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- PDB-5b8f: X-ray Crystal Structure of a 2-C-methyl-D-erythritol 2,4-cyclodip... -

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Basic information

Entry
Database: PDB / ID: 5b8f
TitleX-ray Crystal Structure of a 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Pseudomonas aeruginosa
Components2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
KeywordsLYASE / SSGCID / Psuedomonas aeruginosa / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
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
CYTIDINE-5'-MONOPHOSPHATE / PHOSPHATE ION / 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: to be published
Title: X-ray Crystal Structure of a 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Pseudomonas aeruginosa
Authors: SSGCID / Fairman, J.W. / Dranow, D.M. / Lorimer, D. / Edwards, T.E.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Sep 27, 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
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_symmetry

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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)54,30814
Polymers52,7673
Non-polymers1,54111
Water10,611589
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-87 kcal/mol
Surface area17810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.560, 100.210, 54.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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 / / MECPS


Mass: 17589.127 Da / Num. of mol.: 3 / Fragment: PsaeA.01620.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (strain ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228) (bacteria)
Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: ispF, PA3627 / Plasmid: PsaeA.01620.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P57708, 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase

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Non-polymers , 5 types, 600 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-C5P / CYTIDINE-5'-MONOPHOSPHATE / Cytidine monophosphate


Mass: 323.197 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H14N3O8P
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 589 / 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: 2.1 Å3/Da / Density % sol: 41.33 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Morpheus C12: 12.5% PEG-1000, 12.5% PEG-3350, 12.5% MPD, 0.1M Bicine/Trizma base, pH=8.5, 0.03M each sodium nitrate, disodium hydrogen phosphate, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Feb 25, 2015
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 79313 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 7.31 % / Biso Wilson estimate: 13.3 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.053 / Χ2: 1.028 / Net I/σ(I): 23.44 / Num. measured all: 579986
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.45-1.490.8990.53.6341576579157920.538100
1.49-1.530.9280.3984.6841426566556650.429100
1.53-1.570.9540.3115.9640271549354920.335100
1.57-1.620.9680.2647.0139309535553550.284100
1.62-1.670.9780.2158.6838180518451840.231100
1.67-1.730.9840.17810.5536790499549920.19299.9
1.73-1.80.9910.13513.8635891486548640.145100
1.8-1.870.9930.11416.3834490467246710.123100
1.87-1.960.9960.08721.2133243450345020.094100
1.96-2.050.9980.06826.5431557427342710.073100
2.05-2.160.9980.05631.6930274410641060.06100
2.16-2.290.9980.0534.9328639388838870.054100
2.29-2.450.9990.04637.9626888364836470.049100
2.45-2.650.9990.04141.8925070341734160.044100
2.65-2.90.9990.03546.823117315031490.038100
2.9-3.240.9990.0352.7621008288028810.032100
3.24-3.740.9990.02658.1818339253425340.028100
3.74-4.5910.02361.7415691219321920.025100
4.59-6.4810.02360.7212018171317120.02599.9
6.48-500.9990.02357.636209101310010.02598.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata processing
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GX1

1gx1


Resolution: 1.45→36.981 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 14.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1692 3926 4.95 %RANDOM
Rwork0.138 75361 --
obs0.1395 79287 99.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 62.94 Å2 / Biso mean: 18.3779 Å2 / Biso min: 7.09 Å2
Refinement stepCycle: final / Resolution: 1.45→36.981 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3547 0 94 589 4230
Biso mean--26.13 29.97 -
Num. residues----481
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013829
X-RAY DIFFRACTIONf_angle_d1.2535238
X-RAY DIFFRACTIONf_chiral_restr0.066606
X-RAY DIFFRACTIONf_plane_restr0.006677
X-RAY DIFFRACTIONf_dihedral_angle_d15.8251376
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.46760.20471420.158226502792100
1.4676-1.48620.17681380.148426662804100
1.4862-1.50580.19751370.147126342771100
1.5058-1.52640.20611300.136226872817100
1.5264-1.54820.19291450.13426442789100
1.5482-1.57130.17221510.127926692820100
1.5713-1.59590.17761280.127226432771100
1.5959-1.6220.16151600.121226602820100
1.622-1.650.19831490.12426692818100
1.65-1.680.17311410.126426612802100
1.68-1.71230.17631410.128626582799100
1.7123-1.74730.17371280.126326762804100
1.7473-1.78530.18191350.121226742809100
1.7853-1.82680.18481640.129326652829100
1.8268-1.87250.15781380.126326672805100
1.8725-1.92310.18981190.131226892808100
1.9231-1.97970.17241170.131427032820100
1.9797-2.04360.15991450.128226852830100
2.0436-2.11660.16031430.120827072850100
2.1166-2.20130.1551590.12326422801100
2.2013-2.30150.14971280.129927182846100
2.3015-2.42280.1621280.138527042832100
2.4228-2.57460.16691660.143726962862100
2.5746-2.77330.1821410.152627292870100
2.7733-3.05230.19161250.154227442869100
3.0523-3.49370.17591550.141827342889100
3.4937-4.40050.1511340.132927882922100
4.4005-36.99330.15421390.16062899303899

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