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- PDB-1v0y: Phospholipase D from Streptomyces sp. strain PMF soaked with the ... -

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Basic information

Entry
Database: PDB / ID: 1v0y
TitlePhospholipase D from Streptomyces sp. strain PMF soaked with the substrate dibutyrylphosphatidylcholine.
ComponentsPHOSPHOLIPASE D
KeywordsHYDROLASE / PHOSPHOLIPASE D / SUBSTRATE SOAK / DIBUTYRYLPHOSPHATIDYLCHOLINE / DIC4PC
Function / homology
Function and homology information


phosphatidyltransferase activity / cardiolipin biosynthetic process / phospholipase D / phospholipase D activity
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-HI5 / Phospholipase D
Similarity search - Component
Biological speciesSTREPTOMYCES SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsLeiros, I. / McSweeney, S. / Hough, E.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: The Reaction Mechanism of Phospholipase D from Streptomyces Sp. Strain Pmf. Snapshots Along the Reaction Pathway Reveal a Pentacoordinate Reaction Intermediate and an Unexpected Final Product
Authors: Leiros, I. / Mcsweeney, S. / Hough, E.
#1: Journal: Structure / Year: 2000
Title: The First Crystal Structure of a Phospholipase D
Authors: Leiros, I. / Secundo, F. / Zambonelli, C. / Servi, S. / Hough, E.
History
DepositionApr 2, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)54,3952
Polymers54,0641
Non-polymers3301
Water7,440413
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)57.369, 56.462, 68.762
Angle α, β, γ (deg.)90.00, 93.74, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHOSPHOLIPASE D


Mass: 54064.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) STREPTOMYCES SP. (bacteria) / Strain: PMF / References: UniProt: P84147*PLUS, phospholipase D
#2: Chemical ChemComp-HI5 / 2-(BUTYRYLOXY)-1-{[(TETRAHYDROXYPHOSPHORANYL)OXY]METHYL}ETHYL BUTYRATE


Mass: 330.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H23O9P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 413 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS DATASET DESCRIBES A 30 MINUTE SUBSTRATE SOAK USING 2MM DIBUTYRYLPHOSPHATIDYLCHOLINE. ...THIS DATASET DESCRIBES A 30 MINUTE SUBSTRATE SOAK USING 2MM DIBUTYRYLPHOSPHATIDYLCHOLINE. DIBUTYRYLPHOSPHATIDIC ACID IS FOUND TO BE COVALENTLY LINKED TO AN ACTIVE SITE HISTIDINE, IN A STATE THAT CLOSELY RESEMBLES THE 5-COORDINATED TRANSITION STATE OF THE PHOSPHORUS.
Has protein modificationY
Sequence detailsTHIS SEQUENCE HAS NOT BEEN DEPOSITED TO UNIPROT AT THE TIME OF STRUCTURE DEPOSITION.

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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 Å3/Da / Density % sol: 38.4 %
Crystal growpH: 5.4
Details: 0.2 M NH4AC, 0.1 M CITRATE PHOSPHATE BUFFER AT PH5.4, 27.5% PEG 4000. CRYSTALS WERE THEREAFTER BACKSOAKED TWICE IN A PHOSPHATE- FREE BUFFER TO REMOVE TRACE-AMOUNTS OF PHOSPHATE., pH 5.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM1A / Wavelength: 0.873
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.7→13.71 Å / Num. obs: 45138 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 4.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.473 / Mean I/σ(I) obs: 2 / % possible all: 92.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALAdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: BASED ON PDB ENTRY 1F0I

1f0i


Resolution: 1.71→13.71 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.298 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.104 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS ATOMS THAT HAVE BEEN MODELED WITH AN OCCUPANCY OF 0.00.
RfactorNum. reflection% reflectionSelection details
Rfree0.202 2377 5 %RANDOM
Rwork0.16 ---
obs0.162 45138 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å2-0.44 Å2
2--1.57 Å20 Å2
3----0.83 Å2
Refinement stepCycle: LAST / Resolution: 1.71→13.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3709 0 20 413 4142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213745
X-RAY DIFFRACTIONr_bond_other_d0.0020.023316
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.9555112
X-RAY DIFFRACTIONr_angle_other_deg0.97937720
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8735487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.2586
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024223
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02698
X-RAY DIFFRACTIONr_nbd_refined0.2530.2736
X-RAY DIFFRACTIONr_nbd_other0.2510.23838
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.22071
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2840.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.226
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0291.52447
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71823911
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.6831298
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.2694.51201
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: 1.71→1.75 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.361 149
Rwork0.3 2984

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