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- PDB-4nae: PcrB from Geobacillus kaustophilus, with bound G1P -

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Basic information

Entry
Database: PDB / ID: 4nae
TitlePcrB from Geobacillus kaustophilus, with bound G1P
Components(Heptaprenylglyceryl phosphate synthase) x 2
KeywordsTRANSFERASE / PcrB / GGGp
Function / homology
Function and homology information


: / heptaprenylglyceryl phosphate synthase activity / glycerophospholipid biosynthetic process / prenyltransferase activity / 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
SN-GLYCEROL-1-PHOSPHATE / Heptaprenylglyceryl phosphate synthase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPeterhoff, D. / Beer, B. / Rajendran, C. / Kumpula, E.P. / Kapetaniou, E. / Guldan, H. / Wierenga, R.K. / Sterner, R. / Babinger, P.
CitationJournal: Mol.Microbiol. / Year: 2014
Title: A comprehensive analysis of the geranylgeranylglyceryl phosphate synthase enzyme family identifies novel members and reveals mechanisms of substrate specificity and quaternary structure organization.
Authors: Peterhoff, D. / Beer, B. / Rajendran, C. / Kumpula, E.P. / Kapetaniou, E. / Guldan, H. / Wierenga, R.K. / Sterner, R. / Babinger, P.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Heptaprenylglyceryl phosphate synthase
B: Heptaprenylglyceryl phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5506
Polymers50,4972
Non-polymers1,0534
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-22 kcal/mol
Surface area17440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.350, 157.970, 38.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 25118.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: pcrB, GK0274 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: Q5L3C1, Transferases; Transferring alkyl or aryl groups, other than methyl groups
#2: Protein Heptaprenylglyceryl phosphate synthase / HepGP synthase / Glycerol-1-phosphate heptaprenyltransferase


Mass: 25378.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Gene: pcrB, GK0274 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5L3C1
#3: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O6P
#4: Chemical ChemComp-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000


Mass: 354.436 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H34O8 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.62 %
Crystal growMethod: vapor diffusion, hanging drop / Details: 19% w/v PEG4000, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1 Å
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→29 Å / Num. all: 28722 / Num. obs: 151551 / % possible obs: 80 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 5 / Redundancy: 5 % / Rmerge(I) obs: 0.038

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1422) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→27.416 Å / SU ML: 0.32 / σ(F): 1.4 / σ(I): 2 / Phase error: 28.73 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2428 1458 5.08 %
Rwork0.2023 --
obs0.2043 28718 80.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→27.416 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 46 212 3510
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063373
X-RAY DIFFRACTIONf_angle_d1.1574603
X-RAY DIFFRACTIONf_dihedral_angle_d15.5271163
X-RAY DIFFRACTIONf_chiral_restr0.066545
X-RAY DIFFRACTIONf_plane_restr0.005585
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.07150.42381070.40322269X-RAY DIFFRACTION68
2.0715-2.15440.27891660.24912799X-RAY DIFFRACTION84
2.1544-2.25240.2833780.25181571X-RAY DIFFRACTION78
2.2524-2.37110.26361110.22932368X-RAY DIFFRACTION84
2.3711-2.51960.25481850.21653032X-RAY DIFFRACTION92
2.5196-2.7140.31011860.21983094X-RAY DIFFRACTION92
2.714-2.98680.27861790.21323136X-RAY DIFFRACTION93
2.9868-3.41830.2411610.20553196X-RAY DIFFRACTION93
3.4183-4.3040.19821330.16312516X-RAY DIFFRACTION73
4.304-27.41870.19091520.16823279X-RAY DIFFRACTION90
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.63230.08790.27592.2382-0.27711.34450.04-0.01920.1969-0.3156-0.0725-0.30520.07630.16610.0150.30220.04880.02030.2419-0.01180.38127.678611.922-7.3718
21.08370.7312-0.32930.7188-0.31830.2635-0.0391-0.0328-0.0399-0.1746-0.0102-0.36720.01640.15120.02540.2420.02440.01860.27940.00310.360534.03083.7305-7.7514
31.4591-0.5664-0.5381.6185-0.27850.71450.01010.22050.0116-0.2092-0.1217-0.14620.0249-0.0590.08210.30010.00240.03190.2707-0.01490.26523.4267-9.2615-10.6814
40.71890.3904-0.21891.2971-0.20630.3851-0.02880.01530.12940.00990.06530.0854-0.0539-0.1514-0.00280.24650.0203-0.00830.3105-0.00750.289613.64913.1558-3.7657
51.42480.2535-0.08081.87530.46651.3282-0.2825-0.15050.1497-0.060.1030.2513-0.3436-0.06170.10810.3608-0.0006-0.01050.27630.00130.232720.0556-36.338210.1197
60.6598-0.2522-0.37841.9983-0.13610.2777-0.0281-0.1436-0.06830.1516-0.04990.29380.081-0.00150.02720.3111-0.01660.05010.2806-0.01040.295214.1338-39.359213.4303
71.45280.8247-1.37620.7727-0.49031.8776-0.15250.1833-0.09170.04890.1080.2483-0.0981-0.33420.070.26570.00610.01970.2884-0.02010.305212.0978-27.16555.039
81.8441-0.09790.38091.6624-0.43660.8644-0.0763-0.062-0.417-0.12-0.0490.28960.2016-0.22040.01520.2296-0.02380.00430.2829-0.02180.266812.364-20.5036-5.9889
91.051-0.04340.33531.4638-0.34660.2212-0.05520.0873-0.0009-0.02550.0534-0.02820.026-0.11560.00310.2841-0.01740.01940.2598-0.00190.227525.1763-24.5849-2.7342
102.44980.64460.11443.2954-0.31960.8915-0.31510.2962-0.1336-0.47260.2553-0.5785-0.04950.24020.08270.272-0.01830.02530.2866-0.01490.310936.1463-31.6370.2577
111.5229-0.18320.18743.029-0.38741.12060.0185-0.2438-0.07860.1933-0.1046-0.26360.17530.11920.06590.3229-0.0150.01860.2828-0.00420.266232.4695-33.08526.4533
121.51661.08380.06272.645-0.59530.76930.0159-0.0936-0.30210.0044-0.0241-0.14250.12660.17190.00280.30950.01880.0050.2728-0.01810.267628.4867-41.24659.4273
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 44 )
2X-RAY DIFFRACTION2chain 'A' and (resid 45 through 84 )
3X-RAY DIFFRACTION3chain 'A' and (resid 85 through 138 )
4X-RAY DIFFRACTION4chain 'A' and (resid 139 through 227 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 20 )
6X-RAY DIFFRACTION6chain 'B' and (resid 21 through 66 )
7X-RAY DIFFRACTION7chain 'B' and (resid 67 through 84 )
8X-RAY DIFFRACTION8chain 'B' and (resid 85 through 107 )
9X-RAY DIFFRACTION9chain 'B' and (resid 108 through 161 )
10X-RAY DIFFRACTION10chain 'B' and (resid 162 through 178 )
11X-RAY DIFFRACTION11chain 'B' and (resid 179 through 200 )
12X-RAY DIFFRACTION12chain 'B' and (resid 201 through 227 )

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