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- PDB-4qjb: Crystal structure of the sugar phosphatase PfHAD1 from Plasmodium... -

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Basic information

Entry
Database: PDB / ID: 4qjb
TitleCrystal structure of the sugar phosphatase PfHAD1 from Plasmodium falciparum
ComponentsHaloacid dehalogenase-like hydrolase
KeywordsHYDROLASE / HAD-like hydrolase / HAD Rossmanoid fold / three-layered alpha-beta-alpha sandwich / Sugar Phosphatase
Function / homology
Function and homology information


Hydrolases; Acting on halide bonds; In carbon-halide compounds / negative regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / sugar-phosphatase activity / dephosphorylation / magnesium ion binding / cytoplasm / cytosol
Similarity search - Function
Hypothetical cof family signature 1. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Hypothetical cof family signature 1. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Haloacid dehalogenase-like hydrolase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsTolia, N.H. / Park, J.
CitationJournal: Nat Commun / Year: 2014
Title: A sugar phosphatase regulates the methylerythritol phosphate (MEP) pathway in malaria parasites.
Authors: Guggisberg, A.M. / Park, J. / Edwards, R.L. / Kelly, M.L. / Hodge, D.M. / Tolia, N.H. / Odom, A.R.
History
DepositionJun 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 13, 2014Group: Database references
Revision 1.2Feb 28, 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_ref_seq_dif / 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_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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Haloacid dehalogenase-like hydrolase
B: Haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9496
Polymers67,8292
Non-polymers1204
Water4,179232
1
A: Haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9743
Polymers33,9151
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Haloacid dehalogenase-like hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9743
Polymers33,9151
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)77.900, 43.800, 83.900
Angle α, β, γ (deg.)90.00, 101.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Haloacid dehalogenase-like hydrolase


Mass: 33914.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: genomic DNA
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: 3D7 / Gene: PF10_0325, PF3D7_1033400 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8IJ74
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.07 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES, 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 4.2.2 / Wavelength: 1 Å
DetectorType: NOIR-1 / Detector: CCD / Date: Apr 25, 2013
RadiationMonochromator: Rosenbaum-Rock Si(111) sagitally focused monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→20 Å / Num. all: 35349 / Num. obs: 35166 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→19.459 Å / SU ML: 0.25 / σ(F): 1.36 / Phase error: 27.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2418 1768 5.03 %RANDOM
Rwork0.2019 ---
all0.204 35349 --
obs0.204 35143 99.6 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.05→19.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4434 0 4 232 4670
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034519
X-RAY DIFFRACTIONf_angle_d0.6476094
X-RAY DIFFRACTIONf_dihedral_angle_d11.6211698
X-RAY DIFFRACTIONf_chiral_restr0.039692
X-RAY DIFFRACTIONf_plane_restr0.002787
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.10540.38831220.33372529X-RAY DIFFRACTION99
2.1054-2.16730.30761390.27152541X-RAY DIFFRACTION100
2.1673-2.23710.30691480.25452527X-RAY DIFFRACTION99
2.2371-2.3170.26911280.25842527X-RAY DIFFRACTION99
2.317-2.40960.27951250.21762563X-RAY DIFFRACTION100
2.4096-2.5190.27331360.21612547X-RAY DIFFRACTION100
2.519-2.65150.28291370.22922562X-RAY DIFFRACTION100
2.6515-2.81720.29081220.22762575X-RAY DIFFRACTION100
2.8172-3.03390.25541360.2182575X-RAY DIFFRACTION100
3.0339-3.33790.24081300.20412593X-RAY DIFFRACTION100
3.3379-3.81770.24431550.18652557X-RAY DIFFRACTION99
3.8177-4.7980.19941580.1572582X-RAY DIFFRACTION100
4.798-19.460.18281320.17662697X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.744 Å / Origin y: 29.9459 Å / Origin z: 19.8528 Å
111213212223313233
T0.2254 Å2-0.0124 Å20.0222 Å2-0.206 Å20.0162 Å2--0.172 Å2
L1.5486 °2-0.278 °20.2741 °2-0.6645 °2-0.1588 °2--0.8374 °2
S-0.0447 Å °-0.4134 Å °-0.0461 Å °0.1249 Å °0.0482 Å °0.0151 Å °0.0114 Å °-0.0335 Å °-0.0003 Å °
Refinement TLS groupSelection details: all

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