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- PDB-6ymu: Imidazole Glycerol Phosphate Synthase -

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Basic information

Entry
Database: PDB / ID: 6ymu
TitleImidazole Glycerol Phosphate Synthase
Components
  • Imidazole glycerol phosphate synthase subunit HisF
  • Imidazole glycerol phosphate synthase subunit HisH
KeywordsISOMERASE / Imidazole glycerol phosphate synthase
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / glutaminase / L-histidine biosynthetic process / glutaminase activity / glutamine metabolic process / lyase activity / cytoplasm
Similarity search - Function
Imidazole glycerol phosphate synthase, subunit H / Histidine biosynthesis, HisF / Histidine biosynthesis protein / Histidine biosynthesis protein / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Ribulose-phosphate binding barrel / Class I glutamine amidotransferase-like / Aldolase-type TIM barrel
Similarity search - Domain/homology
Imidazole glycerol phosphate synthase subunit HisF / Imidazole glycerol phosphate synthase subunit HisH
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsSterner, R. / Rajendran, C. / Andrea, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)STE891/12-2 Germany
CitationJournal: Biochemistry / Year: 2020
Title: Significance of the Protein Interface Configuration for Allostery in Imidazole Glycerol Phosphate Synthase.
Authors: Kneuttinger, A.C. / Rajendran, C. / Simeth, N.A. / Bruckmann, A. / Konig, B. / Sterner, R.
History
DepositionApr 9, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Advisory / Data collection ...Advisory / 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_validate_polymer_linkage / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Imidazole glycerol phosphate synthase subunit HisF
B: Imidazole glycerol phosphate synthase subunit HisH
C: Imidazole glycerol phosphate synthase subunit HisF
D: Imidazole glycerol phosphate synthase subunit HisH
E: Imidazole glycerol phosphate synthase subunit HisF
F: Imidazole glycerol phosphate synthase subunit HisH


Theoretical massNumber of molelcules
Total (without water)152,8556
Polymers152,8556
Non-polymers00
Water8,017445
1
A: Imidazole glycerol phosphate synthase subunit HisF


Theoretical massNumber of molelcules
Total (without water)27,7541
Polymers27,7541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Imidazole glycerol phosphate synthase subunit HisH


Theoretical massNumber of molelcules
Total (without water)23,1981
Polymers23,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Imidazole glycerol phosphate synthase subunit HisF


Theoretical massNumber of molelcules
Total (without water)27,7541
Polymers27,7541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Imidazole glycerol phosphate synthase subunit HisH


Theoretical massNumber of molelcules
Total (without water)23,1981
Polymers23,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Imidazole glycerol phosphate synthase subunit HisF


Theoretical massNumber of molelcules
Total (without water)27,7541
Polymers27,7541
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Imidazole glycerol phosphate synthase subunit HisH


Theoretical massNumber of molelcules
Total (without water)23,1981
Polymers23,1981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.417, 85.901, 128.745
Angle α, β, γ (deg.)90.000, 108.240, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Imidazole glycerol phosphate synthase subunit HisF / IGP synthase cyclase subunit / IGP synthase subunit HisF / ImGP synthase subunit HisF / IGPS subunit HisF


Mass: 27753.871 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hisF, TM_1036 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0C6, imidazole glycerol-phosphate synthase
#2: Protein Imidazole glycerol phosphate synthase subunit HisH / IGP synthase glutaminase subunit / IGP synthase subunit HisH / ImGP synthase subunit HisH / IGPS ...IGP synthase glutaminase subunit / IGP synthase subunit HisH / ImGP synthase subunit HisH / IGPS subunit HisH / TmHisH


Mass: 23197.652 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: hisH, TM_1038 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0C8, imidazole glycerol-phosphate synthase, glutaminase
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 445 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.77 Å3/Da / Density % sol: 55.63 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / Details: PEG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.11→40 Å / Num. obs: 95686 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 0.99 / CC star: 1 / Net I/σ(I): 14
Reflection shellResolution: 2.11→2.18 Å / Rmerge(I) obs: 1.5 / Num. unique obs: 9472 / CC1/2: 0.55

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1gpw

1gpw


Resolution: 2.11→40 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.25 --
Rwork0.21 --
obs-95686 99 %
Displacement parametersBiso mean: 50.69 Å2
Refinement stepCycle: LAST / Resolution: 2.11→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10441 0 0 445 10886
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009410640
X-RAY DIFFRACTIONf_angle_d1.056714344
X-RAY DIFFRACTIONf_chiral_restr0.07051623
X-RAY DIFFRACTIONf_plane_restr0.0061855
X-RAY DIFFRACTIONf_dihedral_angle_d22.08883934

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