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- PDB-3qhd: Crystal structure of 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE... -

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Basic information

Entry
Database: PDB / ID: 3qhd
TitleCrystal structure of 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE Synthase from BURKHOLDERIA PSEUDOMALLEI bound to CYTIDINE, FOL795 and FOL955
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / SSGCID / ISPF / CYTIDINE / FOL795 / FOL955 / MEP PATHWAY / METAL-BINDING
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 / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / 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
2-(pyridin-3-yl)-1,3-thiazole-4-carbaldehyde / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / : / 4-(1H-IMIDAZOL-1-YL)PHENOL / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Citation
Journal: J Struct Funct Genomics / Year: 2011
Title: Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.
Authors: Begley, D.W. / Hartley, R.C. / Davies, D.R. / Edwards, T.E. / Leonard, J.T. / Abendroth, J. / Burris, C.A. / Bhandari, J. / Myler, P.J. / Staker, B.L. / Stewart, L.J.
#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 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2013Group: Database references
Revision 1.3Sep 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)59,81213
Polymers58,4613
Non-polymers1,35110
Water6,900383
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8950 Å2
ΔGint-141 kcal/mol
Surface area16070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.820, 67.950, 60.220
Angle α, β, γ (deg.)90.000, 96.300, 90.000
Int Tables number5
Space group name H-MC121

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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, BURPS1710b_2511 / Production host: Escherichia coli (E. coli)
References: UniProt: Q3JRA0, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 7 types, 393 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CTN / 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE / CYTIDINE / Cytidine


Mass: 243.217 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H13N3O5
#5: Chemical ChemComp-MSR / 4-(1H-IMIDAZOL-1-YL)PHENOL


Mass: 160.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8N2O
#6: Chemical ChemComp-795 / 2-(pyridin-3-yl)-1,3-thiazole-4-carbaldehyde


Mass: 190.222 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6N2OS
#7: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.05 Å3/Da / Density % sol: 39.98 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: BupsA.00122.a.A1 W29971. 27 MG/ML PROTEIN IN 20% PEG 4000, 100 MM TRIS, 200 MM NACL, 5 MM ZNCL2. CRYSTALS SOAKED IN 25 MM LIGANDS IN SAME BUFFER FOR 3 WEEKS, pH 8.0, VAPOR DIFFUSION, SITTING ...Details: BupsA.00122.a.A1 W29971. 27 MG/ML PROTEIN IN 20% PEG 4000, 100 MM TRIS, 200 MM NACL, 5 MM ZNCL2. CRYSTALS SOAKED IN 25 MM LIGANDS IN SAME BUFFER 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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 50822 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.006 Å2 / Rmerge(I) obs: 0.023 / Net I/σ(I): 30.36
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.740.1255.595187306680.5
1.74-1.790.0986.686923365598
1.79-1.840.0817.947125361099
1.84-1.90.0758.827156350699.6
1.9-1.960.06711.017165335798.9
1.96-2.030.05313.557425331399.8
2.03-2.110.04617.387279316198.2
2.11-2.190.03723.968613303099.2
2.19-2.290.03827.68873288798
2.29-2.40.03131.79447282999.4
2.4-2.530.02836.989476267499.7
2.53-2.690.02641.539693251699.4
2.69-2.870.02547.5810882241499.3
2.87-3.10.02255.310830218999.4
3.1-3.40.0262.0110266206899.8
3.4-3.80.01870.349106185899.5
3.8-4.390.01875.147870161799.3
4.39-5.380.01779.626919140899.9
5.38-7.60.01778.745313109499.9
7.60.01979.28247557092.5

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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: PDB entry 3MBM

3mbm


Resolution: 1.7→19.95 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1786 / WRfactor Rwork: 0.1518 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8899 / SU B: 3.576 / SU ML: 0.058 / SU R Cruickshank DPI: 0.0955 / SU Rfree: 0.093 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1864 2590 5.1 %RANDOM
Rwork0.1569 ---
obs0.1584 50777 97.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 85.69 Å2 / Biso mean: 22.0549 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3457 0 81 383 3921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213621
X-RAY DIFFRACTIONr_angle_refined_deg1.3981.9924921
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2425473
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.80222.839155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.43815548
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9041537
X-RAY DIFFRACTIONr_chiral_restr0.0890.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212782
X-RAY DIFFRACTIONr_mcbond_it0.5921.52332
X-RAY DIFFRACTIONr_mcangle_it1.00523683
X-RAY DIFFRACTIONr_scbond_it1.6931289
X-RAY DIFFRACTIONr_scangle_it2.6594.51236
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.244 142 -
Rwork0.219 2898 -
all-3040 -
obs--80.36 %
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)
11.70290.17410.32411.6960.4851.7666-0.03580.15780.1601-0.1811-0.01590.0458-0.18110.08460.05170.0662-0.0127-0.01340.03760.02970.07811.7791-33.9065-12.5228
21.62980.09370.19360.70510.47571.3754-0.07190.05420.21-0.0454-0.03480.0663-0.12-0.02340.10660.0841-0.0089-0.00220.02250.02720.08397.3638-31.9325-10.6553
30.4748-0.549-3.23217.44822.837422.14520.19970.3003-0.0126-0.6229-0.29240.2453-1.3155-1.99790.09270.25320.1076-0.04020.3150.03110.157-2.8466-27.2503-17.8497
41.31190.11550.44790.98260.25091.47010.05390.0779-0.0087-0.0355-0.0086-0.00530.065-0.0984-0.04520.072-0.00980.01260.02730.01630.04685.087-40.2491-10.9344
51.41550.3967-0.18752.2777-0.26571.55980.0852-0.282-0.1090.1927-0.1233-0.12550.04770.0010.03810.0897-0.0090.0050.06530.02150.05989.1421-40.00051.0322
61.90620.91730.4391.748-0.4621.28030.00370.0385-0.01340.1078-0.0586-0.1475-0.01960.16210.05490.08180.00350.00750.0222-0.00020.077518.6578-36.6183-4.5513
71.96041.91271.35417.30532.69982.5745-0.00850.2542-0.0021-0.09630.03020.03420.10480.1273-0.02170.0648-0.00340.01040.0426-0.00260.047512.9278-40.9095-13.7437
81.98070.19491.13382.2151-0.22681.5985-0.25410.79340.1696-0.22360.1312-0.1948-0.14290.4470.12290.113-0.09860.04840.40530.0640.077123.6474-34.0904-28.057
93.1628-0.23581.12012.3392-1.24771.7827-0.18631.03710.1316-0.25890.1518-0.30130.03550.430.03450.1226-0.07570.05320.52140.00890.095827.4821-38.2415-28.2539
1010.8729-4.53825.30736.3091-1.56835.5039-0.23961.48280.077-0.5126-0.1839-0.4554-0.02580.67430.42350.2156-0.04890.16410.6677-0.03630.227634.0053-42.9529-31.9718
112.72591.12020.23411.5335-0.44142.24-0.20591.1146-0.4589-0.52810.2441-0.33620.28660.5921-0.03820.254-0.01050.11590.6938-0.22730.186126.4871-50.348-33.4394
122.23350.87521.34772.35630.83081.727-0.24180.720.0776-0.30050.20810.1203-0.14340.54910.03370.1032-0.08310.00790.30890.01970.022514.877-37.5139-29.8324
131.96720.84371.65793.32171.48741.6792-0.09370.42430.1948-0.1155-0.04360.0722-0.10370.24940.13740.0958-0.05990.01960.1880.05890.046115.5103-34.541-23.6047
142.0751.64490.823114.2422-0.69721.1823-0.01150.4881-0.0004-0.281-0.1129-0.32050.01350.40620.12440.0563-0.02860.02970.21770.01720.031321.8101-38.2313-22.329
156.65864.04641.04385.26890.4060.77320.12450.0713-0.01220.1887-0.116-0.22460.03110.1862-0.00840.09350.0128-0.00870.059-0.00560.060127.6885-41.3678-7.202
163.36351.3843-0.15593.082-0.04470.70120.08060.1067-0.01050.2238-0.0672-0.4907-0.07180.2958-0.01330.12050.0102-0.03330.1620.01040.212737.5598-40.6615-5.8263
174.3428-0.69821.52692.83340.28042.3275-0.0447-0.3690.02580.30450.052-0.06320.1066-0.0191-0.00730.12830.0344-0.01570.0693-0.01020.102320.3403-47.00920.9599
185.4737-5.0198-3.85744.70114.919425.3685-1.27-1.23570.43561.16221.2458-0.3685-0.7012.67050.02410.73940.1189-0.18790.879-0.30490.419332.078-46.51048.7699
192.05830.23080.28541.5161-0.44881.00870.00650.2746-0.2333-0.0891-0.0098-0.26660.14740.19140.00330.09760.0644-0.00050.0847-0.0410.147732.3944-50.009-8.9512
201.75560.32570.4943.8260.02361.2106-0.04460.4557-0.0079-0.10920.0314-0.29130.00410.3480.01320.0488-0.00770.02190.1866-0.01280.108933.0745-39.5218-15.4797
216.01255.0221.49169.58410.9830.77380.14840.044-0.35050.0112-0.138-0.10430.15320.0848-0.01030.11120.02910.01540.0753-0.04080.130821.8392-49.8988-10.6091
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 19
2X-RAY DIFFRACTION2A20 - 62
3X-RAY DIFFRACTION3A63 - 70
4X-RAY DIFFRACTION4A71 - 105
5X-RAY DIFFRACTION5A106 - 122
6X-RAY DIFFRACTION6A123 - 145
7X-RAY DIFFRACTION7A146 - 159
8X-RAY DIFFRACTION8B1 - 29
9X-RAY DIFFRACTION9B30 - 59
10X-RAY DIFFRACTION10B60 - 75
11X-RAY DIFFRACTION11B76 - 92
12X-RAY DIFFRACTION12B93 - 122
13X-RAY DIFFRACTION13B123 - 143
14X-RAY DIFFRACTION14B144 - 159
15X-RAY DIFFRACTION15C1 - 18
16X-RAY DIFFRACTION16C19 - 50
17X-RAY DIFFRACTION17C51 - 62
18X-RAY DIFFRACTION18C63 - 74
19X-RAY DIFFRACTION19C75 - 122
20X-RAY DIFFRACTION20C123 - 148
21X-RAY DIFFRACTION21C149 - 159

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