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- PDB-1n1d: Glycerol-3-phosphate cytidylyltransferase complexed with CDP-glycerol -

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Basic information

Entry
Database: PDB / ID: 1n1d
TitleGlycerol-3-phosphate cytidylyltransferase complexed with CDP-glycerol
Componentsglycerol-3-phosphate cytidylyltransferase
KeywordsTRANSFERASE / alpha/beta fold / cytidylyltransferase / nucleotidyltransferase / negative cooperativity / CDP-glycerol
Function / homology
Function and homology information


glycerol-3-phosphate cytidylyltransferase / glycerol-3-phosphate cytidylyltransferase activity / teichoic acid biosynthetic process / cell wall organization / metal ion binding / cytoplasm
Similarity search - Function
Glycerol-3-phosphate cytidylyltransferase / : / Cytidylyltransferase-like / Cytidyltransferase-like domain / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-C2G / Glycerol-3-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPattridge, K.A. / Weber, C.H. / Friesen, J.A. / Sankar, S. / Kent, C. / Ludwig, M.L.
Citation
Journal: J.Biol.Chem. / Year: 2003
Title: Glycerol-3-phosphate cytidylyltransferase. Structural changes induced by binding of CDP-glycerol and the role of lysine residues in catalysis
Authors: Pattridge, K.A. / Weber, C.H. / Friesen, J.A. / Sanker, S. / Kent, C. / Ludwig, M.L.
#1: Journal: Structure / Year: 1999
Title: A prototypical cytidylyltransferase: CTP:glycerol-3-phosphate cytidylyltransferase from Bacillus subtilis
Authors: Weber, C.H. / Park, Y.S. / Sanker, S. / Kent, C. / Ludwig, M.L.
History
DepositionOct 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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 / 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: glycerol-3-phosphate cytidylyltransferase
B: glycerol-3-phosphate cytidylyltransferase
C: glycerol-3-phosphate cytidylyltransferase
D: glycerol-3-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,37911
Polymers61,1824
Non-polymers2,1977
Water3,045169
1
A: glycerol-3-phosphate cytidylyltransferase
B: glycerol-3-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7386
Polymers30,5912
Non-polymers1,1474
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4410 Å2
ΔGint-65 kcal/mol
Surface area11870 Å2
MethodPISA
2
C: glycerol-3-phosphate cytidylyltransferase
D: glycerol-3-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6425
Polymers30,5912
Non-polymers1,0513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4250 Å2
ΔGint-46 kcal/mol
Surface area11760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.795, 55.929, 63.701
Angle α, β, γ (deg.)88.99, 75.03, 82.54
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
glycerol-3-phosphate cytidylyltransferase / GCT / CDP-glycerol pyrophosphorylase / Teichoic acid biosynthesis protein D


Mass: 15295.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: P27623, glycerol-3-phosphate cytidylyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-C2G / [CYTIDINE-5'-PHOSPHATE] GLYCERYLPHOSPHORIC ACID ESTER / CYTIDINE 5'-DIPHOSPHOGLYCEROL


Mass: 477.255 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H21N3O13P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.03 Å3/Da / Density % sol: 38.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 3350, lithium sulfate, Tris, EDTA, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
2100 mMTris1droppH8.5
31 mMEDTA1drop
41 mMdithiothreitol1drop
55-10 mMCDP-glycerol1drop
630 %PEG33501reservoir
7200 mM1reservoirLi2SO4
8100 mMTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 140 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 10, 1998 / Details: mirrors
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→99 Å / Num. all: 40625 / Num. obs: 40625 / % possible obs: 87.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Rsym value: 0.051 / Net I/σ(I): 20.6
Reflection shellResolution: 1.8→1.87 Å / Mean I/σ(I) obs: 5.7 / Rsym value: 0.191 / % possible all: 82.1
Reflection
*PLUS
Num. obs: 40610 / Num. measured all: 121437 / Rmerge(I) obs: 0.051
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 82.1 % / Rmerge(I) obs: 0.191

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
CNSrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COZ

1coz


Resolution: 2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2944 3031 -RANDOM
Rwork0.2409 ---
all0.2463 30174 --
obs0.2463 30174 89.6 %-
Displacement parametersBiso mean: 12.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.52 Å21.615 Å20.764 Å2
2--1.537 Å2-0.254 Å2
3----0.017 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4248 0 135 169 4552
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0075
X-RAY DIFFRACTIONc_angle_deg1.317
X-RAY DIFFRACTIONc_dihedral_angle_d22.21
X-RAY DIFFRACTIONc_improper_angle_d0.783
X-RAY DIFFRACTIONc_mcangle_it1.342
X-RAY DIFFRACTIONc_mcbond_it0.9141.5
X-RAY DIFFRACTIONc_scangle_it1.4672.5
X-RAY DIFFRACTIONc_scbond_it2.1432.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2cdg.paramcdg.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 15 Å / Num. reflection obs: 40610 / Num. reflection Rfree: 2032
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.21
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.783

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