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- PDB-1ox4: TOWARDS UNDERSTANDING THE MECHANISM OF THE COMPLEX CYCLIZATION RE... -

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Basic information

Entry
Database: PDB / ID: 1ox4
TitleTOWARDS UNDERSTANDING THE MECHANISM OF THE COMPLEX CYCLIZATION REACTION CATALYZED BY IMIDAZOLE GLYCEROPHOSPHATE SYNTHASE
Components(Imidazole glycerol phosphate synthase ...) x 2
KeywordsTRANSFERASE / LYASE / COMPLEX CYCLIZATION / IMIDAZOLE GLYCEROPHOSPHATE SYNTHASE
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / oxo-acid-lyase activity / imidazoleglycerol-phosphate synthase activity / glutaminase / L-histidine biosynthetic process / glutaminase activity / glutamine metabolic process / cytoplasm
Similarity search - Function
Imidazole glycerol phosphate synthase HisHF / Imidazole glycerol phosphate synthase, subunit H / Histidine biosynthesis, HisF / : / Histidine biosynthesis protein / Histidine biosynthesis protein / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain ...Imidazole glycerol phosphate synthase HisHF / Imidazole glycerol phosphate synthase, subunit H / Histidine biosynthesis, HisF / : / Histidine biosynthesis protein / Histidine biosynthesis protein / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Ribulose-phosphate binding barrel / Class I glutamine amidotransferase-like / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICKEL (II) ION / PYROPHOSPHATE 2- / Imidazole glycerol phosphate synthase hisHF
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChaudhuri, B.N. / Smith, J.L.
Citation
Journal: Biochemistry / Year: 2003
Title: Towards Understanding the Mechanism of the Complex Cyclization Reaction Catalyzed by Imidazole Glycerophosphate Synthase: Crystal Structures of a Ternary Complex and the Free Enzyme
Authors: Chaudhuri, B.N. / Lange, C. / Myers, R.S. / Davisson, V.J. / Smith, J.L.
#1: Journal: Biochemistry / Year: 2003
Title: Substrate-induced changes in the ammonia channel for imidazole glycerol phosphate synthase.
Authors: Myers, R.S. / Jensen, J.R. / Deras, I.L. / Smith, J.L. / Davisson, V.J.
History
DepositionApr 1, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_conn_type / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn_type.id / _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

Downloads & links

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Assembly

Deposited unit
A: Imidazole glycerol phosphate synthase hisHF
B: Imidazole glycerol phosphate synthase hisHF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,84110
Polymers122,9872
Non-polymers8548
Water3,423190
1
A: Imidazole glycerol phosphate synthase hisHF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,8495
Polymers61,4221
Non-polymers4274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Imidazole glycerol phosphate synthase hisHF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9925
Polymers61,5651
Non-polymers4274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.5, 112.0, 115.30
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.8351, 0.1588, -0.5266), (0.0974, 0.985, 0.1426), (0.5414, 0.0678, -0.838)
Vector: 130.87511, -62.405, -15.1443)

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Components

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Imidazole glycerol phosphate synthase ... , 2 types, 2 molecules AB

#1: Protein Imidazole glycerol phosphate synthase hisHF / E.C.2.4.2.-, E.C.4.1.3.- / HISTIDINE BIOSYNTHESIS BIFUNCTIONAL AMIDOTRANSFERASE / IGP synthase / ImGP synthase / IGPS / ...HISTIDINE BIOSYNTHESIS BIFUNCTIONAL AMIDOTRANSFERASE / IGP synthase / ImGP synthase / IGPS / glutamine amidotransferase:cyclase


Mass: 61422.164 Da / Num. of mol.: 1 / Fragment: AMIDOTRANSFERASE AND CYCLASE DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HIS7 / Production host: Escherichia coli (E. coli)
References: UniProt: P33734, Transferases; Glycosyltransferases; Pentosyltransferases, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Protein Imidazole glycerol phosphate synthase hisHF / E.C.2.4.2.-, E.C.4.1.3.- / HISTIDINE BIOSYNTHESIS BIFUNCTIONAL AMIDOTRANSFERASE / IGP synthase / ImGP synthase / IGPS / ...HISTIDINE BIOSYNTHESIS BIFUNCTIONAL AMIDOTRANSFERASE / IGP synthase / ImGP synthase / IGPS / glutamine amidotransferase:cyclase


Mass: 61565.297 Da / Num. of mol.: 1 / Fragment: AMIDOTRANSFERASE AND CYCLASE DOMAINS
Source method: isolated from a genetically manipulated source
Details: modified CYS 83
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HIS7 / Production host: Escherichia coli (E. coli)
References: UniProt: P33734, Transferases; Glycosyltransferases; Pentosyltransferases, Lyases; Carbon-carbon lyases; Oxo-acid-lyases

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Non-polymers , 4 types, 198 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-POP / PYROPHOSPHATE 2-


Mass: 175.959 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O7P2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / 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: 2.65 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, PEG MME 5000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop / Details: Chaudhuri, B.N., (2001) Structure, 9, 987. / PH range low: 7 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
20.2 Mammonium sulfate1reservoir
322-28 %PEG5000 MME1reservoir
40.1 MMES1reservoirpH6.5-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 45173 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.5 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 16.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 3 / % possible all: 99.8
Reflection
*PLUS
Highest resolution: 2.5 Å
Reflection shell
*PLUS
Highest resolution: 2.5 Å / % possible obs: 99.8 %

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JVN

1jvn


Resolution: 2.5→50 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 2250 5 %RANDOM
Rwork0.228 ---
obs0.2281 44777 99.8 %-
all-44777 --
Displacement parametersBiso mean: 37.6 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8342 0 40 190 8572
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINED
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.32 381 5.2 %
Rwork0.287 6990 -
obs--99.8 %
Refinement
*PLUS
Highest resolution: 2.5 Å / Rfactor Rfree: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.26

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