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- PDB-3d8h: Crystal structure of phosphoglycerate mutase from Cryptosporidium... -

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Basic information

Entry
Database: PDB / ID: 3d8h
TitleCrystal structure of phosphoglycerate mutase from Cryptosporidium parvum, cgd7_4270
ComponentsGlycolytic phosphoglycerate mutase
KeywordsISOMERASE / structural genomics / malaria / cryptosporidium / Glycolysis / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / glycolytic process
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglycerate mutase
Similarity search - Component
Biological speciesCryptosporidium parvum (eukaryote)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsWernimont, A.K. / Lew, J. / Wasney, G. / Alam, Z. / Kozieradzki, I. / Cossar, D. / Schapiro, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. ...Wernimont, A.K. / Lew, J. / Wasney, G. / Alam, Z. / Kozieradzki, I. / Cossar, D. / Schapiro, M. / Bochkarev, A. / Arrowsmith, C.H. / Bountra, C. / Wilkstrom, M. / Edwards, A.M. / Hui, R. / Artz, J.D. / Hills, T. / Structural Genomics Consortium (SGC)
CitationJournal: Mol.Biochem.Parasitol. / Year: 2011
Title: Characterization of a new phosphatase from Plasmodium.
Authors: Hills, T. / Srivastava, A. / Ayi, K. / Wernimont, A.K. / Kain, K. / Waters, A.P. / Hui, R. / Pizarro, J.C.
History
DepositionMay 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Aug 24, 2011Group: Database references
Revision 1.3Sep 7, 2011Group: Database references
Revision 1.4Oct 25, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycolytic phosphoglycerate mutase
B: Glycolytic phosphoglycerate mutase


Theoretical massNumber of molelcules
Total (without water)60,4112
Polymers60,4112
Non-polymers00
Water3,711206
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-10.7 kcal/mol
Surface area20420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.248, 158.365, 140.249
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 3 / Auth seq-ID: 197 - 205 / Label seq-ID: 197 - 205

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Glycolytic phosphoglycerate mutase


Mass: 30205.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium parvum (eukaryote) / Strain: Iowa II / Gene: cgd7_4270 / Plasmid: pET28a-thrombin-lic / Production host: Escherichia coli (E. coli) / References: UniProt: Q5CXZ9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.4 Å3/Da / Density % sol: 48.77 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25% PEG 3350, 0.2 M NH4OAc, 0.1 M Hepes pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 18, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. all: 39125 / Num. obs: 39125 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.046 / Χ2: 1.25 / Net I/σ(I): 9.6
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.796 / Mean I/σ(I) obs: 2.32 / Num. unique all: 3847 / Rsym value: 0.796 / Χ2: 1.011 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XQ9

1xq9


Resolution: 2.01→40.5 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.933 / SU B: 10.193 / SU ML: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.2 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1958 5 %RANDOM
Rwork0.231 ---
all0.233 39074 --
obs0.233 39074 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.774 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å20 Å2
2---0.25 Å20 Å2
3----1.55 Å2
Refinement stepCycle: LAST / Resolution: 2.01→40.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3641 0 0 206 3847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223755
X-RAY DIFFRACTIONr_angle_refined_deg1.1411.9755112
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.925469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.57824.474152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.96715652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1091517
X-RAY DIFFRACTIONr_chiral_restr0.0810.2582
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022785
X-RAY DIFFRACTIONr_nbd_refined0.1850.21747
X-RAY DIFFRACTIONr_nbtor_refined0.2990.22560
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.212
X-RAY DIFFRACTIONr_mcbond_it0.3841.52416
X-RAY DIFFRACTIONr_mcangle_it0.64723777
X-RAY DIFFRACTIONr_scbond_it1.0231582
X-RAY DIFFRACTIONr_scangle_it1.5044.51331
Refine LS restraints NCS

Dom-ID: 2 / Auth asym-ID: B / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
36TIGHT POSITIONAL0.030.05
26LOOSE POSITIONAL0.125
36TIGHT THERMAL0.10.5
26LOOSE THERMAL0.8110
LS refinement shellResolution: 2.01→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 134 -
Rwork0.282 2630 -
all-2764 -
obs--97.29 %

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