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- PDB-1jn1: Structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase... -

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Basic information

Entry
Database: PDB / ID: 1jn1
TitleStructure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Haemophilus influenzae (HI0671)
Components2C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE SYNTHASE
KeywordsSTRUCTURAL GENOMICS / unknown function / 2C-METHYL-D-ERYTHRITOL 2 / 4-CYCLODIPHOSPHATE SYNTHASE / MECPS / isoprenoid biosynthesis / Structure 2 Function Project / S2F
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-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsLehmann, C. / Lim, K. / Toedt, J. / Krajewski, W. / Howard, A. / Eisenstein, E. / Herzberg, O. / Structure 2 Function Project (S2F)
Citation
Journal: Proteins / Year: 2002
Title: Structure of 2C-methyl-D-erythrol-2,4-cyclodiphosphate synthase from Haemophilus influenzae: activation by conformational transition.
Authors: Lehmann, C. / Lim, K. / Toedt, J. / Krajewski, W. / Howard, A. / Eisenstein, E. / Herzberg, O.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2000
Title: Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes
Authors: Lange, B.M. / Rujan, T. / Martin, W. / Croteau, R.
History
DepositionJul 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9828
Polymers51,6503
Non-polymers3325
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7070 Å2
ΔGint-34 kcal/mol
Surface area19920 Å2
MethodPISA
2
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

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

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

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)207,92732
Polymers206,60012
Non-polymers1,32720
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_666-y+1,-x+1,-z+11
crystal symmetry operation10_665-x+1,-y+1,z1
crystal symmetry operation15_556y,x,-z+11
Buried area48730 Å2
ΔGint-212 kcal/mol
Surface area59210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.3, 112.3, 187.6
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number98
Space group name H-MI4122
DetailsThe protein is a trimer in solution. The asymmetric unit contains the homotrimer / A tetramer of trimers is formed in the crystal. The biological significance is unknown. To form a tetramer of trimers, use the following: X,Y,Z; 1-Y,1-X,1-Z; 1-X,1-Y,Z; Y,X,1-Z

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Components

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


Mass: 17216.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: ISPF / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P44815
#2: Chemical
ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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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: 2.86 Å3/Da / Density % sol: 57.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 40% sat. ammonium sulfate, 0.1 MES, 15 mM CoCl2, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
11.7 Mammonium sulfate1reservoir
20.1 MMES1reservoirpH6.5
31 mM1reservoirCoCl2
415 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 30, 2001
RadiationMonochromator: Cryogenically-cooled Si(111) double-crystal system
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. all: 13670 / Num. obs: 13670 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 18.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 9.4
Reflection shellResolution: 2.9→3.03 Å / Rmerge(I) obs: 0.294 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 29 Å / % possible obs: 100 % / Num. measured all: 399292 / Rmerge(I) obs: 0.053
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.294 / Mean I/σ(I) obs: 9.4

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Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: structure from MIR data in P6(3) space group

Resolution: 2.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: engh & huber
RfactorNum. reflectionSelection details
Rfree0.29 1076 random
Rwork0.198 --
all-13331 -
obs-12725 -
Displacement parametersBiso mean: 57 Å2
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 9 0 3603
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2
LS refinement shellResolution: 2.9→3 Å / Rfactor Rfree: 0.387 / Rfactor Rwork: 0.294
Refinement
*PLUS
Highest resolution: 2.9 Å / σ(F): 2 / % reflection Rfree: 8 % / Rfactor Rfree: 0.29 / Rfactor Rwork: 0.198
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.387 / Rfactor Rwork: 0.294

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