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- PDB-6fwh: Acanthamoeba IGPD in complex with R-C348 to 1.7A resolution -

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Basic information

Entry
Database: PDB / ID: 6fwh
TitleAcanthamoeba IGPD in complex with R-C348 to 1.7A resolution
ComponentsImidazoleglycerol-phosphate dehydratase
KeywordsLYASE / Inhibitor / Histidine biosynthesis / Acanthamoeba
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process
Similarity search - Function
Imidazole glycerol phosphate dehydratase; domain 1 / Imidazoleglycerol-phosphate dehydratase signature 1. / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase, conserved site / Imidazole glycerol phosphate dehydratase domain superfamily / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase signature 2. / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-5LD / : / Imidazoleglycerol-phosphate dehydratase / Imidazoleglycerol-phosphate dehydratase
Similarity search - Component
Biological speciesAcanthamoeba castellanii (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsRoberts, C.W. / Bisson, C. / Baker, P.J.
CitationJournal: PLoS ONE / Year: 2018
Title: Structural and functional studies of histidine biosynthesis in Acanthamoeba spp. demonstrates a novel molecular arrangement and target for antimicrobials.
Authors: Rice, C.A. / Campbell, S.J. / Bisson, C. / Owen, H.J. / Sedelnikova, S.E. / Baker, P.J. / Rice, D.W. / Henriquez, F.L. / Roberts, C.W.
History
DepositionMar 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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.ptnr3_symmetry / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Imidazoleglycerol-phosphate dehydratase
B: Imidazoleglycerol-phosphate dehydratase
C: Imidazoleglycerol-phosphate dehydratase
D: Imidazoleglycerol-phosphate dehydratase
E: Imidazoleglycerol-phosphate dehydratase
F: Imidazoleglycerol-phosphate dehydratase
G: Imidazoleglycerol-phosphate dehydratase
H: Imidazoleglycerol-phosphate dehydratase
I: Imidazoleglycerol-phosphate dehydratase
J: Imidazoleglycerol-phosphate dehydratase
K: Imidazoleglycerol-phosphate dehydratase
L: Imidazoleglycerol-phosphate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,06549
Polymers257,23712
Non-polymers3,82837
Water27,3471518
1
A: Imidazoleglycerol-phosphate dehydratase
B: Imidazoleglycerol-phosphate dehydratase
C: Imidazoleglycerol-phosphate dehydratase
D: Imidazoleglycerol-phosphate dehydratase
E: Imidazoleglycerol-phosphate dehydratase
F: Imidazoleglycerol-phosphate dehydratase
G: Imidazoleglycerol-phosphate dehydratase
H: Imidazoleglycerol-phosphate dehydratase
I: Imidazoleglycerol-phosphate dehydratase
J: Imidazoleglycerol-phosphate dehydratase
K: Imidazoleglycerol-phosphate dehydratase
L: Imidazoleglycerol-phosphate dehydratase
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase
B: Imidazoleglycerol-phosphate dehydratase
C: Imidazoleglycerol-phosphate dehydratase
D: Imidazoleglycerol-phosphate dehydratase
E: Imidazoleglycerol-phosphate dehydratase
F: Imidazoleglycerol-phosphate dehydratase
G: Imidazoleglycerol-phosphate dehydratase
H: Imidazoleglycerol-phosphate dehydratase
I: Imidazoleglycerol-phosphate dehydratase
J: Imidazoleglycerol-phosphate dehydratase
K: Imidazoleglycerol-phosphate dehydratase
L: Imidazoleglycerol-phosphate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)522,13198
Polymers514,47424
Non-polymers7,65774
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y,-z+31
Buried area88280 Å2
ΔGint-459 kcal/mol
Surface area132210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)167.690, 156.100, 117.120
Angle α, β, γ (deg.)90.00, 125.42, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11F-427-

HOH

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Components

#1: Protein
Imidazoleglycerol-phosphate dehydratase / / IGPD


Mass: 21436.416 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acanthamoeba castellanii (eukaryote) / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A1P7ZJC8, UniProt: L8H477*PLUS, imidazoleglycerol-phosphate dehydratase
#2: Chemical...
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-5LD / [(2R)-2-hydroxy-3-(1H-1,2,4-triazol-1-yl)propyl]phosphonic acid / (R)-C348


Mass: 207.124 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C5H10N3O4P
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1518 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / Details: 0.2 M calcium acetate and 20 % (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.79→95.44 Å / Num. obs: 228093 / % possible obs: 99.7 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.058 / Net I/σ(I): 11
Reflection shellResolution: 1.79→1.84 Å / Rmerge(I) obs: 0.535 / Rpim(I) all: 0.309

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EKW

5ekw


Resolution: 1.79→95.44 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.316 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.104 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19016 11433 5 %RANDOM
Rwork0.14921 ---
obs0.15129 216659 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 19.762 Å2
Baniso -1Baniso -2Baniso -3
1-0.37 Å20 Å2-0.05 Å2
2---0.24 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.79→95.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17826 0 181 1518 19525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01918286
X-RAY DIFFRACTIONr_bond_other_d0.0020.0217415
X-RAY DIFFRACTIONr_angle_refined_deg1.5121.97424691
X-RAY DIFFRACTIONr_angle_other_deg0.901340254
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.75152334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.57423.239781
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.642153174
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.40615144
X-RAY DIFFRACTIONr_chiral_restr0.0870.22834
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0220406
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023662
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.1311.6339348
X-RAY DIFFRACTIONr_mcbond_other6.1111.6339347
X-RAY DIFFRACTIONr_mcangle_it5.4252.41511666
X-RAY DIFFRACTIONr_mcangle_other5.4312.41511667
X-RAY DIFFRACTIONr_scbond_it19.1822.1678938
X-RAY DIFFRACTIONr_scbond_other19.1842.1688936
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other14.22.94413022
X-RAY DIFFRACTIONr_long_range_B_refined13.11220.65820113
X-RAY DIFFRACTIONr_long_range_B_other13.11120.65720114
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.793→1.84 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 854 -
Rwork0.235 15968 -
obs--99.9 %

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