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- PDB-7myv: Plasmodium falciparum HAD5/PMM -

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Basic information

Entry
Database: PDB / ID: 7myv
TitlePlasmodium falciparum HAD5/PMM
ComponentsPhosphomannomutase
KeywordsHYDROLASE / phosphomannomutase / HAD Superfamily / Rossmannoid fold
Function / homology
Function and homology information


Synthesis of GDP-mannose / phosphomannomutase / phosphomannomutase activity / GDP-mannose biosynthetic process / mannose metabolic process / protein N-linked glycosylation / metal ion binding / cytosol
Similarity search - Function
Phosphomannomutase / Phosphomannomutase, cap domain / Eukaryotic phosphomannomutase / HAD-superfamily hydrolase, subfamily IIB / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.51 Å
AuthorsFrasse, P.M. / Odom John, A.R. / Goldberg, D.E.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI103280 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI123808 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21-AI130584 United States
Wellcome Trust United States
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Enzymatic and structural characterization of HAD5, an essential phosphomannomutase of malaria-causing parasites.
Authors: Frasse, P.M. / Miller, J.J. / Polino, A.J. / Soleimani, E. / Zhu, J.S. / Jakeman, D.L. / Jez, J.M. / Goldberg, D.E. / Odom John, A.R.
History
DepositionMay 21, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 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

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Assembly

Deposited unit
A: Phosphomannomutase
B: Phosphomannomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8924
Polymers57,8442
Non-polymers492
Water00
1
A: Phosphomannomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9462
Polymers28,9221
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphomannomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9462
Polymers28,9221
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)161.255, 161.255, 109.738
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Phosphomannomutase


Mass: 28921.934 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Strain: isolate 3D7 / Gene: PF3D7_1017400 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): DE3 / Variant (production host): BL21 Gold / References: UniProt: Q8IJM5, phosphomannomutase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN

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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: 3.56 Å3/Da / Density % sol: 65.45 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2ul drops containing 1:1 mixture of protein (6mg/mL) and crystallization buffer (0.1M bis -tris-propane pH 6.5, 0.1 M calcium acetate, 16% (w/v) PEG 8000, and 2% (v/v) benzamidine hydrochloride)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jul 30, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→40.3164 Å / Num. obs: 11030 / % possible obs: 99.9 % / Redundancy: 32.1 % / Rsym value: 0.334 / Net I/σ(I): 18.5
Reflection shellResolution: 3.5→3.56 Å / Redundancy: 30.1 % / Mean I/σ(I) obs: 2.7 / Num. unique obs: 543 / Rsym value: 1.43 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CFR

6cfr


Resolution: 3.51→40.31 Å / SU ML: 0.5 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3071 1096 10 %
Rwork0.2544 9860 -
obs0.2593 10956 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 164.07 Å2 / Biso mean: 86.4114 Å2 / Biso min: 44.48 Å2
Refinement stepCycle: final / Resolution: 3.51→40.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 2 0 3949
Biso mean--70.62 --
Num. residues----477
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.51-3.670.35771360.316112151351100
3.67-3.860.32821300.299511881318100
3.86-4.10.33831350.27812111346100
4.1-4.420.29351360.252812221358100
4.42-4.860.26241360.216912271363100
4.86-5.560.26951380.24412401378100
5.56-70.36921400.288112541394100
7.01-40.310.29591450.22791303144897

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