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- PDB-4zew: Crystal structure of PfHAD1 in complex with glucose-6-phosphate -

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Basic information

Entry
Database: PDB / ID: 4zew
TitleCrystal structure of PfHAD1 in complex with glucose-6-phosphate
ComponentsPfHAD1
KeywordsUNKNOWN FUNCTION / C2 HAD / sugar phosphatase / haloacid-dehalogenase / glucose-6-phosphate
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 / metal ion binding / cytoplasm
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
6-O-phosphono-alpha-D-glucopyranose / PHOSPHATE ION / Haloacid dehalogenase-like hydrolase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPark, J. / Tolia, N.H.
Funding support United States, 3items
OrganizationGrant numberCountry
Children's Discovery Institue of Washington University and St. Louis Children's HospitalMD-LI-2011-171 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI103280 United States
Burroughs Wellcome Fund1013514 United States
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2015
Title: Cap-domain closure enables diverse substrate recognition by the C2-type haloacid dehalogenase-like sugar phosphatase Plasmodium falciparum HAD1.
Authors: Park, J. / Guggisberg, A.M. / Odom, A.R. / Tolia, N.H.
History
DepositionApr 20, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Revision 1.3Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PfHAD1
B: PfHAD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,1456
Polymers67,7412
Non-polymers4044
Water5,188288
1
A: PfHAD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1553
Polymers33,8711
Non-polymers2842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PfHAD1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9903
Polymers33,8711
Non-polymers1192
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.700, 44.500, 84.800
Angle α, β, γ (deg.)90.00, 101.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PfHAD1


Mass: 33870.641 Da / Num. of mol.: 2 / Mutation: D27A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (isolate 3D7) (eukaryote)
Gene: PF10_0325 / Plasmid: BG1861 / Production host: Escherichia coli BL21(DE3) (bacteria) / 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: Sugar ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H13O9P
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.34 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M HEPES, pH 7.5, 20% PEG8000

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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: May 16, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 44805 / % possible obs: 98.9 % / Redundancy: 3.77 % / Rsym value: 0.072 / Net I/σ(I): 16.1
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 2.42 / % possible all: 98.3

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
PHASERphasing
XDSdata reduction
XDSdata scaling
Blu-Icedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4QJB

4qjb


Resolution: 1.9→19.62 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 2185 4.88 %Random selection
Rwork0.179 ---
obs0.181 44805 99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4472 0 23 288 4783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084614
X-RAY DIFFRACTIONf_angle_d1.1876236
X-RAY DIFFRACTIONf_dihedral_angle_d14.2071743
X-RAY DIFFRACTIONf_chiral_restr0.052711
X-RAY DIFFRACTIONf_plane_restr0.008802
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.94130.33571320.26472613X-RAY DIFFRACTION97
1.9413-1.98640.28111340.23492617X-RAY DIFFRACTION100
1.9864-2.0360.28831390.22172622X-RAY DIFFRACTION98
2.036-2.0910.24781330.21292637X-RAY DIFFRACTION99
2.091-2.15250.26191390.19972618X-RAY DIFFRACTION98
2.1525-2.22190.22791430.18982653X-RAY DIFFRACTION98
2.2219-2.30120.26381280.19342652X-RAY DIFFRACTION100
2.3012-2.39310.23411400.17932631X-RAY DIFFRACTION99
2.3931-2.50180.22061500.17892648X-RAY DIFFRACTION99
2.5018-2.63350.22511250.19192678X-RAY DIFFRACTION99
2.6335-2.7980.26031450.19322669X-RAY DIFFRACTION99
2.798-3.01330.22831220.19382673X-RAY DIFFRACTION100
3.0133-3.31530.25211420.18462697X-RAY DIFFRACTION100
3.3153-3.7920.20531340.16822676X-RAY DIFFRACTION99
3.792-4.76620.15321390.13652734X-RAY DIFFRACTION100
4.7662-19.61710.16831400.15412802X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 25.7635 Å / Origin y: 29.9674 Å / Origin z: 20.2434 Å
111213212223313233
T0.1732 Å2-0.0145 Å20.0175 Å2-0.1279 Å20.0233 Å2--0.1349 Å2
L0.9536 °2-0.158 °20.1462 °2-0.4019 °2-0.0918 °2--0.4237 °2
S-0.0308 Å °-0.1573 Å °-0.0505 Å °-0.0002 Å °0.016 Å °-0.0027 Å °0.0726 Å °0.0061 Å °0.0151 Å °
Refinement TLS groupSelection details: ALL

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