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- PDB-3vz3: Structural insights into substrate and cofactor selection by sp2771 -

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Basic information

Entry
Database: PDB / ID: 3vz3
TitleStructural insights into substrate and cofactor selection by sp2771
ComponentsSuccinate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / substrate selection / cofactor preference
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 4-oxobutanoic acid / Succinate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesSynechococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å
AuthorsYuan, Y.A. / Yuan, Z. / Yin, B. / Wei, D.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Structural basis for cofactor and substrate selection by cyanobacterium succinic semialdehyde dehydrogenase
Authors: Yuan, Z. / Yin, B. / Wei, D. / Yuan, Y.A.
History
DepositionOct 9, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 10, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_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)100,3196
Polymers98,6282
Non-polymers1,6914
Water20,6991149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-28 kcal/mol
Surface area31340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.957, 117.181, 181.980
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 Succinate-semialdehyde dehydrogenase


Mass: 49314.203 Da / Num. of mol.: 2 / Mutation: C262A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechococcus (bacteria) / Strain: ATCC 27264 / PCC 7002 / PR-6 / Gene: SYNPCC7002_A2771 / Production host: Escherichia coli (E. coli) / References: UniProt: B1XMM6
#2: Chemical ChemComp-SSN / 4-oxobutanoic acid / Succinic semialdehyde


Mass: 102.089 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O3
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1149 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: PEG 5000 MME, tascimate, HEPES, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. obs: 89961 / % possible obs: 92.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 12.2 % / Rsym value: 0.043
Reflection shellResolution: 1.7→1.73 Å / % possible all: 75.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3JZ4

3jz4


Resolution: 1.69→42.41 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.344 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.111 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20342 4735 5 %RANDOM
Rwork0.16564 ---
obs0.16751 89961 91.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.19 Å20 Å20 Å2
2---0.18 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.69→42.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6890 0 110 1149 8149
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227152
X-RAY DIFFRACTIONr_angle_refined_deg1.2571.9849736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6325904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43324.564298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.533151142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1251538
X-RAY DIFFRACTIONr_chiral_restr0.0840.21104
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025410
X-RAY DIFFRACTIONr_nbd_refined0.1990.23694
X-RAY DIFFRACTIONr_nbtor_refined0.3070.24950
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2755
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1840.2149
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.2156
X-RAY DIFFRACTIONr_mcbond_it0.6791.54646
X-RAY DIFFRACTIONr_mcangle_it1.03527228
X-RAY DIFFRACTIONr_scbond_it2.03332846
X-RAY DIFFRACTIONr_scangle_it3.2444.52508
LS refinement shellResolution: 1.695→1.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 304 -
Rwork0.21 5337 -
obs--75.06 %
Refinement TLS params.

T33: -0.0559 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.21840.0326-0.00020.4365-0.16910.44670.0032-0.02670.00680.05840.01010.015-0.0228-0.0028-0.0133-0.07250.00550.0001-0.0637-0.004533.673566.210563.112
20.23520.0213-0.01890.4361-0.10050.50350.0034-0.03110.00310.06490.00930.0191-0.00460.0037-0.0127-0.0750.0042-0.0007-0.0613-0.006833.53857.57827.957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 454
2X-RAY DIFFRACTION2B3 - 454

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