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- PDB-4mu4: The form B structure of an E21Q catalytic mutant of A. thaliana I... -

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Basic information

Entry
Database: PDB / ID: 4mu4
TitleThe form B structure of an E21Q catalytic mutant of A. thaliana IGPD2 in complex with Mn2+ and its substrate, 2R3S-IGP, to 1.41 A resolution
ComponentsImidazoleglycerol-phosphate dehydratase 2, chloroplastic
KeywordsLYASE / hydro-lyase / histidine biosynthesis / manganese binding / chloroplastic
Function / homology
Function and homology information


imidazoleglycerol-phosphate dehydratase / imidazoleglycerol-phosphate dehydratase activity / L-histidine biosynthetic process / chloroplast / metal ion binding
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-IYP / : / Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.41 Å
AuthorsBisson, C. / Britton, K.L. / Sedelnikova, S.E. / Baker, P.J. / Rice, D.W.
CitationJournal: Structure / Year: 2015
Title: Crystal Structures Reveal that the Reaction Mechanism of Imidazoleglycerol-Phosphate Dehydratase Is Controlled by Switching Mn(II) Coordination.
Authors: Bisson, C. / Britton, K.L. / Sedelnikova, S.E. / Rodgers, H.F. / Eadsforth, T.C. / Viner, R.C. / Hawkes, T.R. / Baker, P.J. / Rice, D.W.
History
DepositionSep 20, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 2023Group: 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 / 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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _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_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_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_symmetry / _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: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,9247
Polymers22,3901
Non-polymers5346
Water3,531196
1
A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)550,185168
Polymers537,36324
Non-polymers12,821144
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation6_555z,-x,-y1
crystal symmetry operation7_555-z,-x,y1
crystal symmetry operation8_555-z,x,-y1
crystal symmetry operation9_555y,z,x1
crystal symmetry operation10_555-y,z,-x1
crystal symmetry operation11_555y,-z,-x1
crystal symmetry operation12_555-y,-z,x1
crystal symmetry operation13_555y,x,-z1
crystal symmetry operation14_555-y,-x,-z1
crystal symmetry operation15_555y,-x,z1
crystal symmetry operation16_555-y,x,z1
crystal symmetry operation17_555x,z,-y1
crystal symmetry operation18_555-x,z,y1
crystal symmetry operation19_555-x,-z,-y1
crystal symmetry operation20_555x,-z,y1
crystal symmetry operation21_555z,y,-x1
crystal symmetry operation22_555z,-y,x1
crystal symmetry operation23_555-z,y,x1
crystal symmetry operation24_555-z,-y,-x1
Buried area115740 Å2
ΔGint-174 kcal/mol
Surface area130140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.900, 112.900, 112.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432
Components on special symmetry positions
IDModelComponents
11A-206-

ARG

21A-472-

HOH

31A-590-

HOH

41A-591-

HOH

51A-595-

HOH

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Components

#1: Protein Imidazoleglycerol-phosphate dehydratase 2, chloroplastic / IGPD 2 / Protein HISTIDINE BIOSYNTHESIS 5B


Mass: 22390.143 Da / Num. of mol.: 1 / Fragment: short construct (UNP residues 69-272) / Mutation: E21Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: At4g14910, dl3495c, HISN5B / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O23346, imidazoleglycerol-phosphate dehydratase
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-IYP / (2R,3S)-2,3-dihydroxy-3-(1H-imidazol-5-yl)propyl dihydrogen phosphate


Mass: 238.135 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11N2O6P
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05% PEG2000, 0.4 M succinic acid, pH 7.0, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2011 / Details: two K-B pairs of bimorph type mirrors
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.41→65.183 Å / Num. all: 47547 / Num. obs: 47547 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 12.197 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 17.7
Reflection shellResolution: 1.41→1.45 Å / Redundancy: 10.8 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 3.4 / Num. unique all: 3450 / % possible all: 100

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.7.0032refinement
XDS(XIA2)data reduction
XSCALE(XIA2)data scaling
SCALA(XIA2)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F1D

2f1d


Resolution: 1.41→65.183 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.972 / SU B: 1.454 / SU ML: 0.026 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.045 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1536 2303 4.8 %RANDOM
Rwork0.12347 ---
obs0.12495 45244 99.93 %-
all-47547 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.769 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.41→65.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1533 0 29 196 1758
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191657
X-RAY DIFFRACTIONr_bond_other_d0.0020.021596
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.9342254
X-RAY DIFFRACTIONr_angle_other_deg0.8212.9863678
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5025222
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.96723.20578
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.98415285
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8881515
X-RAY DIFFRACTIONr_chiral_restr0.0910.2258
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021903
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02397
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_it5.0171.107819
X-RAY DIFFRACTIONr_mcbond_other5.011.105818
X-RAY DIFFRACTIONr_mcangle_it5.4151.6731028
X-RAY DIFFRACTIONr_mcangle_other5.4161.6741029
X-RAY DIFFRACTIONr_scbond_it7.9151.502838
X-RAY DIFFRACTIONr_scbond_other7.911.501839
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.092.0621215
X-RAY DIFFRACTIONr_long_range_B_refined6.82910.9511942
X-RAY DIFFRACTIONr_long_range_B_other6.83810.9541943
X-RAY DIFFRACTIONr_rigid_bond_restr12.7733252
X-RAY DIFFRACTIONr_sphericity_free35.447549
X-RAY DIFFRACTIONr_sphericity_bonded32.86353365
LS refinement shellResolution: 1.41→1.45 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.231 155 -
Rwork0.186 3295 -
obs--99.91 %

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