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- PDB-3etf: Crystal structure of a putative succinate-semialdehyde dehydrogen... -

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Basic information

Entry
Database: PDB / ID: 3etf
TitleCrystal structure of a putative succinate-semialdehyde dehydrogenase from salmonella typhimurium lt2
ComponentsPutative succinate-semialdehyde dehydrogenase
KeywordsOXIDOREDUCTASE / PUTATIVE SUCCINATE-SEMIALDEHYDE DEHYDROGENASE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID
Function / homology
Function and homology information


succinate-semialdehyde dehydrogenase (NAD+) activity / aldehyde dehydrogenase [NAD(P)+] activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / 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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family ...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, cysteine active site / Aldehyde dehydrogenases cysteine active site. / 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
Succinate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsBrunzelle, J.S. / Evdokimova, E. / Kudritska, M. / Wawrzak, Z. / Anderson, W.F. / Savchenk, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Proteins / Year: 2013
Title: Structure and activity of the NAD(P)(+) -dependent succinate semialdehyde dehydrogenase YneI from Salmonella typhimurium.
Authors: Zheng, H. / Beliavsky, A. / Tchigvintsev, A. / Brunzelle, J.S. / Brown, G. / Flick, R. / Evdokimova, E. / Wawrzak, Z. / Mahadevan, R. / Anderson, W.F. / Savchenko, A. / Yakunin, A.F.
History
DepositionOct 7, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Dec 19, 2012Group: Database references
Revision 1.3Jun 12, 2013Group: Database references
Revision 1.4Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.5Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.6Dec 27, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative succinate-semialdehyde dehydrogenase
B: Putative succinate-semialdehyde dehydrogenase
C: Putative succinate-semialdehyde dehydrogenase
D: Putative succinate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)198,8614
Polymers198,8614
Non-polymers00
Water35,7601985
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative succinate-semialdehyde dehydrogenase
D: Putative succinate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)99,4312
Polymers99,4312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-30 kcal/mol
Surface area32260 Å2
MethodPISA, PQS
3
B: Putative succinate-semialdehyde dehydrogenase
C: Putative succinate-semialdehyde dehydrogenase


Theoretical massNumber of molelcules
Total (without water)99,4312
Polymers99,4312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4890 Å2
ΔGint-29 kcal/mol
Surface area32270 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)133.875, 133.875, 247.028
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein
Putative succinate-semialdehyde dehydrogenase /


Mass: 49715.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / Gene: yneI, STM1524 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8ZPI3, Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1985 / 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: 3.21 Å3/Da / Density % sol: 61.72 %
Crystal growTemperature: 298 K / pH: 4.6
Details: 2M NA FORMATE, 0.1M NA ACETATE, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9787
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 4, 2008 / Details: BE LENS
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.85→30 Å / Num. obs: 206465 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 20.65
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 11.42 % / Rmerge(I) obs: 0.469 / Mean I/σ(I) obs: 5.97 / % possible all: 100

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Processing

Software
NameVersionClassification
BLU-MAXdata collection
PHENIXSHARPmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→30 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.06 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.105 / ESU R Free: 0.102
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.194 10912 5 %RANDOM
Rwork0.167 ---
obs0.168 206465 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.42 Å2-0.21 Å20 Å2
2---0.42 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.85→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13556 0 0 1985 15541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02214181
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4041.94919341
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.62451906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.08824.66603
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.292152235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1081583
X-RAY DIFFRACTIONr_chiral_restr0.1070.22188
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210983
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.26882
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.210003
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.21587
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.280
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2810.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0241.59578
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.342214789
X-RAY DIFFRACTIONr_scbond_it2.59935267
X-RAY DIFFRACTIONr_scangle_it3.9724.54552
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.9 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 787 -
Rwork0.194 15035 -
obs--99.03 %

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