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- PDB-9ddy: The Crystal Structure of Geranyltranstransferase from Streptococc... -

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Basic information

Entry
Database: PDB / ID: 9ddy
TitleThe Crystal Structure of Geranyltranstransferase from Streptococcus pneumoniae TIGR4
ComponentsGeranyltranstransferase
KeywordsTRANSFERASE / ISOPRENOID SYNTHASE / CSBID / STRUCTURAL GENOMICS / Center for Structural Biology of Infectious Diseases
Function / homology
Function and homology information


isoprenoid biosynthetic process / (2E,6E)-farnesyl diphosphate synthase activity / cytoplasm
Similarity search - Function
: / Polyprenyl synthases signature 1. / Polyprenyl synthases signature 2. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Isoprenoid synthase domain superfamily
Similarity search - Domain/homology
Geranyltranstransferase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsKim, Y. / Tan, A. / Endres, M. / Tan, K. / Joachimik, A. / Center for Structural Biology of Infectious Diseases (CSBID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: The Crystal Structure of Geranyltranstransferase from Streptococcus pneumoniae TIGR4
Authors: Kim, Y. / Tan, A. / Endres, M. / Tan, K. / Joachimik, A.
History
DepositionAug 28, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Geranyltranstransferase
B: Geranyltranstransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4373
Polymers64,3452
Non-polymers921
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-43 kcal/mol
Surface area21940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.643, 101.496, 119.889
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Geranyltranstransferase / Geranylgeranyl diphosphate synthase


Mass: 32172.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: ispA, SP_1205 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): GOLD / References: UniProt: A0A0H2UQ53
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Sodium chloride, 0.1 M BIS-TRIS, 25%w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97936 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97936 Å / Relative weight: 1
ReflectionResolution: 2.32→50 Å / Num. obs: 28000 / % possible obs: 100 % / Redundancy: 6 % / Biso Wilson estimate: 43.15 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rmerge(I) obs: 0.111 / Rpim(I) all: 0.049 / Rrim(I) all: 0.122 / Χ2: 0.535 / Net I/σ(I): 12.5
Reflection shellResolution: 2.32→2.36 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.909 / Mean I/σ(I) obs: 1.04 / Num. unique obs: 1383 / CC1/2: 0.57 / CC star: 0.852 / Rpim(I) all: 0.436 / Rrim(I) all: 1.011 / Χ2: 0.362 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.32→46.73 Å / SU ML: 0.2927 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.2538
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2536 1307 4.68 %
Rwork0.2092 26627 -
obs0.2113 27934 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.99 Å2
Refinement stepCycle: LAST / Resolution: 2.32→46.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4255 0 6 49 4310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214328
X-RAY DIFFRACTIONf_angle_d0.44445853
X-RAY DIFFRACTIONf_chiral_restr0.035695
X-RAY DIFFRACTIONf_plane_restr0.0032759
X-RAY DIFFRACTIONf_dihedral_angle_d17.53151606
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.32-2.410.34591170.28422724X-RAY DIFFRACTION92.09
2.41-2.520.31491630.27242915X-RAY DIFFRACTION99.97
2.52-2.650.31771400.25792957X-RAY DIFFRACTION100
2.65-2.820.30481420.24442932X-RAY DIFFRACTION100
2.82-3.030.29431470.25372976X-RAY DIFFRACTION99.97
3.03-3.340.27971500.24282960X-RAY DIFFRACTION99.97
3.34-3.820.26031470.2082985X-RAY DIFFRACTION99.97
3.82-4.810.2221470.1683026X-RAY DIFFRACTION99.62
4.82-46.730.1981540.17563152X-RAY DIFFRACTION99.49
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)
12.80398885564-2.71960877147-1.187747717333.894993823631.543448879391.882817439550.182723758020.5868684346-0.490641808223-0.456818206754-0.2915502172580.5228491751240.266595401382-0.3342535423860.1217091982850.425901515745-0.0850264960003-0.1039872807330.518746592563-0.07859442739860.4365462654649.551939313843.3904156489913.3555515006
22.70315147865-2.91668594954-0.7966851511097.836377800160.9800198081331.97713262001-0.04229851650240.297729821309-0.302524520421-0.236402001123-0.04365578967620.2927587775140.301682417492-0.3685436222230.08538412191090.302801476202-0.0776231385677-0.009996382561160.333097882043-0.06714764255110.31038439793921.19570637071.3012710518215.8010452289
36.982329004162.806820270331.400307747841.445344794891.292670049035.9262249340.07419175788591.164787722070.20070255814-0.395761056712-0.0749531215430.133418062753-0.152470766261-0.1163420740220.02329961684050.5794965734220.175137747317-0.05917648269240.7970774252850.07812516203640.3486743213513.65065760120.74973429396.33534242787
42.90436403719-0.7302021175390.3804501718882.861455261780.3114492203921.904552687290.02897513553120.162201486033-0.107064524507-0.02246821779160.020544887018-0.0335428027910.0506841025258-0.0815983442243-0.04462821428010.241006510951-0.01625513628170.01161489301530.2706434534430.01813923500510.24159808673620.617631851911.525479736223.8277046361
54.065040735511.79752686749-1.063055014455.472148706750.4862473076972.225025052820.03897981043810.5810424306660.84952177612-0.727994950662-0.178283573899-0.688333659364-1.045699565920.374719421697-0.2591148747380.6129327693810.01098865729460.1590898110510.5677961284440.1513272598660.66006985761436.499118923322.18647907612.3846739685
64.737466951750.542969925693-0.6791917660165.214425335810.4202282362593.611482485870.1395174395710.902891452126-0.0978632840802-0.543858991879-0.0389929874066-0.2746962138230.03668783286870.2411509429850.01276719720430.4792025946660.04767313831430.02688414741190.523789874466-0.05351264537990.40613148523536.35025695044.09892699610.4626108143
74.305323797070.890387961194-1.132353139643.75144116558-3.287045359936.219020966240.346220708356-1.019817278970.5512539536030.729883653197-0.2297131020110.187563897439-1.187672040950.732628644793-0.04704145320910.44403747446-0.1071482008540.008495301800990.441039779752-0.08050498586970.40984822326126.349060461224.817501875637.1724125432
83.88004048831-0.2353456484-0.3628663492842.87283818651-1.098404440362.798128478450.0935056319728-0.4715094915580.2695055146610.2203129224160.0885546353870.0307053844408-0.454819175950.103513237911-0.1500387813590.310587946426-0.001646864159680.05410878448590.3188464304760.003076397051490.286034234715.904014342519.830383244641.5832452227
92.88277525587-2.12833943241-0.5349938971554.3851417629-0.572966924770.707832441720.1732259780720.1373243952650.38325541996-0.161521728235-0.0708675865092-0.0657785724246-0.263396547998-0.151359506592-0.0818970227840.390675211593-0.003819093874540.02077496636010.2839003267940.006184030776970.39678136841817.168002896128.171886362225.8677656653
104.47186039398-1.387523323670.5948272679771.82569475579-0.2508031958642.82978313847-0.236737881393-0.3332597419980.2623359934770.2206364364210.0571152275870.0466362957681-0.147913625675-0.4459581764070.1867679419120.347497422626-0.03262134523380.007522966412690.3680398922370.01805600150320.3795927017332.0561187159818.868136589440.3454335352
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid -2 through 37 )AA-2 - 371 - 40
22chain 'A' and (resid 38 through 80 )AA38 - 8041 - 83
33chain 'A' and (resid 81 through 102 )AA81 - 10284 - 105
44chain 'A' and (resid 103 through 156 )AA103 - 156106 - 159
55chain 'A' and (resid 157 through 175 )AA157 - 175160 - 178
66chain 'A' and (resid 176 through 290 )AA176 - 290179 - 280
77chain 'B' and (resid 1 through 36 )BC1 - 361 - 36
88chain 'B' and (resid 37 through 81 )BC37 - 8137 - 81
99chain 'B' and (resid 82 through 122 )BC82 - 12282 - 122
1010chain 'B' and (resid 123 through 290 )BC123 - 290123 - 274

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