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- PDB-2ze9: Crystal structure of H168A mutant of phospholipase D from Strepto... -

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Basic information

Entry
Database: PDB / ID: 2ze9
TitleCrystal structure of H168A mutant of phospholipase D from Streptomyces antibioticus, as a complex with phosphatidylcholine
ComponentsPhospholipase D
KeywordsHYDROLASE / ALPHA-BETA-BETA-ALPHA SANDWICH / Lipid degradation / Secreted
Function / homology
Function and homology information


phosphatidyltransferase activity / cardiolipin biosynthetic process / phospholipase D / phospholipase D activity / lipid catabolic process / extracellular region
Similarity search - Function
Phospholipase D-like domain / PLD-like domain / Phospholipase D. Active site motifs. / Phospholipase D/Transphosphatidylase / Phospholipase D phosphodiesterase active site profile. / Endonuclease Chain A / Endonuclease; Chain A / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-PD7 / Phospholipase D
Similarity search - Component
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsSuzuki, A. / Toda, H. / Iwasaki, Y. / Yamane, T. / Yamane, T.
Citation
Journal: To be Published
Title: Crystal structure of phospholipase D from streptomyces antibioticus.
Authors: Suzuki, A. / Toda, H. / Iwasaki, Y. / Yamane, T. / Yamane, T.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Crystallization and preliminary X-ray diffraction studies of phospholipase D from Streptomyces antibioticus
Authors: Suzuki, A. / Kakuno, K. / Iwasaki, Y. / Yamane, T. / Yamane, T.
#2: Journal: Chembiochem / Year: 2008
Title: Streptomyces phospholipase D mutants with altered substrate specificity capable of phosphatidylinositol synthesis
Authors: Masayama, A. / Takahashi, T. / Tsukada, K. / Nishikawa, S. / Takahashi, R. / Adachi, M. / Koga, K. / Suzuki, A. / Yamane, T. / Nakano, H. / Iwasaki, Y.
History
DepositionDec 6, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.5Apr 30, 2025Group: Database references / Category: citation / Item: _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase D
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,5613
Polymers53,9691
Non-polymers5922
Water6,575365
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.868, 78.232, 98.603
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 Phospholipase D / Choline phosphatase


Mass: 53968.992 Da / Num. of mol.: 1 / Mutation: H168A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces antibioticus (bacteria) / Plasmid: pPELB-PLD3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53728, phospholipase D
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PD7 / (2R)-3-(phosphonooxy)propane-1,2-diyl diheptanoate


Mass: 396.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H33O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 365 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHERE ARE DIFFERENCES BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. ACCORDING TO THE DEPOSITOR, THE ...THERE ARE DIFFERENCES BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. ACCORDING TO THE DEPOSITOR, THE SEQUENCE IN Q53728 CONTAINS SOME ERRORS AND RESIDUE NUMBER 107 IS SER, 211 IS ARG. THESE ERRORS WILL BE FIXED LATER.

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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: 2.17 Å3/Da / Density % sol: 43.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 15% PEG 6000, 0.1M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 1, 1999 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→61.31 Å / Num. all: 21448 / Num. obs: 20805 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 17.2
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 5.5 / Num. unique all: 2726 / % possible all: 88.8

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
CrystalCleardata collection
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2ZE4

2ze4


Resolution: 2.3→48.04 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.879 / SU B: 6.9 / SU ML: 0.17 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.481 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25137 1071 5.2 %RANDOM
Rwork0.17029 ---
all0.17448 21555 --
obs0.17448 19582 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: 13.618 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å20 Å20 Å2
2--0.5 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3758 0 38 365 4161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213883
X-RAY DIFFRACTIONr_angle_refined_deg1.8941.9725299
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2185503
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10524.177158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.62915587
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.2621526
X-RAY DIFFRACTIONr_chiral_restr0.1190.2590
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022975
X-RAY DIFFRACTIONr_nbd_refined0.2150.21885
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22529
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1770.2378
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2250.213
X-RAY DIFFRACTIONr_mcbond_it0.9281.52593
X-RAY DIFFRACTIONr_mcangle_it1.51224019
X-RAY DIFFRACTIONr_scbond_it2.32931505
X-RAY DIFFRACTIONr_scangle_it3.5844.51280
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 61 -
Rwork0.184 1242 -
obs--83.74 %

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