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- PDB-3vz2: Structural insights into substrate and cofactor selection by sp2771 -

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Basic information

Entry
Database: PDB / ID: 3vz2
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, 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
Succinate-semialdehyde dehydrogenase
Similarity search - Component
Biological speciesSynechococcus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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.R.
History
DepositionOct 9, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 16, 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)101,7142
Polymers101,7142
Non-polymers00
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-17 kcal/mol
Surface area32930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.928, 116.963, 180.604
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: 50856.938 Da / Num. of mol.: 2 / Mutation: S419A
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.: 218 / 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: 2.44 Å3/Da / Density % sol: 49.52 %
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: 2.5→50 Å / Num. obs: 32970 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 14.2 % / Rsym value: 0.072
Reflection shellResolution: 2.5→2.54 Å / % possible all: 100

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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: 2.5→42.12 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.911 / SU B: 17.509 / SU ML: 0.192 / Cross valid method: THROUGHOUT / ESU R: 0.585 / ESU R Free: 0.282 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23658 1755 5.1 %RANDOM
Rwork0.17693 ---
obs0.18002 32967 97.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.84 Å2-0 Å2-0 Å2
2---0.2 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6951 0 0 218 7169
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197099
X-RAY DIFFRACTIONr_bond_other_d0.0010.026870
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9669649
X-RAY DIFFRACTIONr_angle_other_deg0.829315799
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8375912
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03824.5300
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.851151153
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0771539
X-RAY DIFFRACTIONr_chiral_restr0.0870.21097
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0218126
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021575
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3090.24943
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2291
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.237
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.210
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.651.54672
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1327293
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.96132728
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.2854.52356
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.498→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 112 -
Rwork0.226 1906 -
obs--79.26 %
Refinement TLS params.

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)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.04680.07960.09680.3230.0560.58570.00350.0161-0.02210.0524-0.0122-0.0293-0.02620.0040.00880.01460.0059-0.00460.08260.00910.1238-14.7462-7.6313-26.9878
20.0399-0.0153-0.10570.2049-0.13620.5353-0.0086-0.01110.0298-0.05110.0006-0.01560.08530.00070.00790.0191-0.00630.00340.09550.01070.1175-11.79261.2398-62.1
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 454
2X-RAY DIFFRACTION2B2 - 454

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