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- PDB-2ze4: Crystal structure of phospholipase D from streptomyces antibioticus -

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Basic information

Entry
Database: PDB / ID: 2ze4
TitleCrystal structure of phospholipase D from streptomyces antibioticus
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
Biological speciesStreptomyces antibioticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsSuzuki, A. / Kakuno, K. / Saito, R. / Iwasaki, Y. / Yamane, T. / Yamane, T.
Citation
Journal: To be Published
Title: Crystal structure of phospholipase D from streptomyces antibioticus
Authors: Suzuki, A. / Kakuno, K. / Saito, R. / 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 5, 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 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)54,2312
Polymers54,0361
Non-polymers1951
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.004, 85.008, 99.343
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: 54036.059 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.5 Å3/Da / Density % sol: 50.8 %
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: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: FUJI / Detector: IMAGE PLATE / Date: Dec 8, 1997 / Details: mirrors
RadiationMonochromator: DOUBLE-CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. all: 19350 / Num. obs: 17415 / % possible obs: 90 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.151 / % possible all: 78.6

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Processing

Software
NameVersionClassification
REFMAC5.3.0040refinement
WeissenbergCamera Control Softwaredata collection
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→64.55 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.948 / SU B: 5.979 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 2.239 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17101 856 5.1 %RANDOM
Rwork0.12111 ---
all0.12374 18600 --
obs0.12374 15916 90.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.338 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å20 Å20 Å2
2--1.19 Å20 Å2
3----1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 12 204 3959
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0213844
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.9645248
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0785500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.62424.114158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.00615586
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.5651526
X-RAY DIFFRACTIONr_chiral_restr0.1150.2585
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022953
X-RAY DIFFRACTIONr_nbd_refined0.2210.21659
X-RAY DIFFRACTIONr_nbtor_refined0.3130.22605
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2245
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.211
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.25
X-RAY DIFFRACTIONr_mcbond_it1.1441.52547
X-RAY DIFFRACTIONr_mcangle_it1.94223995
X-RAY DIFFRACTIONr_scbond_it3.15931480
X-RAY DIFFRACTIONr_scangle_it5.2964.51253
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 64 -
Rwork0.153 1012 -
obs--79.53 %

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