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- PDB-2huc: Structural Studies Examining the Substrate Specificity Profiles o... -

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Basic information

Entry
Database: PDB / ID: 2huc
TitleStructural Studies Examining the Substrate Specificity Profiles of PC-PLCBc Protein Variants
ComponentsPhospholipase C
KeywordsHYDROLASE / PLC / bacillus cereus / substrate specificity / E4G
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 / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBenfield, A.P. / Martin, S.F. / Antikainen, N.M.
CitationJournal: Arch.Biochem.Biophys. / Year: 2007
Title: Structural studies examining the substrate specificity profiles of PC-PLC(Bc) protein variants.
Authors: Benfield, A.P. / Goodey, N.M. / Phillips, L.T. / Martin, S.F.
History
DepositionJul 26, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5484
Polymers28,3511
Non-polymers1963
Water3,585199
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.973, 89.973, 71.957
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 / PLC / Phosphatidylcholine cholinephosphohydrolase / Cereolysin A


Mass: 28351.355 Da / Num. of mol.: 1 / Fragment: PC-PLC / Mutation: E4G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: plc / Plasmid: pMAL-C2 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5-alpha / 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.: 199 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.36 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 45% Ammonium Sulfate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 23834 / Num. obs: 23254 / % possible obs: 98.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.036 / Χ2: 1.056 / Net I/σ(I): 31.9
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.162 / Num. unique all: 22236 / Χ2: 1.073 / % possible all: 96.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20 Å / FOM work R set: 0.877 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1172 4.9 %5%
Rwork0.187 ---
obs0.208 23221 97.4 %-
all-23834 --
Solvent computationBsol: 58.048 Å2
Displacement parametersBiso mean: 19.419 Å2
Baniso -1Baniso -2Baniso -3
1-1.478 Å20 Å20 Å2
2--1.478 Å20 Å2
3----2.956 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1997 0 3 199 2199
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.13
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_mcangle_it1.5762
X-RAY DIFFRACTIONc_scangle_it2.8062.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs
1.9-1.930.15300.185650680
1.93-1.960.238500.191925975
1.96-1.990.199500.199934984
1.99-2.020.228440.194950994
2.02-2.060.188650.1719361001
2.06-2.10.203350.171952987
2.1-2.140.229620.1859461008
2.14-2.190.218600.1729401000
2.19-2.240.209420.1749731015
2.24-2.30.225520.1759581010
2.3-2.360.21530.1789791032
2.36-2.430.211630.1879521015
2.43-2.510.197460.1799781024
2.51-2.60.254610.1949681029
2.6-2.70.185480.1939771025
2.7-2.820.223500.1829921042
2.82-2.970.229360.21210021038
2.97-3.160.188500.1949851035
3.16-3.40.213630.1989951058
3.4-3.740.232470.18410121059
3.74-4.280.162660.1679961062
4.28-5.390.211550.16910141069
5.39-300.226440.2310351079
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.paramCNS_TOPPAR:protein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top

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