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- PDB-3vzx: Crystal structure of PcrB from bacillus subtilis subap. subtilis ... -

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Basic information

Entry
Database: PDB / ID: 3vzx
TitleCrystal structure of PcrB from bacillus subtilis subap. subtilis str. 168
ComponentsHeptaprenylglyceryl phosphate synthase
KeywordsTRANSFERASE / biosynthesis / prenyltransferases / enzyme catalysis
Function / homology
Function and homology information


: / heptaprenylglyceryl phosphate synthase activity / glycerophospholipid biosynthetic process / magnesium ion binding
Similarity search - Function
GGGP/HepGP synthase group I / FMN-linked oxidoreductases / Geranylgeranylglyceryl phosphate synthase/Heptaprenylglyceryl phosphate synthase / GGGP/HepGP synthase superfamily / PcrB family / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Heptaprenylglyceryl phosphate synthase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsRen, F. / Feng, X. / Ko, T.P. / Huang, C.H. / Hu, Y. / Chan, H.C. / Liu, Y.L. / Wang, K. / Chen, C.C. / Pang, X. ...Ren, F. / Feng, X. / Ko, T.P. / Huang, C.H. / Hu, Y. / Chan, H.C. / Liu, Y.L. / Wang, K. / Chen, C.C. / Pang, X. / He, M. / Li, Y. / Oldfield, E. / Guo, R.T.
CitationJournal: Chembiochem / Year: 2013
Title: Insights into TIM-barrel prenyl transferase mechanisms: crystal structures of PcrB from Bacillus subtilis and Staphylococcus aureus
Authors: Ren, F. / Feng, X. / Ko, T.P. / Huang, C.H. / Hu, Y. / Chan, H.C. / Liu, Y.L. / Wang, K. / Chen, C.C. / Pang, X. / He, M. / Li, Y. / Oldfield, E. / Guo, R.T.
History
DepositionOct 17, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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_asym_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_asym_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_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: Heptaprenylglyceryl phosphate synthase
B: Heptaprenylglyceryl phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,64217
Polymers50,2212
Non-polymers42015
Water9,512528
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-126 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.116, 55.953, 77.271
Angle α, β, γ (deg.)90.00, 108.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Heptaprenylglyceryl phosphate synthase / PcrB / HepGP synthase / Glycerol-1-phosphate heptaprenyltransferase


Mass: 25110.629 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: pcrB / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: O34790, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 528 / 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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 2.5M NaCl, 14% PEG6000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.54→25 Å / Num. obs: 63317 / % possible obs: 97.9 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.7
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.442 / Mean I/σ(I) obs: 3 / Num. unique all: 6150 / % possible all: 95.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VIZ

1viz


Resolution: 1.54→24.57 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.225 4969 RANDOM
Rwork0.182 --
all-64925 -
obs-61084 -
Refinement stepCycle: LAST / Resolution: 1.54→24.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3508 0 15 528 4051
LS refinement shellResolution: 1.54→1.6 Å
RfactorNum. reflection
Rfree0.283 268
Rwork0.248 -
obs-5237

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