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- PDB-4mu3: The form A structure of an E21Q catalytic mutant of A. thaliana I... -

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Basic information

Entry
Database: PDB / ID: 4mu3
TitleThe form A structure of an E21Q catalytic mutant of A. thaliana IGPD2 in complex with Mn2+ and a mixture of its substrate, 2R3S-IGP, and an inhibitor, 2S3S-IGP, to 1.12 A resolution
ComponentsImidazoleglycerol-phosphate dehydratase 2, chloroplastic
KeywordsLYASE/LYASE INHIBITOR / hydro-lyase / histidine biosynthesis / manganese binding / chloroplastic / LYASE-LYASE INHIBITOR complex
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-IG2 / Chem-IYP / : / Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 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
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_alt_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_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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

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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)23,28710
Polymers22,3901
Non-polymers8969
Water3,693205
1
A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules
x 24


Theoretical massNumber of molelcules
Total (without water)558,879240
Polymers537,36324
Non-polymers21,516216
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 area105680 Å2
ΔGint30 kcal/mol
Surface area137230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.100, 113.100, 113.100
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-496-

HOH

21A-559-

HOH

31A-560-

HOH

41A-564-

HOH

51A-584-

HOH

61A-597-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 214 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-IG2 / (2S,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-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
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 205 / 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: 2.69 Å3/Da / Density % sol: 54.31 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 25% ethylene glycol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2011 / Details: Kirkpatrick Baez bimorph mirror pair
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.12→46.17 Å / Num. all: 94992 / Num. obs: 94992 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.5 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 30.8
Reflection shellResolution: 1.12→1.14 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.5 / % possible all: 93.9

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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: 1.12→46.17 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 0.568 / SU ML: 0.012 / Cross valid method: THROUGHOUT / ESU R: 0.022 / ESU R Free: 0.022 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13856 4612 4.9 %RANDOM
Rwork0.12511 ---
obs0.12577 89279 99.08 %-
all-94992 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.019 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.12→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1443 0 52 205 1700
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191577
X-RAY DIFFRACTIONr_bond_other_d0.0020.021516
X-RAY DIFFRACTIONr_angle_refined_deg1.7151.9692141
X-RAY DIFFRACTIONr_angle_other_deg0.87633489
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5765205
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13323.46775
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.44715266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.5481513
X-RAY DIFFRACTIONr_chiral_restr0.1120.2246
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021785
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02377
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_it2.3180.932763
X-RAY DIFFRACTIONr_mcbond_other2.3210.926762
X-RAY DIFFRACTIONr_mcangle_it1.7251.402957
X-RAY DIFFRACTIONr_mcangle_other1.7361.402958
X-RAY DIFFRACTIONr_scbond_it10.2871.344814
X-RAY DIFFRACTIONr_scbond_other10.2471.345814
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.8071.8281175
X-RAY DIFFRACTIONr_long_range_B_refined6.3389.1081827
X-RAY DIFFRACTIONr_long_range_B_other6.3369.1191828
X-RAY DIFFRACTIONr_rigid_bond_restr18.3433092
X-RAY DIFFRACTIONr_sphericity_free38.849545
X-RAY DIFFRACTIONr_sphericity_bonded34.04253224
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 316 -
Rwork0.231 6155 -
obs--93.91 %

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