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- PDB-1vpa: Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidyly... -

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Basic information

Entry
Database: PDB / ID: 1vpa
TitleCrystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (TM1393) from Thermotoga maritima at 2.67 A resolution
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
KeywordsTRANSFERASE / TM1393 / 2-C-methyl-d-erythritol 4-phosphate cytidylyltransferase / structural genomics / JCSG / Joint Center for Structural Genomics / PSI / protein structure initiative
Function / homology
Function and homology information


cytidylyltransferase activity / 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 / terpenoid biosynthetic process / cytosol
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
ACETIC ACID / CYTIDINE-5'-TRIPHOSPHATE / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (TM1393) from Thermotoga maritima at 2.67 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionOct 14, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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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)54,8778
Polymers53,7422
Non-polymers1,1356
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-47 kcal/mol
Surface area17830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.230, 144.230, 53.724
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALAAA1 - 13513 - 147
21METMETALAALABB1 - 13513 - 147
12LEULEUGLUGLUAA136 - 145148 - 157
22LEULEUGLUGLUBB136 - 145148 - 157
13TYRTYRGLUGLUAA146 - 219158 - 231
23TYRTYRTRPTRPBB146 - 218158 - 230

NCS ensembles :
ID
1
2
3

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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: 26870.945 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM1393, ispD / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X1B3, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 3.18 Å3/Da / Density % sol: 61.04 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8
Details: 0.2M Ca(OAc)2, 10.0% PEG-8000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979127
DetectorType: APS / Detector: CCD / Date: Feb 20, 2004
Details: sagitally focusing 2nd crystal, Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979127 Å / Relative weight: 1
ReflectionResolution: 2.67→49.35 Å / Num. obs: 18105 / % possible obs: 98.28 % / Redundancy: 4.51 % / Biso Wilson estimate: 53.97 Å2 / Rsym value: 0.109 / Net I/σ(I): 11.46
Reflection shellResolution: 2.67→2.77 Å / Redundancy: 3.66 % / Mean I/σ(I) obs: 1.97 / Num. unique all: 1772 / Rsym value: 0.523 / % possible all: 98.23

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vgz

1vgz


Resolution: 2.67→49.35 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.887 / SU B: 18.909 / SU ML: 0.213 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.687 / ESU R Free: 0.317 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. POOR DENSITY FOR REGION 139-143 IN CHAIN A AND B. UNACCOUNTED DIFFERENCE DENSITY NEXT TO ASP102 AND ARG105 CURRENTLY MODELED AS WATER. ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. POOR DENSITY FOR REGION 139-143 IN CHAIN A AND B. UNACCOUNTED DIFFERENCE DENSITY NEXT TO ASP102 AND ARG105 CURRENTLY MODELED AS WATER. UNACCOUNTED DENSITY NEXT TO ARG14 CTP AND LYS201 MODELLED AS ACETATE (PRESENT IN CRYSTALIZATION SOLUTION). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24783 1313 7.3 %RANDOM
Rwork0.19879 ---
obs0.20234 16781 98.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.048 Å2
Baniso -1Baniso -2Baniso -3
1-1.9 Å20.95 Å20 Å2
2--1.9 Å20 Å2
3----2.85 Å2
Refinement stepCycle: LAST / Resolution: 2.67→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3434 0 68 119 3621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223570
X-RAY DIFFRACTIONr_bond_other_d0.0010.023336
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9814843
X-RAY DIFFRACTIONr_angle_other_deg0.77837677
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0715439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26722.886149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.02115603
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3691528
X-RAY DIFFRACTIONr_chiral_restr0.0750.2551
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02739
X-RAY DIFFRACTIONr_nbd_refined0.2070.2784
X-RAY DIFFRACTIONr_nbd_other0.1790.23548
X-RAY DIFFRACTIONr_nbtor_other0.0850.22293
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2158
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2620.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.241
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.28
X-RAY DIFFRACTIONr_mcbond_it0.4111.52268
X-RAY DIFFRACTIONr_mcbond_other0.0821.5896
X-RAY DIFFRACTIONr_mcangle_it0.67223529
X-RAY DIFFRACTIONr_scbond_it0.98431479
X-RAY DIFFRACTIONr_scangle_it1.6174.51314
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21707
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12016medium positional0.430.5
12016medium thermal0.382
2138medium positional0.370.5
2138medium thermal0.212
31114medium positional0.320.5
31114medium thermal0.332
LS refinement shellResolution: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.382 90 7.01 %
Rwork0.301 1193 -
obs--97.34 %
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)
13.3020.7326-0.55021.9374-0.35471.86590.0410.1991-0.2372-0.06440.0365-0.15280.10250.1967-0.0775-0.1604-0.03010.0003-0.1655-0.0252-0.0772-9.5182118.4907-7.6958
234.6953-10.3424-9.062826.553913.76167.57910.0254-1.56170.6090.9742-0.27041.2935-1.1225-0.10630.2450.32350.01010.08920.01350.04590.1204-36.1449117.316110.7784
32.18790.27170.25283.2666-0.68372.34410.05360.0565-0.207-0.03560.02910.01260.128-0.0658-0.0827-0.1456-0.0528-0.0383-0.09980.0031-0.1034-21.4555117.5078-5.5236
42.24181.8705-0.12324.88510.32680.51810.2151-0.253-0.26170.5031-0.2854-0.20230.23540.03930.07030.005-0.0716-0.0284-0.01520.0364-0.0411-34.796292.16866.9232
57.8673-0.69627.929838.6958-5.97438.71230.36610.20860.5069-1.4480.58511.8251-0.7626-1.9344-0.9513-0.13530.0513-0.00380.34860.16270.27-34.4120.5216-8.3803
62.19882.0084-0.37844.26031.26532.19230.28190.02860.10910.6479-0.1780.05630.1984-0.0869-0.10390.0083-0.0697-0.0087-0.04660.015-0.0612-33.4648104.89046.4067
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 13513 - 147
22AA136 - 144148 - 156
33AA145 - 219157 - 231
44BB1 - 13513 - 147
55BB136 - 144148 - 156
66BB145 - 218157 - 230

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