACTION99
3.8933-4.28260.19082680.1484784X-RAY DIFFRACTION99
4.2826-4.89660.14872450.12824822X-RAY DIFFRACTION99
4.8966-6.14750.19852460.16584884X-RAY DIFFRACTION100
6.1475-22.25860.18142210.1745103X-RAY DIFFRACTION100

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