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- PDB-4naf: PrcB from Geobacillus kaustophilus, apo structure -

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Basic information

Entry
Database: PDB / ID: 4naf
TitlePrcB from Geobacillus kaustophilus, apo structure
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
Heptaprenylglyceryl phosphate synthase
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 1.1Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.source
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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


Theoretical massNumber of molelcules
Total (without water)50,6082
Polymers50,6082
Non-polymers00
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-20 kcal/mol
Surface area18360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.114, 157.840, 38.170
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: 25232.525 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: 25375.666 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS HAVE INDICATED THAT THE CORRECT RESIDUE SHOULD BE A GLU RESIDUE

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.44 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.9→27.435 Å / Num. all: 151551 / Num. obs: 41523 / % possible obs: 99.9 % / Observed criterion σ(F): 1.45 / 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: 1.9→27.435 Å / SU ML: 0.23 / σ(F): 1.35 / Phase error: 25.21 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 2092 5.04 %Random
Rwork0.2125 ---
obs0.2139 41513 99.92 %-
all-151551 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→27.435 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 0 290 3634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053412
X-RAY DIFFRACTIONf_angle_d0.9324664
X-RAY DIFFRACTIONf_dihedral_angle_d13.0851175
X-RAY DIFFRACTIONf_chiral_restr0.064548
X-RAY DIFFRACTIONf_plane_restr0.004603
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94420.35371300.32922558X-RAY DIFFRACTION100
1.9442-1.99280.31821520.28882580X-RAY DIFFRACTION100
1.9928-2.04670.28141310.26912572X-RAY DIFFRACTION100
2.0467-2.10690.30151350.2392620X-RAY DIFFRACTION100
2.1069-2.17490.28841280.23582575X-RAY DIFFRACTION100
2.1749-2.25260.24631290.23492625X-RAY DIFFRACTION100
2.2526-2.34270.30411310.23412585X-RAY DIFFRACTION100
2.3427-2.44930.23121470.22882591X-RAY DIFFRACTION100
2.4493-2.57830.30241640.22942615X-RAY DIFFRACTION100
2.5783-2.73970.27431470.21932639X-RAY DIFFRACTION100
2.7397-2.9510.23621580.22322600X-RAY DIFFRACTION100
2.951-3.24760.24281260.21842639X-RAY DIFFRACTION100
3.2476-3.71650.22781500.1942653X-RAY DIFFRACTION100
3.7165-4.67870.18451340.16842711X-RAY DIFFRACTION100
4.6787-27.43780.1921300.192858X-RAY DIFFRACTION100
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)
10.3656-0.11230.0450.26090.10790.18850.0807-0.00070.2561-0.0855-0.1703-0.14980.0629-0.0047-0.00640.25050.03840.01550.19180.00730.324927.080312.5077-7.5758
20.21350.01350.04550.0518-0.05560.0714-0.0205-0.18380.2647-0.15090.2271-0.2669-0.010.29460.00210.20780.01380.00590.1937-0.01590.277928.34439.5191-6.6385
30.0399-0.0356-0.03530.2113-0.1280.1549-0.01380.00390.1121-0.21110.0454-0.29160.02090.067900.22190.023-0.00940.231-0.01120.351835.54115.2686-8.7288
40.0481-0.1114-0.03360.61620.00370.0829-0.0332-0.03-0.0881-0.2349-0.1141-0.3150.0876-0.0113-0.00160.17170.00890.03610.17670.01420.220827.7147-11.6491-10.6194
50.3181-0.0808-0.11811.4158-0.03680.4943-0.00360.0555-0.011-0.11-0.0066-0.0085-0.0398-0.103-00.18510.0092-0.00860.2275-0.02460.16216.4212-7.4116-6.7503
60.53710.3091-0.06770.49550.29990.38490.0677-0.07020.2072-0.0811-0.12860.2269-0.0604-0.0855-00.16540.0612-0.02710.223-0.04650.239912.4935.5854-4.8896
70.0509-0.0345-0.0140.0546-0.01470.0166-0.0961-0.13090.23220.11820.0719-0.0217-0.3119-0.1168-00.25660.03550.00470.2345-0.01240.379218.303718.3248-4.7089
80.6221-0.2941-0.15511.0729-0.22840.25360.0221-0.1302-0.07790.0438-0.06690.12280.0273-0.047200.2633-0.0356-0.00920.2260.00130.179614.5552-36.972710.8677
90.3161-0.32110.36850.5155-0.50480.4946-0.00620.1045-0.0934-0.09710.050.11150.1661-0.16200.1819-0.02180.00920.2343-0.01130.155213.8044-21.9299-4.2574
100.27870.23540.16060.6083-0.21090.3495-0.0331-0.0387-0.0499-0.03150.0158-0.02920.0705-0.0072-00.2334-0.01020.04350.1905-0.00870.189721.3775-27.5482-4.0503
111.03320.4098-0.03820.7316-0.45490.88970.0258-0.0424-0.1075-0.0047-0.0953-0.41060.02930.08810.00010.201-0.00750.00740.20040.02370.218931.3487-31.78063.9914
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 28 )
2X-RAY DIFFRACTION2chain 'A' and (resid 29 through 44 )
3X-RAY DIFFRACTION3chain 'A' and (resid 45 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 107 )
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 161 )
6X-RAY DIFFRACTION6chain 'A' and (resid 162 through 215 )
7X-RAY DIFFRACTION7chain 'A' and (resid 216 through 228 )
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 77 )
9X-RAY DIFFRACTION9chain 'B' and (resid 78 through 107 )
10X-RAY DIFFRACTION10chain 'B' and (resid 108 through 138 )
11X-RAY DIFFRACTION11chain 'B' and (resid 139 through 228 )

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