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- PDB-4it9: Structure of Bacterial Enzyme -

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Basic information

Entry
Database: PDB / ID: 4it9
TitleStructure of Bacterial Enzyme
ComponentsSuccinate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann fold
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, N-terminal / Aldehyde dehydrogenase, C-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, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Succinate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesSynechococcus sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Succinate-semialdehyde dehydrogenase
B: Succinate-semialdehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,63235
Polymers98,5182
Non-polymers2,11433
Water10,989610
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11030 Å2
ΔGint62 kcal/mol
Surface area31510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.779, 115.340, 179.267
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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / 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: 2.24 Å3/Da / Density % sol: 45.2 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Type: OTHER / Wavelength: 0.97935 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 98424 / % possible obs: 99.5 % / Redundancy: 14.3 % / Rmerge(I) obs: 0.174 / Χ2: 0.949 / Net I/σ(I): 3.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.7-1.7614.70.58996770.847199.4
1.76-1.8314.70.48996990.879199.5
1.83-1.9114.70.38397490.924199.7
1.91-2.0214.70.397660.948199.8
2.02-2.1414.70.24698290.966199.9
2.14-2.3114.70.20797890.97199.9
2.31-2.5414.50.18298751.003199.9
2.54-2.9114.40.15599161.004199.9
2.91-3.6613.60.12799550.985199.5
3.66-5012.30.113101690.969197.4

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→39.141 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.2 / σ(F): 1.34 / Phase error: 24.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2059 1997 2.03 %
Rwork0.1833 --
obs0.1838 98292 99.44 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.88 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 61.94 Å2 / Biso mean: 14.6407 Å2 / Biso min: 3.76 Å2
Baniso -1Baniso -2Baniso -3
1-4.712 Å2-0 Å2-0 Å2
2---4.0032 Å2-0 Å2
3----0.7088 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.141 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6882 0 134 610 7626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067129
X-RAY DIFFRACTIONf_angle_d1.19626
X-RAY DIFFRACTIONf_chiral_restr0.0731086
X-RAY DIFFRACTIONf_plane_restr0.0051254
X-RAY DIFFRACTIONf_dihedral_angle_d13.8992589
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 (%)
1.6993-1.74180.28181390.22516717685699
1.7418-1.78890.24791410.209868406981100
1.7889-1.84150.26871410.1996782692399
1.8415-1.9010.20441410.179867796920100
1.901-1.96890.20711410.170968416982100
1.9689-2.04770.211430.166168577000100
2.0477-2.14090.19481420.167968576999100
2.1409-2.25380.21051430.166368707013100
2.2538-2.3950.21671430.169168847027100
2.395-2.57990.21781420.176268747016100
2.5799-2.83940.21261450.182369517096100
2.8394-3.25010.18341440.185369527096100
3.2501-4.09410.19741430.18186964710799
4.0941-39.15170.18651490.20147127727697

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