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- PDB-9pzk: Crystal structure of Petunia x hybrida benzaldehyde synthase in c... -

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Basic information

Entry
Database: PDB / ID: 9pzk
TitleCrystal structure of Petunia x hybrida benzaldehyde synthase in complex with NADP
Components
  • Benzaldehyde synthase, alpha subunit
  • Benzaldehyde synthase, beta subunit
KeywordsPLANT PROTEIN / NADP+ bound / heterotetrameric
Function / homologyNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Function and homology information
Biological speciesPetunia x hybrida (garden petunia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsMatos, J.O. / Prem Kumar, R. / Weng, J.K.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Structural and Biochemical Characterization of Benzaldehyde Synthase from P. hybrida
Authors: Matos, J.O. / Huang, X.Q. / Kumar, R.P. / Han, J. / Sherk, J. / Keswani, V. / Dudareva, N. / Weng, J.K.
History
DepositionAug 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Benzaldehyde synthase, alpha subunit
B: Benzaldehyde synthase, beta subunit
C: Benzaldehyde synthase, alpha subunit
D: Benzaldehyde synthase, beta subunit
E: Benzaldehyde synthase, alpha subunit
F: Benzaldehyde synthase, beta subunit
G: Benzaldehyde synthase, alpha subunit
H: Benzaldehyde synthase, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,59612
Polymers242,6228
Non-polymers2,9744
Water15,079837
1
A: Benzaldehyde synthase, alpha subunit
B: Benzaldehyde synthase, beta subunit
C: Benzaldehyde synthase, alpha subunit
D: Benzaldehyde synthase, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,7986
Polymers121,3114
Non-polymers1,4872
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23240 Å2
ΔGint-136 kcal/mol
Surface area34290 Å2
MethodPISA
2
E: Benzaldehyde synthase, alpha subunit
F: Benzaldehyde synthase, beta subunit
G: Benzaldehyde synthase, alpha subunit
H: Benzaldehyde synthase, beta subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,7986
Polymers121,3114
Non-polymers1,4872
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23580 Å2
ΔGint-129 kcal/mol
Surface area33800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.976, 73.744, 134.064
Angle α, β, γ (deg.)90.64, 103.73, 114.95
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Benzaldehyde synthase, alpha subunit


Mass: 31128.471 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petunia x hybrida (garden petunia) / Production host: Escherichia coli (E. coli)
#2: Protein
Benzaldehyde synthase, beta subunit


Mass: 29527.137 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petunia x hybrida (garden petunia) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 837 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.42 Å3/Da / Density % sol: 49.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1 M sodium chloride, 0.1 M sodium formate, 0.1 M Bis-Tris propane, pH 8.5, 25 % v/v PEG Smear Medium

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: 7B2 / Wavelength: 0.9686 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.51→30 Å / Num. obs: 75466 / % possible obs: 97.4 % / Redundancy: 3.5 % / CC1/2: 1 / Rmerge(I) obs: 0.178 / Net I/σ(I): 3.8
Reflection shellResolution: 2.51→2.57 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3968 / CC1/2: 0.6 / % possible all: 86

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
Aimlessdata scaling
DIALSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.51→29.7 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2131 3835 5.08 %
Rwork0.1644 --
obs0.1669 75451 97.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.51→29.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16240 0 192 837 17269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00216679
X-RAY DIFFRACTIONf_angle_d0.4622533
X-RAY DIFFRACTIONf_dihedral_angle_d12.6896330
X-RAY DIFFRACTIONf_chiral_restr0.0412596
X-RAY DIFFRACTIONf_plane_restr0.0042853
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.550.32541190.28462200X-RAY DIFFRACTION79
2.55-2.580.33411410.25642614X-RAY DIFFRACTION98
2.58-2.610.26571470.23742684X-RAY DIFFRACTION98
2.61-2.650.29111660.23012621X-RAY DIFFRACTION98
2.65-2.690.33091410.21642640X-RAY DIFFRACTION98
2.69-2.730.2771500.21712724X-RAY DIFFRACTION98
2.73-2.780.23911280.20572614X-RAY DIFFRACTION98
2.78-2.830.26961620.20272727X-RAY DIFFRACTION98
2.83-2.880.25321500.20212592X-RAY DIFFRACTION98
2.88-2.930.28491700.18652678X-RAY DIFFRACTION98
2.93-2.990.27011290.1842670X-RAY DIFFRACTION98
2.99-3.060.25141370.18452712X-RAY DIFFRACTION99
3.06-3.130.2761550.17612632X-RAY DIFFRACTION98
3.13-3.210.22671510.17192725X-RAY DIFFRACTION98
3.21-3.290.21441500.16922613X-RAY DIFFRACTION98
3.29-3.390.22181190.1692713X-RAY DIFFRACTION98
3.39-3.50.22271160.15912708X-RAY DIFFRACTION98
3.5-3.620.18821300.15312680X-RAY DIFFRACTION98
3.62-3.770.20921400.14212654X-RAY DIFFRACTION97
3.77-3.940.18621310.13932683X-RAY DIFFRACTION98
3.94-4.150.17031490.13652656X-RAY DIFFRACTION98
4.15-4.410.15571300.12472701X-RAY DIFFRACTION98
4.41-4.740.1731380.12582663X-RAY DIFFRACTION98
4.74-5.220.17831600.13912695X-RAY DIFFRACTION98
5.22-5.970.18071510.15822666X-RAY DIFFRACTION99
5.97-7.50.17621370.162696X-RAY DIFFRACTION98
7.5-29.70.16591380.15032655X-RAY DIFFRACTION98

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