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- PDB-3vz1: Structural insights into substrate and cofactor selelction by sp2771 -

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Basic information

Entry
Database: PDB / ID: 3vz1
TitleStructural insights into substrate and cofactor selelction 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
Succinate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesSynechococcus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)98,6932
Polymers98,6932
Non-polymers00
Water12,791710
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4670 Å2
ΔGint-15 kcal/mol
Surface area31820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.986, 115.626, 180.533
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: 49346.266 Da / Num. of mol.: 2
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / 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: 45.89 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 48792 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rsym value: 0.062
Reflection shellResolution: 2.1→2.14 Å / % possible all: 96.2

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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: 2.1→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / SU B: 8.898 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.239 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22586 2594 5 %RANDOM
Rwork0.17186 ---
obs0.17461 48792 95.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.755 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.36 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6882 0 0 710 7592
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227028
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9669552
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3525902
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34824.564298
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.985151144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6741538
X-RAY DIFFRACTIONr_chiral_restr0.090.21086
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025350
X-RAY DIFFRACTIONr_nbd_refined0.2090.23511
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24858
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2571
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.235
X-RAY DIFFRACTIONr_mcbond_it0.6991.54654
X-RAY DIFFRACTIONr_mcangle_it1.12427216
X-RAY DIFFRACTIONr_scbond_it2.14532708
X-RAY DIFFRACTIONr_scangle_it3.4294.52336
LS refinement shellResolution: 2.101→2.156 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 191 -
Rwork0.189 3518 -
obs--94.18 %
Refinement TLS params.

S33: -0.0188 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.16820.12480.01670.5083-0.17160.39030.011-0.02070.030.07350.00780.0439-0.0070.0096-0.06160.00380.0158-0.0624-0.015-0.049212.4578122.687462.8366
20.2111-0.02670.0420.40560.00710.4026-0.00160.0175-0.0233-0.06130.02040.0305-0.02450.011-0.0551-0.00810.0006-0.0606-0.0083-0.051412.0841115.193427.5972
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 454
2X-RAY DIFFRACTION2B3 - 454

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