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- PDB-4itb: Structure of bacterial enzyme in complex with cofactor and substrate -

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Basic information

Entry
Database: PDB / ID: 4itb
TitleStructure of bacterial enzyme in complex with cofactor and substrate
ComponentsSuccinate-semialdehyde dehydrogenase
Keywordsoxidoreductase/substrate / Rossmann fold / OXIDOREDUCTASE / oxidoreductase-substrate complex
Function / homology
Function and homology information


succinate-semialdehyde dehydrogenase (NAD+) activity / aldehyde dehydrogenase [NAD(P)+] activity / nucleotide binding
Similarity search - Function
Succinate-semialdehyde dehydrogenase GabD1-like / : / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal ...Succinate-semialdehyde dehydrogenase GabD1-like / : / 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 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-NDP / 4-oxobutanoic acid / Succinate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / Soaking / Resolution: 1.4 Å
AuthorsRhee, S. / Park, J.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for a Cofactor-dependent Oxidation Protection and Catalysis of Cyanobacterial Succinic Semialdehyde Dehydrogenase.
Authors: Park, J. / Rhee, S.
History
DepositionJan 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Succinate-semialdehyde dehydrogenase
B: Succinate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,70330
Polymers98,5182
Non-polymers3,18528
Water12,268681
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11480 Å2
ΔGint38 kcal/mol
Surface area30740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.003, 115.434, 180.102
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 Succinate-semialdehyde dehydrogenase


Mass: 49259.188 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus sp. (bacteria) / Strain: ATCC 27264 / PCC 7002 / PR-6 / Production host: Escherichia coli (E. coli) / References: UniProt: B1XMM6
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-SSN / 4-oxobutanoic acid / Succinic semialdehyde


Mass: 102.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O3
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 681 / 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: 2.27 Å3/Da / Density % sol: 45.78 %

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Data collection

Diffraction sourceWavelength: 0.97948 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97948 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 177093 / % possible obs: 99.9 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.105 / Χ2: 1.023 / Net I/σ(I): 5.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.4514.50.458174770.6061100
1.45-1.5114.50.346175070.6641100
1.51-1.5814.60.277175540.7121100
1.58-1.6614.60.227176080.7671100
1.66-1.7614.70.182175760.8351100
1.76-1.914.70.142176190.941100
1.9-2.0914.70.111177031.0971100
2.09-2.3914.70.109177921.4611100
2.39-3.0214.50.11178681.881100
3.02-5013.90.062183891.251199.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: Soaking / Resolution: 1.4→41.947 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.1 / σ(F): 1.34 / Phase error: 21.42 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1899 1999 1.13 %
Rwork0.1742 --
obs0.1744 176908 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.821 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 49.11 Å2 / Biso mean: 12.9633 Å2 / Biso min: 5.36 Å2
Baniso -1Baniso -2Baniso -3
1-1.3489 Å20 Å20 Å2
2---1.3237 Å2-0 Å2
3----0.0252 Å2
Refinement stepCycle: LAST / Resolution: 1.4→41.947 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6892 0 206 681 7779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067228
X-RAY DIFFRACTIONf_angle_d1.1239786
X-RAY DIFFRACTIONf_chiral_restr0.071108
X-RAY DIFFRACTIONf_plane_restr0.0051268
X-RAY DIFFRACTIONf_dihedral_angle_d14.0022624
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 (%)
1.4003-1.43530.23961410.20251238712528100
1.4353-1.47410.21431410.18161229712438100
1.4741-1.51750.17381420.16691240712549100
1.5175-1.56650.17931410.16331234912490100
1.5665-1.62250.19031420.16181240812550100
1.6225-1.68750.19511420.15741239812540100
1.6875-1.76430.17691420.1651241912561100
1.7643-1.85730.2141420.16311244912591100
1.8573-1.97360.19411430.16851248612629100
1.9736-2.1260.19551420.16681246912611100
2.126-2.340.17191430.16551252312666100
2.34-2.67850.18231440.17911263312777100
2.6785-3.37440.211450.18861266512810100
3.3744-41.96630.17681490.1802130191316899

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