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- PDB-4ys8: Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidyly... -

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Basic information

Entry
Database: PDB / ID: 4ys8
TitleCrystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
KeywordsTRANSFERASE / SSGCID / ispD / isoprenoid biosynthesis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
ACETATE ION / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesBurkholderia thailandensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Burkholderia thailandensis
Authors: Dranow, D.M. / Fairman, J.W. / Pierce, P.G. / Lorimer, D. / Edwards, T.E. / SSGCID
History
DepositionMar 16, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2015Group: Other
Revision 1.2Oct 28, 2015Group: Database references
Revision 1.3Oct 11, 2017Group: Data collection / Derived calculations / Category: pdbx_struct_oper_list / reflns_shell
Item: _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.percent_possible_all
Revision 1.4Nov 3, 2021Group: Data collection / Database references
Category: database_2 / diffrn_detector ...database_2 / diffrn_detector / diffrn_radiation_wavelength / diffrn_source
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_detector.type / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_wavelength_list / _diffrn_source.type
Revision 1.5Sep 27, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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


Theoretical massNumber of molelcules
Total (without water)103,80510
Polymers103,2864
Non-polymers5206
Water3,675204
1
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0063
Polymers25,8211
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9733
Polymers25,8211
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0063
Polymers25,8211
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase


Theoretical massNumber of molelcules
Total (without water)25,8211
Polymers25,8211
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
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)51,9786
Polymers51,6432
Non-polymers3354
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-15 kcal/mol
Surface area18790 Å2
MethodPISA
6
C: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
D: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8274
Polymers51,6432
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4440 Å2
ΔGint-16 kcal/mol
Surface area18170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.650, 138.310, 78.590
Angle α, β, γ (deg.)90.000, 101.890, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 25821.379 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia thailandensis (bacteria) / Strain: E264 / ATCC 700388 / DSM 13276 / CIP 106301 / Gene: ispD, BTH_I2089 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2SWT6, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.35 Å3/Da / Density % sol: 47.67 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: ButhA.00168.a.A1.PW33338 at 30.46 mg/ml was incuabted with 6mM MgCl2 and 6mM ATP, then mixed 1:1 with JCSG+(e11): 14.4% PEG-8000, 80mM Sodium Cacodylate/ HCl, pH=6.5, 160mM Calcium acetate, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 25, 2015 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 34999 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 37.04 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.077 / Rrim(I) all: 0.089 / Χ2: 0.966 / Net I/σ(I): 14.76 / Num. measured all: 134066
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.45-2.510.8490.5512.879986259025930.64100
2.51-2.580.8740.4663.249612249924930.54199.8
2.58-2.660.8760.423.639555247524800.488100
2.66-2.740.9140.3454.319163237723700.499.7
2.74-2.830.9450.2795.298932231723150.32499.9
2.83-2.930.960.2266.658535221822100.26299.6
2.93-3.040.9830.1698.448373218121770.19699.8
3.04-3.160.9890.12410.797921205820590.144100
3.16-3.30.9930.09713.327644199919940.11399.7
3.3-3.460.9940.07616.967272189218930.089100
3.46-3.650.9960.06219.676817179117850.07399.7
3.65-3.870.9970.0522.856595173117270.05899.8
3.87-4.140.9980.04325.926244164116420.05100
4.14-4.470.9980.03730.125590146914660.04499.8
4.47-4.90.9990.03232.645265139613900.03899.6
4.9-5.480.9980.03531.574770125012490.04199.9
5.48-6.330.9980.03928.394225111311100.04599.7
6.33-7.750.9990.02933.735469459380.03499.3
7.75-10.960.9990.02143.7827057307240.02599.2
10.960.9990.02238.3213164143840.02692.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VGW
Resolution: 2.45→29.529 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2629 1744 4.99 %
Rwork0.2157 33173 -
obs0.2181 34917 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.57 Å2 / Biso mean: 47.7916 Å2 / Biso min: 12.93 Å2
Refinement stepCycle: final / Resolution: 2.45→29.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6617 0 34 205 6856
Biso mean--71.19 41.02 -
Num. residues----887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046818
X-RAY DIFFRACTIONf_angle_d0.789269
X-RAY DIFFRACTIONf_chiral_restr0.0371061
X-RAY DIFFRACTIONf_plane_restr0.0041224
X-RAY DIFFRACTIONf_dihedral_angle_d11.7162429
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.45-2.5220.33461490.2812772292199
2.522-2.60330.30181330.27227302863100
2.6033-2.69630.33921470.25928282975100
2.6963-2.80420.2671480.252527092857100
2.8042-2.93170.30321400.251927632903100
2.9317-3.08610.30951500.245127602910100
3.0861-3.27920.29561430.243827762919100
3.2792-3.5320.30261580.224327502908100
3.532-3.88680.271380.207127762914100
3.8868-4.44760.21411460.180327632909100
4.4476-5.59720.20741460.174527842930100
5.5972-29.53120.22811460.19672762290898
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
16.6366-2.00381.27038.242-1.5253.7784-0.14930.0907-0.5809-0.03420.00590.03930.04150.18620.16210.1622-0.03260.06850.2559-0.02340.280446.523785.944842.7634
23.10040.44690.15363.4916-0.38955.46190.0127-0.1211-0.0559-0.0066-0.0245-0.4132-0.20380.40620.00550.1647-0.04240.03590.2152-0.01840.279547.154793.378446.7688
30.5031.3724-0.37034.9031-0.71970.98870.0018-0.03390.08370.28130.03660.4074-0.00990.0158-0.02950.19680.0003-0.00610.2536-0.03630.309530.71381.932748.6686
45.227-0.2631-2.02716.47382.14142.0287-0.061-0.1671-0.14720.20760.0352-0.16210.24130.1280.01220.31530.01280.01160.28250.09960.203535.527878.799747.6029
52.6389-0.0340.78774.0167-1.79525.3432-0.00820.2015-0.2291-0.01820.07450.0182-0.2926-0.0139-0.13960.42990.0395-0.00170.31140.01460.285631.480251.324933.0461
63.59651.5486-0.54833.40660.60514.7514-0.0580.24020.1881-0.37650.01430.2426-0.235-0.3324-0.11720.3610.0411-0.07190.2351-0.03160.237827.308945.823629.909
71.4648-0.59310.55835.1238-0.67013.4389-0.0612-0.0771-0.2188-0.09430.03480.3270.4046-0.2375-0.05910.2382-0.00480.0230.25930.00270.18427.559445.718240.8961
81.19890.1221-0.09231.29270.16412.0628-0.0666-0.3875-0.05080.5865-0.0332-0.0458-0.02610.49690.06080.30250.0025-0.04210.3096-0.02110.359639.131350.912748.5056
90.4299-0.6138-0.00764.42330.28660.5221-0.069-0.1409-0.13880.4496-0.06730.81230.1866-0.14720.08650.3422-0.03870.06570.27720.00620.344725.697761.469851.5497
104.8515-1.36310.02926.6165-1.96924.2596-0.0217-0.41040.10140.41380.05370.5793-0.1182-0.24210.01170.38560.04970.05640.2118-0.08530.297627.598656.518848.6875
114.75623.1046-2.57374.67960.80027.4318-0.3742-0.07740.7739-1.90360.6551-0.7325-0.67690.5496-0.08920.7123-0.11760.13290.33390.050.511833.9468.136630.7859
124.10691.67511.45752.4629-0.98181.85010.00320.23090.15820.02570.07160.0478-0.0627-0.2123-0.05720.4296-0.0183-0.04080.3145-0.07320.301423.589107.2778-8.5506
135.71950.3453-0.37123.168-1.40664.1606-0.07420.45660.2538-0.1080.0016-0.0750.4327-0.05660.03210.38110.0193-0.06470.289-0.00330.286824.5309112.5855-13.4789
142.29970.88570.40693.75580.47523.3918-0.15040.09790.3213-0.1113-0.0179-0.3843-0.38660.04030.20490.4647-0.0487-0.1690.228-0.03850.395333.5622116.7641-4.8467
151.97441.33440.37952.2857-0.79323.48420.2909-0.4550.00860.8951-0.2639-0.02650.2891-0.44250.05130.43050.0256-0.03890.3125-0.03740.240227.5417105.98565.0974
162.85820.65130.99958.4394-1.99270.9461-0.24970.0683-0.5858-1.176-0.0267-0.58420.0456-0.0010.0130.4795-0.03730.02990.25430.090.246641.067181.87430.5198
172.3743-0.9867-0.19652.4247-0.50220.1969-0.0332-0.3927-0.28920.2121-0.2432-0.321-0.37940.0839-0.17970.4899-0.0314-0.17760.36070.03530.22839.161689.73846.0978
183.66291.498-0.77038.96561.70939.30350.22660.5701-0.2794-0.2087-0.401-1.385-0.6170.31240.16970.4702-0.0279-0.17960.4046-0.0020.665341.7534114.1505-1.4933
198.82842.76652.09097.95281.7084.08560.1317-0.0682-0.57720.2291-0.061-1.166-0.00290.3113-0.07520.35130.0445-0.13010.26840.06760.431136.8457102.17650.8649
202.9359-2.1144-1.41612.71382.5932.7453-0.1493-0.679-0.84610.07730.76640.6270.94140.0193-0.40060.5191-0.0914-0.00090.4540.12270.508219.481890.9514-8.2381
215.453-1.2463-0.93656.6179-0.29922.7231-0.03660.06840.2535-0.31050.41211.10190.3777-0.2833-0.29950.4469-0.081-0.10290.31570.16770.509919.351168.44477.8635
222.56990.3248-0.45476.1701-0.87420.45270.00550.0621-0.0612-0.1130.1240.56880.0306-0.0586-0.18290.4851-0.0427-0.0910.32910.08680.304925.392566.48387.2367
231.3163-0.23950.26387.58350.7430.5789-0.35140.0520.24010.03520.3371-0.28940.10990.32450.02540.4687-0.0693-0.05850.34420.0850.326238.904587.56022.8989
241.7241-0.5798-0.4294.4252-2.54442.9148-0.0617-0.2984-0.07580.175-0.178-1.1402-0.21310.47470.20510.4892-0.0194-0.17640.43870.15090.597340.045568.3599.683
255.0913-2.514-3.055.2643.74423.8623-0.46250.74750.5969-0.4746-0.12820.3515-0.0783-0.3750.39890.7377-0.0089-0.21860.34320.0830.297928.01182.38161.057
265.2718-1.6287-3.75089.3196-2.62774.2958-0.03770.28950.57691.17071.33961.5063-0.47890.9432-0.75740.5824-0.0879-0.13210.5260.10770.565916.754388.84775.3513
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 43 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 96 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 97 through 185 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 186 through 231 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 43 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 44 through 81 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 82 through 115 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 116 through 138 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 139 through 185 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 186 through 218 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 219 through 230 )B0
12X-RAY DIFFRACTION12chain 'C' and (resid 0 through 43 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 44 through 81 )C0
14X-RAY DIFFRACTION14chain 'C' and (resid 82 through 107 )C0
15X-RAY DIFFRACTION15chain 'C' and (resid 108 through 138 )C0
16X-RAY DIFFRACTION16chain 'C' and (resid 139 through 152 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 153 through 168 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 169 through 186 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 187 through 218 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 219 through 231 )C0
21X-RAY DIFFRACTION21chain 'D' and (resid 1 through 65 )D0
22X-RAY DIFFRACTION22chain 'D' and (resid 66 through 126 )D0
23X-RAY DIFFRACTION23chain 'D' and (resid 127 through 168 )D0
24X-RAY DIFFRACTION24chain 'D' and (resid 169 through 204 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 205 through 218 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 219 through 230 )D0

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