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- PDB-4kt7: The crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythrito... -

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Basic information

Entry
Database: PDB / ID: 4kt7
TitleThe crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritolsynthase from Anaerococcus prevotii DSM 20548
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
KeywordsTRANSFERASE / structural genomics / PSI-Biology / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
Similarity search - Function
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site / Cytidylyltransferase IspD/TarI / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature. / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A / Nucleotide-diphospho-sugar transferases / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesAnaerococcus prevotii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsBorek, D. / Tan, K. / Stols, L. / Eschenfeidt, W.H. / Otwinoski, Z. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritolsynthase from Anaerococcus prevotii DSM 20548
Authors: Borek, D. / Tan, K. / Stols, L. / Eschenfeidt, W.H. / Otwinoski, Z. / Joachimiak, A.
History
DepositionMay 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)54,9524
Polymers54,8932
Non-polymers582
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3980 Å2
ΔGint-34 kcal/mol
Surface area21080 Å2
MethodPISA
2
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules

A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,9048
Polymers109,7874
Non-polymers1174
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area10040 Å2
ΔGint-90 kcal/mol
Surface area40150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.858, 145.509, 36.719
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-301-

NA

21B-465-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 229
2010B3 - 229
DetailsExperimentally unknown. The chains A and B is predicted to form a dimer.

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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: 27446.707 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Anaerococcus prevotii (bacteria) / Strain: DSM 20548 / Gene: Apre_0175, ispD / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: C7RFG6, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 3.0 Sodium Chloride, 0.1M Bis-TrisHCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 20, 2012 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→75 Å / Num. all: 32747 / Num. obs: 32747 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.4 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 20.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.8.1_1168refinement
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 2.001→33.61 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.92 / SU ML: 0.2 / σ(F): 1.35 / Phase error: 22.99 / Stereochemistry target values: ML / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.2281 1494 5.01 %
Rwork0.1808 --
obs0.1832 29845 91.21 %
all-28356 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.848 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.79 Å20 Å2
3----0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.001→33.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 2 250 3858
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083699
X-RAY DIFFRACTIONf_angle_d1.0824993
X-RAY DIFFRACTIONf_dihedral_angle_d14.0821402
X-RAY DIFFRACTIONf_chiral_restr0.078578
X-RAY DIFFRACTIONf_plane_restr0.003635
Refine LS restraints NCS

Ens-ID: 1 / Number: 7934 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0014-2.0660.2515750.21591378X-RAY DIFFRACTION50
2.066-2.13980.26431090.20571960X-RAY DIFFRACTION71
2.1398-2.22550.2891210.21212382X-RAY DIFFRACTION87
2.2255-2.32670.25421480.20422686X-RAY DIFFRACTION96
2.3267-2.44940.25081330.19572800X-RAY DIFFRACTION99
2.4494-2.60280.22531370.19252798X-RAY DIFFRACTION100
2.6028-2.80370.24271580.20052801X-RAY DIFFRACTION100
2.8037-3.08560.27831520.19392821X-RAY DIFFRACTION100
3.0856-3.53170.20511590.16782811X-RAY DIFFRACTION100
3.5317-4.44790.22061430.1532888X-RAY DIFFRACTION100
4.4479-33.61490.19511590.17613026X-RAY DIFFRACTION99
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)
14.4342-0.508-0.65961.33411.1663.2371-0.1869-0.8759-0.14980.8856-0.06830.016-0.31080.2460.14310.41620.09240.02360.25640.0490.213919.0681-19.056816.5456
26.01352.3662-0.91746.51672.42291.51410.18310.84420.1459-0.8540.5287-0.2337-1.16420.4016-0.72360.4353-0.17510.15861.03140.15810.812636.8178-4.39281.575
32.95590.9883-0.24052.1165-0.03350.82460.2669-0.009-0.31920.0494-0.2308-0.54770.1320.9927-0.07570.15330.0481-0.01440.49110.03740.364632.5157-14.94526.5832
42.89870.7444-0.2272.9990.96582.28430.0610.0211-0.390.2136-0.1498-0.23060.36280.69560.03230.13120.0173-0.00070.27730.02850.189422.0491-17.34164.0557
51.7851-0.42640.16671.5475-0.18990.9333-0.0399-0.20410.00740.366-0.0653-0.2312-0.13130.17830.07350.114-0.0413-0.03470.1560.0040.083317.2511-1.560114.9726
62.5171-2.43190.01213.8209-1.08510.7450.09530.08050.07960.2339-0.18940.2884-0.17520.02080.09990.2027-0.0448-0.0210.1444-0.07120.232910.041410.90110.2566
73.7236-0.97790.42833.25481.77413.12940.11360.27940.0997-0.1607-0.28340.3482-0.0889-0.25080.15250.1409-0.01860.00710.20240.00850.13018.7211-10.7883.1419
82.13740.4230.49741.58770.19131.0641-0.253-0.076-0.0743-0.1011-0.021-0.0447-0.47850.09420.10470.1867-0.1232-0.03990.2041-0.00120.195715.1635-2.856412.248
96.40070.6157-0.80615.6496-0.78378.3418-0.3391-0.38940.158-0.33060.1098-0.8284-1.22760.74690.21840.6439-0.34790.02230.62690.02890.593335.80766.521610.173
103.4922-0.4119-2.05363.98560.87411.8038-0.12530.05270.1183-0.12090.2742-0.8254-0.34231.1455-0.230.4882-0.0454-0.06860.3655-0.11970.354127.10631.942611.5034
112.6899-0.9244-1.18632.6337-1.60662.314-0.2305-0.51170.5227-0.14350.5965-0.9556-1.15641.14220.31430.506-0.42530.00460.4052-0.22730.510229.955536.346112.2301
122.6263-0.6692-0.03732.81840.85162.92210.1864-0.22010.5441-0.120.0063-0.2069-0.95470.2635-0.02670.5642-0.0598-0.02070.1234-0.04220.324319.334737.567814.9647
131.20950.70650.08693.20440.24532.0479-0.17880.15590.0221-0.31030.1644-0.0426-0.2168-0.0815-0.03370.1245-0.0039-0.02560.1092-0.02150.100113.864116.64825.6356
142.3787-0.032-0.89263.33771.91494.4498-0.0627-0.16480.05460.3015-0.25620.5025-0.2482-0.58220.24710.26320.03210.01490.2114-0.04990.25529.520227.034712.1319
155.47350.0017-0.19736.53021.49083.0965-0.08080.75890.12120.36360.2357-1.2620.15880.7204-0.10490.31760.1727-0.06810.82450.00240.536136.508916.40537.6573
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 35 )
3X-RAY DIFFRACTION3chain 'A' and (resid 36 through 71 )
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 107 )
5X-RAY DIFFRACTION5chain 'A' and (resid 108 through 146 )
6X-RAY DIFFRACTION6chain 'A' and (resid 147 through 165 )
7X-RAY DIFFRACTION7chain 'A' and (resid 166 through 196 )
8X-RAY DIFFRACTION8chain 'A' and (resid 197 through 217 )
9X-RAY DIFFRACTION9chain 'A' and (resid 218 through 230 )
10X-RAY DIFFRACTION10chain 'B' and (resid 3 through 35 )
11X-RAY DIFFRACTION11chain 'B' and (resid 36 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 107 )
13X-RAY DIFFRACTION13chain 'B' and (resid 108 through 165 )
14X-RAY DIFFRACTION14chain 'B' and (resid 166 through 217 )
15X-RAY DIFFRACTION15chain 'B' and (resid 218 through 230 )

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