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- PDB-4qnk: The structure of wt A. thaliana IGPD2 in complex with Mn2+ and ph... -

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Basic information

Entry
Database: PDB / ID: 4qnk
TitleThe structure of wt A. thaliana IGPD2 in complex with Mn2+ and phosphate
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
: / PHOSPHATE ION / Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsBisson, C. / Britton, K.L. / Sedelnikova, S.E. / Rodgers, H.F. / Eadsforth, T.C. / Viner, R. / Hawkes, T.R. / 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
DepositionJun 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 24, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2015Group: 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_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_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.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_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 / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
B: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
C: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
D: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
E: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
F: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
G: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
H: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,58244
Polymers177,5118
Non-polymers2,07136
Water23,4921304
1
A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
B: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
C: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
D: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
E: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
F: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
G: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
H: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
B: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
C: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
D: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
E: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
F: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
G: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
H: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules

A: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
B: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
C: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
D: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
E: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
F: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
G: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
H: Imidazoleglycerol-phosphate dehydratase 2, chloroplastic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)538,745132
Polymers532,53324
Non-polymers6,213108
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Unit cell
Length a, b, c (Å)225.130, 225.130, 225.130
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
Components on special symmetry positions
IDModelComponents
11B-526-

HOH

21B-539-

HOH

31B-540-

HOH

41B-562-

HOH

51F-517-

HOH

61F-527-

HOH

71F-529-

HOH

81F-534-

HOH

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

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


Mass: 22188.855 Da / Num. of mol.: 8 / Fragment: UNP residues 70-272, SEE REMARK 999
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 BL21(DE3) (bacteria)
References: UniProt: O23346, imidazoleglycerol-phosphate dehydratase

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Non-polymers , 5 types, 1340 molecules

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


Mass: 54.938 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Mn
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1304 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsEXPRESSED N-TERMINAL SEQUENCE MASPPPGDNGFPAITTA WAS PROTEOLYTICALLY CLEAVED PRIOR TO CRYSTALLIZATION.

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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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.1 M Bicine, pH 9.0, 10% w/v PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9507 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 11, 2008
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9507 Å / Relative weight: 1
ReflectionResolution: 1.75→71.19 Å / Num. all: 187811 / Num. obs: 187811 / % possible obs: 99.4 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 11.7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 4 % / Rmerge(I) obs: 0.579 / Mean I/σ(I) obs: 2.2 / % possible all: 99.4

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Processing

Software
NameVersionClassification
GDAdata collection
PHASERphasing
REFMAC5.8.0073refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→45.98 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.919 / SU ML: 0.055 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17949 9330 5 %RANDOM
Rwork0.12901 ---
obs0.13154 178465 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.568 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11506 0 80 1304 12890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01912083
X-RAY DIFFRACTIONr_bond_other_d0.0030.0211467
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.94616195
X-RAY DIFFRACTIONr_angle_other_deg1.171326292
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3851507
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.59123.356581
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.256152028
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.23915101
X-RAY DIFFRACTIONr_chiral_restr0.1020.21876
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213576
X-RAY DIFFRACTIONr_gen_planes_other0.010.022861
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_it3.3461.6775944
X-RAY DIFFRACTIONr_mcbond_other3.3381.6775943
X-RAY DIFFRACTIONr_mcangle_it3.4832.8067425
X-RAY DIFFRACTIONr_mcangle_other3.1962.8027426
X-RAY DIFFRACTIONr_scbond_it9.2662.426139
X-RAY DIFFRACTIONr_scbond_other9.0282.3965995
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.6933.6228753
X-RAY DIFFRACTIONr_long_range_B_refined6.2514.41113501
X-RAY DIFFRACTIONr_long_range_B_other6.2514.41213502
X-RAY DIFFRACTIONr_rigid_bond_restr16.299323550
X-RAY DIFFRACTIONr_sphericity_free21.5455370
X-RAY DIFFRACTIONr_sphericity_bonded36.666524142
LS refinement shellResolution: 1.75→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 669 -
Rwork0.207 13110 -
obs--99.25 %

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