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- PDB-1h47: Structures of MECP synthase in complex with (i) CMP and (ii) CMP ... -

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Basic information

Entry
Database: PDB / ID: 1h47
TitleStructures of MECP synthase in complex with (i) CMP and (ii) CMP and product
Components2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
KeywordsSYNTHASE / ISOPRENOID / LYASE / 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 / ubiquinone biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / manganese ion binding / zinc ion binding / metal ion binding / identical protein 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
CYTIDINE-5'-MONOPHOSPHATE / GERANYL DIPHOSPHATE / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsKemp, L.E. / Alphey, M.S. / Bond, C.S. / Hunter, W.N.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2005
Title: The Identification of Isoprenoids that Bind in the Intersubunit Cavity of Escherichia Coli 2C-Methyl-D-Erythritol-2,4-Cyclodiphosphate Synthase by Complementary Biophysical Methods
Authors: Kemp, L.E. / Alphey, M.S. / Bond, C.S. / Ferguson, M. / Hecht, S. / Bacher, A. / Eisenreich, W. / Rohdich, F. / Hunter, W.N.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2002
Title: Structure of 2C-Methyl-D-Erythritol 2,4 Cyclodiphosphate Synthase
Authors: Kemp, L.E. / Alphey, M.S. / Bond, C.S. / Hunter, W.N.
History
DepositionFeb 24, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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_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_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_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
B: 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
C: 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
D: 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
E: 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
F: 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,93720
Polymers102,9776
Non-polymers2,96014
Water3,081171
1
A: 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
B: 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
C: 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,96810
Polymers51,4883
Non-polymers1,4807
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
E: 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
F: 2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,96810
Polymers51,4883
Non-polymers1,4807
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)88.082, 117.582, 54.215
Angle α, β, γ (deg.)90.00, 90.21, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.478057, 0.125674, -0.869291), (0.12625, 0.989265, 0.073588), (0.869208, -0.074569, -0.488792)78.545, -6.803, 93.8
2given(-0.999954, 0.006622, 0.006882), (-0.006796, -0.999648, -0.025663), (0.006709, -0.025709, 0.999647)27.131, 0.445, 5.798

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Components

#1: Protein
2C-METHYL-D-ERYTHRITOL-2,4-CYCLODIPHOSPHATE SYNTHASE / MECPS / MECDP-SYNTHASE / ISPF / MECS


Mass: 17162.805 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: BL21 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P62617, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
#2: Chemical ChemComp-GPP / GERANYL DIPHOSPHATE


Mass: 314.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O7P2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE


Mass: 323.197 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H14N3O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: CONVERTS 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D- ERYTHRITOL 2-PHOSPHATE INTO 2-C-METHYL-D- ...FUNCTION: CONVERTS 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D- ERYTHRITOL 2-PHOSPHATE INTO 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE (MECDP) AND CMP (BY SIMILARITY). PATHWAY: NONMEVALONATE TERPENOID BIOSYNTHESIS PATHWAY; FIFTH STEP.

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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: 2.5 Å3/Da / Density % sol: 50 %
Crystal growpH: 5.6
Details: 10-20% PEG 2000 MONOETHYL ETHER, 0.1M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE, pH 5.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.282
DetectorDate: Feb 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.282 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 141167 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 91

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GX1

1gx1


Resolution: 1.99→87.71 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.267 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.187 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 3708 5 %RANDOM
Rwork0.214 ---
obs0.216 69794 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å2-0.33 Å2
2--4.25 Å20 Å2
3----2.43 Å2
Refinement stepCycle: LAST / Resolution: 1.99→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6974 0 170 171 7315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0217340
X-RAY DIFFRACTIONr_bond_other_d0.0030.026894
X-RAY DIFFRACTIONr_angle_refined_deg1.6252.0059960
X-RAY DIFFRACTIONr_angle_other_deg0.881315910
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5885938
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.21124
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028192
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021454
X-RAY DIFFRACTIONr_nbd_refined0.2080.22210
X-RAY DIFFRACTIONr_nbd_other0.2530.28626
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1390.25650
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2228
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2210.237
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1280.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9941.54632
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8127342
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.63932708
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.3364.52618
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.99→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.332 257
Rwork0.283 4697

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