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- PDB-3q8h: Crystal structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate ... -

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Basic information

Entry
Database: PDB / ID: 3q8h
TitleCrystal structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase from burkholderia pseudomallei in complex with cytidine derivative EBSI01028
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / ISPF / MEP PATHWAY / METAL-BINDING / ISOPRENE BIOSYNTHESIS
Function / homology
Function and homology information


2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity / terpenoid biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / metal ion binding
Similarity search - Function
2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, conserved site / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase superfamily / YgbB family / 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase signature. / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AO9 / : / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.75 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
#1: Journal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Staker, B.L. / Phan, I. / Gillespie, A. / Choi, R. / Nakazawa-Hewitt, S. / Nguyen, M.T. / Napuli, A. / Barrett, L. / Buchko, G.W. / Stacy, R. / Myler, P.J. / Stewart, L.J. / Manoil, C. / Van Voorhis, W.C.
History
DepositionJan 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Dec 11, 2013Group: Database references
Revision 1.4Sep 13, 2023Group: 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 / 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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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

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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 2,4-cyclodiphosphate synthase
B: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
C: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,99812
Polymers58,4613
Non-polymers1,5379
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6590 Å2
ΔGint-15 kcal/mol
Surface area16170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.690, 67.760, 60.020
Angle α, β, γ (deg.)90.000, 96.020, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-167-

HOH

21B-227-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase / MECDP-synthase / MECPS


Mass: 19487.109 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (bacteria) / Strain: 1710B / Gene: ispF, mecS, BPSL2098 / Production host: Escherichia coli (E. coli)
References: UniProt: Q63T71, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 5 types, 315 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-AO9 / 5'-deoxy-5'-[(imidazo[2,1-b][1,3]thiazol-5-ylcarbonyl)amino]cytidine


Mass: 392.390 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H16N6O5S
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.04 Å3/Da / Density % sol: 39.57 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 27 mg/mL protein in 20% PEG 4000, 100 mM Tris, 200 mM NaCl. Crystals soaked in same conditions with 20 mM ligand and 5 mM ZnCl2 for 3 weeks. , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Oct 31, 2010
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.75→19.9 Å / Num. obs: 46878 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.962 Å2 / Rmerge(I) obs: 0.025 / Net I/σ(I): 27.83
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.75-1.80.1764.35677324792.7
1.8-1.840.1384.96525337799.4
1.84-1.90.11366665327999.5
1.9-1.960.0937.46766319299.6
1.96-2.020.0799.46849310899.6
2.02-2.090.06212.36850297699.3
2.09-2.170.052167201291599.2
2.17-2.260.05219.88420280199.5
2.26-2.360.04623.58735267299.3
2.36-2.470.04127.28762254699.4
2.47-2.610.03532.79066246599.6
2.61-2.770.032369048225599.4
2.77-2.960.0343.110480218598.5
2.96-3.20.02451.29953200599.5
3.2-3.50.0260.69357187199.4
3.5-3.910.01870.48458169599.8
3.91-4.520.016787525151499.8
4.52-5.530.015796196125399.5
5.53-7.830.01878.3488999999.6
7.830.01885.7238352392.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ke1

3ke1


Resolution: 1.75→19.9 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / WRfactor Rfree: 0.1695 / WRfactor Rwork: 0.1451 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8868 / SU B: 4.026 / SU ML: 0.062 / SU R Cruickshank DPI: 0.1005 / SU Rfree: 0.0966 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1841 2359 5 %RANDOM
Rwork0.1549 ---
obs0.1564 46844 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 89.73 Å2 / Biso mean: 22.1886 Å2 / Biso min: 2.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3420 0 93 306 3819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0213590
X-RAY DIFFRACTIONr_angle_refined_deg1.8841.9944880
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3735465
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.05222.81153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89515534
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3711536
X-RAY DIFFRACTIONr_chiral_restr0.1080.2561
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212754
X-RAY DIFFRACTIONr_mcbond_it0.8141.52303
X-RAY DIFFRACTIONr_mcangle_it1.37423632
X-RAY DIFFRACTIONr_scbond_it2.15231287
X-RAY DIFFRACTIONr_scangle_it3.4154.51247
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 146 -
Rwork0.215 3073 -
all-3219 -
obs--92.63 %
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)
11.46860.84220.60031.41850.67731.3868-0.06620.0370.1998-0.2159-0.01380.15-0.14880.03320.07990.06930.0085-0.01180.02070.00050.102511.9406-33.4397-12.3642
24.29142.1196-0.08522.6309-0.37650.44110.0438-0.43440.62470.0781-0.19930.394-0.1742-0.15190.15550.13120.0588-0.02220.1127-0.1460.22428.8039-25.9287-1.9025
31.1680.040.24850.3106-0.01071.31310.01680.0630.0419-0.00990.04560.0020.0296-0.15-0.06230.0834-0.00050.00590.0850.01490.07014.4575-38.8116-15.1239
42.98660.7789-0.30471.3773-0.58711.36040.0418-0.41220.05450.1354-0.0694-0.0402-0.0374-0.00140.02760.08280.01880.01240.1171-0.02030.04310.8281-37.21140.4855
52.08871.86860.05452.3585-0.44041.0810.0229-0.16570.02780.1145-0.0904-0.0342-0.0180.07080.06750.08750.016-0.00030.0428-0.01440.084918.5632-36.0063-4.6412
61.76892.03231.31116.26212.82851.94790.01160.04790.0413-0.0692-0.0387-0.03840.05420.03550.02710.0915-0.00130.010.052-0.00680.076513.0877-40.1334-13.4779
71.5026-0.02960.91312.4898-0.36751.0959-0.15280.53280.1064-0.11640.0382-0.3128-0.04330.35470.11460.0787-0.03540.04970.23590.05490.08523.3163-34.4697-28.0459
82.6213-0.78010.61261.5045-1.26211.2242-0.06170.76740.0328-0.1401-0.0408-0.17150.12640.16530.10240.0589-0.01670.05080.3845-0.03570.063727.4142-37.8975-28.0512
916.72760.5221-1.61765.58988.214620.63460.07691.2988-0.1264-0.72580.2643-0.6912-0.77470.2496-0.34120.18510.05220.15940.27580.00280.165935.9632-44.0946-31.9157
101.7305-0.04690.61481.4564-0.22160.6274-0.05790.52040.0043-0.16790.05340.06830.0260.21330.00450.0889-0.00620.02050.2133-0.00330.021118.3197-41.2282-30.7434
117.66911.03061.32583.4797-0.29624.2589-0.27430.08750.5831-0.08240.12930.0799-0.26150.10570.1450.1356-0.0395-0.06890.02030.04220.167521.8288-21.5418-16.7722
121.7092.68130.604118.4351-0.69590.6906-0.03840.38540.0336-0.20980.0444-0.12650.04550.2586-0.0060.11470.01010.02970.17020.00840.102121.357-39.5948-22.7035
134.8822.91410.43033.49140.37570.08570.1068-0.12410.04550.167-0.1026-0.09650.07330.0282-0.00420.1380.0113-0.02250.08730.00220.078727.5964-40.6476-7.1726
144.0943-0.11550.643410.56061.2342.3705-0.1062-0.30050.14430.3520.057-0.5178-0.04150.27090.04930.03590.0073-0.06470.09640.00830.145841.4039-38.4923-5.5537
152.4122-0.010.01930.385-0.18640.61540.0025-0.1607-0.14280.1129-0.0008-0.12560.05360.0153-0.00170.12380.0425-0.02330.08040.00240.116625.2697-45.3947-3.4475
163.4135-1.3478-5.10245.4454-0.96029.6158-0.1445-0.35240.25330.90580.1688-0.4944-0.48320.3587-0.02430.31140.1569-0.18560.1549-0.1170.143429.6299-46.13537.81
171.86480.42860.17491.3649-0.5621.04480.0130.0816-0.2166-0.0473-0.0191-0.21750.17140.16660.00610.08010.0601-0.00440.0512-0.0060.106232.1706-49.4774-9.2882
181.25980.10090.30041.5179-0.10060.842-0.01450.1838-0.0409-0.0028-0.0083-0.16860.05220.21990.02280.06470.01780.00350.0682-0.00350.093430.23-41.7901-14.2927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION2A21 - 37
3X-RAY DIFFRACTION3A38 - 100
4X-RAY DIFFRACTION4A101 - 122
5X-RAY DIFFRACTION5A123 - 145
6X-RAY DIFFRACTION6A146 - 159
7X-RAY DIFFRACTION7B1 - 29
8X-RAY DIFFRACTION8B30 - 58
9X-RAY DIFFRACTION9B59 - 70
10X-RAY DIFFRACTION10B71 - 136
11X-RAY DIFFRACTION11B137 - 144
12X-RAY DIFFRACTION12B145 - 159
13X-RAY DIFFRACTION13C1 - 18
14X-RAY DIFFRACTION14C19 - 38
15X-RAY DIFFRACTION15C39 - 60
16X-RAY DIFFRACTION16C61 - 75
17X-RAY DIFFRACTION17C76 - 121
18X-RAY DIFFRACTION18C122 - 158

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