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- PDB-4myb: Crystal Structure of Francisella tularensis 2-C-methyl-D-erythrit... -

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Basic information

Entry
Database: PDB / ID: 4myb
TitleCrystal Structure of Francisella tularensis 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD)
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
KeywordsTRANSFERASE / alpha and beta protein / nucleotide-diphospho-sugar transferases
Function / homologySpore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Alpha-Beta Complex / Alpha Beta / :
Function and homology information
Biological speciesFrancisella tularensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsNoble, S.M. / Tsang, A.K. / Couch, R.D.
CitationJournal: To be Published
Title: Crystal Structure of Francisella tularensis 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD)
Authors: Noble, S.M. / Tsang, A.K. / Couch, R.D.
History
DepositionSep 27, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)29,4551
Polymers29,4551
Non-polymers00
Water95553
1
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase

A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)58,9112
Polymers58,9112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation26_555-x,-y,z1
Buried area4360 Å2
ΔGint-15 kcal/mol
Surface area20650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.409, 200.409, 200.409
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number210
Space group name H-MF4132
Components on special symmetry positions
IDModelComponents
11A-305-

HOH

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Components

#1: Protein 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase / MEP cytidylyltransferase


Mass: 29455.439 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Francisella tularensis (bacteria) / Gene: ispD, FTL_1525 / Production host: Escherichia coli (E. coli)
References: UniProt: Q2A280, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M citric acid, pH 4.5, 7% PEG6000, 0.5 M lithium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9787 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 17, 2011 / Details: bent conical Si mirror (Rh coated)
RadiationMonochromator: bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 2.4→30.562 Å / Num. all: 13737 / Num. obs: 13737 / % possible obs: 100 % / Redundancy: 1 % / Biso Wilson estimate: 42.06 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.068 / Net I/σ(I): 12.35
Reflection shellResolution: 2.4→2.58 Å / Redundancy: 43 % / Mean I/σ(I) obs: 8.06 / Num. unique all: 1742 / Rsym value: 0.068 / % possible all: 99

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SAINTdata scaling
SAINTdata reduction
PHASERphasing
PHENIX1.8_1069refinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→30.562 Å / Occupancy max: 1 / Occupancy min: 0.67 / SU ML: 0.28 / σ(F): 1.34 / Phase error: 28.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2656 699 5.09 %
Rwork0.2545 --
obs0.2551 13737 97.98 %
all-13737 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.29 Å2 / Biso mean: 73.974 Å2 / Biso min: 26.96 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30.562 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1738 0 0 53 1791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091750
X-RAY DIFFRACTIONf_angle_d1.2672375
X-RAY DIFFRACTIONf_chiral_restr0.077273
X-RAY DIFFRACTIONf_plane_restr0.005301
X-RAY DIFFRACTIONf_dihedral_angle_d15.237636
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.58560.38161480.31262559270799
2.5856-2.84560.31171230.30952571269499
2.8456-3.25690.32251540.2822559271398
3.2569-4.10180.23141160.24962618273498
4.1018-30.56450.23281580.22232731288996
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)
13.03831.9161-1.40751.3512-1.04840.78570.5709-1.301-0.04911.1991-0.53581.00540.7489-1.4156-0.10711.0428-0.48030.26511.01860.12780.9401-17.279216.491651.0641
28.67391.70671.5766.0420.07745.75240.1958-0.13860.20120.6811-0.10120.82490.411-0.6416-0.1140.4525-0.12360.01920.25120.00870.4467-8.7819.671539.301
32.11298.20717.14889.78636.65768.2982-0.78630.0220.7963-0.09090.38820.1481-0.7112-0.18510.40140.58250.12280.10280.51120.09880.88060.1381-6.370632.0897
44.13340.45532.51033.7091-1.28616.4210.47660.2691-0.51150.59690.1119-0.01690.91920.0923-0.49730.5779-0.049-0.22950.18240.05250.528-5.734713.321732.6143
56.17014.0869-1.91977.96581.33232.80360.3938-0.6298-0.72611.0404-0.196-0.27570.4956-0.0763-0.15473.2274-0.7148-0.4625-0.31990.73960.6527-6.62510.234854.4754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:75)A3 - 75
2X-RAY DIFFRACTION2chain 'A' and (resseq 76:136)A76 - 136
3X-RAY DIFFRACTION3chain 'A' and (resseq 137:155)A137 - 155
4X-RAY DIFFRACTION4chain 'A' and (resseq 156:214)A156 - 214
5X-RAY DIFFRACTION5chain 'A' and (resseq 215:227)A215 - 227

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