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- PDB-2o1o: Cryptosporidium parvum putative polyprenyl pyrophosphate synthase... -

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Basic information

Entry
Database: PDB / ID: 2o1o
TitleCryptosporidium parvum putative polyprenyl pyrophosphate synthase (cgd4_2550) in complex with risedronate.
ComponentsPutative farnesyl pyrophosphate synthase
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / putative polyprenyl pyrophosphate synthase / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


farnesyl diphosphate biosynthetic process / dimethylallyltranstransferase activity / (2E,6E)-farnesyl diphosphate synthase activity / metal ion binding / cytoplasm
Similarity search - Function
Farnesyl pyrophosphate synthase-like / Polyprenyl synthases signature 1. / Polyprenyl synthetase, conserved site / Polyprenyl synthetase / Polyprenyl synthetase / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-RIS / Putative farnesyl pyrophosphate synthase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsChruszcz, M. / Artz, J.D. / Dong, A. / Dunford, J. / Lew, J. / Zhao, Y. / Kozieradski, I. / Kavanaugh, K.L. / Oppermann, U. / Sundstrom, M. ...Chruszcz, M. / Artz, J.D. / Dong, A. / Dunford, J. / Lew, J. / Zhao, Y. / Kozieradski, I. / Kavanaugh, K.L. / Oppermann, U. / Sundstrom, M. / Weigelt, J. / Edwards, A.M. / Arrowsmith, C.H. / Bochkarev, A. / Hui, R. / Minor, W. / Structural Genomics Consortium (SGC)
CitationJournal: Chem.Biol. / Year: 2008
Title: Targeting a uniquely nonspecific prenyl synthase with bisphosphonates to combat cryptosporidiosis
Authors: Artz, J.D. / Dunford, J.E. / Arrowood, M.J. / Dong, A. / Chruszcz, M. / Kavanagh, K.L. / Minor, W. / Russell, R.G. / Ebetino, F.H. / Oppermann, U. / Hui, R.
History
DepositionNov 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Refinement description / Structure summary / Category: audit_author / software / Item: _chem_comp.pdbx_synonyms
Revision 1.4Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative farnesyl pyrophosphate synthase
B: Putative farnesyl pyrophosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,65810
Polymers85,9462
Non-polymers7128
Water50428
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-87 kcal/mol
Surface area28540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.758, 101.758, 75.313
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Putative farnesyl pyrophosphate synthase


Mass: 42973.051 Da / Num. of mol.: 2 / Fragment: residues 38-384
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Gene: cgd4_2550 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-(DE3)-CodonPlus-RIL / References: UniProt: Q5CR09
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-RIS / 1-HYDROXY-2-(3-PYRIDINYL)ETHYLIDENE BIS-PHOSPHONIC ACID / Risedronate


Mass: 283.112 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H11NO7P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.6 M ammonium sulfate, 10 mM MgCl2, and 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 5, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.42→50 Å / Num. all: 64868 / Num. obs: 32655 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.066 / Rsym value: 0.046 / Net I/σ(I): 29.7
Reflection shellResolution: 2.42→2.53 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.464 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4061 / Rsym value: 0.49 / % possible all: 100

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Processing

Software
NameClassification
SHELXL-97refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2HER

2her
PDB Unreleased entry


Resolution: 2.42→50 Å / Num. parameters: 21516 / Num. restraintsaints: 21967 / Cross valid method: FREE R / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH AND HUBER
Details: SHELXL-97, RESOLVE, and COOT were used for refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.2126 1695 5.4 %RANDOM
Rwork0.1863 ---
all-31541 --
obs-31541 94.9 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 5378
Refinement stepCycle: LAST / Resolution: 2.42→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5310 0 40 28 5378
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d0.022
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0283
X-RAY DIFFRACTIONs_zero_chiral_vol0.042
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.065
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.129
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.098
X-RAY DIFFRACTIONs_approx_iso_adps0

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