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- PDB-1ah7: PHOSPHOLIPASE C FROM BACILLUS CEREUS -

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Basic information

Entry
Database: PDB / ID: 1ah7
TitlePHOSPHOLIPASE C FROM BACILLUS CEREUS
ComponentsPHOSPHOLIPASE C
KeywordsHYDROLASE / LIPASE / PHOSPHOLIPID HYDROLYSIS
Function / homology
Function and homology information


phospholipase C / phosphatidylcholine phospholipase C activity / killing of cells of another organism / zinc ion binding
Similarity search - Function
Zinc-dependent phospholipase C / Phospholipase C/D / Zinc dependent phospholipase C / Prokaryotic zinc-dependent phospholipase C signature. / Prokaryotic zinc-dependent phospholipase C domain profile. / Zinc dependent phospholipase C (alpha toxin) / P1 Nuclease / P1 Nuclease / Phospholipase C/P1 nuclease domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.501 Å
AuthorsGreaves, R.
Citation
Journal: Nature / Year: 1989
Title: High-resolution (1.5 A) crystal structure of phospholipase C from Bacillus cereus.
Authors: Hough, E. / Hansen, L.K. / Birknes, B. / Jynge, K. / Hansen, S. / Hordvik, A. / Little, C. / Dodson, E. / Derewenda, Z.
#1: Journal: Lipases : Their Structure, Biochemistry, and Application
Year: 1994
Title: Structural Aspects of Phospholipase C from Bacillus Cereus and its Reaction Mechanism
Authors: Hough, E. / Hansen, S.
#2: Journal: J.Mol.Biol. / Year: 1993
Title: Crystal Structure of Phospholipase C from Bacillus Cereus Complexed with a Substrate Analog
Authors: Hansen, S. / Hough, E. / Svensson, L.A. / Wong, Y.L. / Martin, S.F.
#3: Journal: J.Mol.Biol. / Year: 1993
Title: The Crystal Structure of Tris-Inhibited Phospholipase C from Bacillus Cereus at 1.9 A Resolution. The Nature of the Metal Ion in Site 2
Authors: Hansen, S. / Hansen, L.K. / Hough, E.
#4: Journal: J.Mol.Biol. / Year: 1992
Title: Crystal Structures of Phosphate, Iodide and Iodate-Inhibited Phospholipase C from Bacillus Cereus and Structural Investigations of the Binding of Reaction Products and a Substrate Analogue
Authors: Hansen, S. / Hansen, L.K. / Hough, E.
History
DepositionApr 14, 1997Processing site: BNL
Revision 1.0Dec 10, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOLIPASE C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6204
Polymers28,4231
Non-polymers1963
Water4,179232
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.760, 89.760, 74.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein PHOSPHOLIPASE C / PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE C


Mass: 28423.420 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bacillus cereus (bacteria) / References: UniProt: P09598, phospholipase C
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.7 %
Crystal growMethod: vapor diffusion / pH: 7
Details: VAPOR PHASE DIFFUSION FROM SOLUTION OF 5MG/ML PLC IN 35% SATURATED AMMONIUM SULFATE, pH 7, vapor diffusion
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlenzyme1drop
235 %satammonium sulfate1drop
32.5 Mammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Aug 1, 1986 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.5→12.45 Å / Num. obs: 46061 / % possible obs: 95 % / Redundancy: 2.5 % / Rsym value: 0.056
Reflection shellResolution: 1.501→1.57 Å / % possible all: 82
Reflection
*PLUS
Rmerge(I) obs: 0.056
Reflection shell
*PLUS
% possible obs: 82 %

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
CCP4data reduction
CCP4data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.501→12.451 Å / Cross valid method: FREE R / σ(F): 0
Details: PROTEIN MODEL DID NOT INCLUDE HYDROGEN ATOM POSITIONS. INITIAL REFINEMENT WAS PERFORMED USING USING PROTIN AND PROLSQ. THERE IS STILL SOME DOUBT ABOUT THE EXACT POSITIONING OF TYR 156 WHICH ...Details: PROTEIN MODEL DID NOT INCLUDE HYDROGEN ATOM POSITIONS. INITIAL REFINEMENT WAS PERFORMED USING USING PROTIN AND PROLSQ. THERE IS STILL SOME DOUBT ABOUT THE EXACT POSITIONING OF TYR 156 WHICH IS NOT WITHIN THE EXPECTED DISTRIBUTION OF RING PLANARITY FOR TYROSINE RESIDUES. THE DENSITY AROUND THE C-TERMINUS WAS POOR. THE POSITIONING OF RESIDUES ASP 244 AND ARG 245 IS THUS AMBIGUOUS.
RfactorNum. reflection% reflection
Rfree0.23124 2340 5 %
Rwork0.20281 --
obs0.20331 43951 95 %
Refinement stepCycle: LAST / Resolution: 1.501→12.451 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 3 231 2266
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 48722
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.021
X-RAY DIFFRACTIONp_angle_d0.049
X-RAY DIFFRACTIONp_plane_restr0.014

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