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- PDB-1gpw: Structural evidence for ammonia tunneling across the (beta/alpha)... -

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Basic information

Entry
Database: PDB / ID: 1gpw
TitleStructural evidence for ammonia tunneling across the (beta/alpha)8 barrel of the imidazole glycerol phosphate synthase bienzyme complex.
Components
  • AMIDOTRANSFERASE HISH
  • HISF PROTEIN
KeywordsLYASE/TRANSFERASE / COMPLEX (LYASE-TRANSFERASE) / HISTIDINE BIOSYNTHESIS / GLUTAMINASE / GLUTAMINE AMIDOTRANSFERASE / CYCLASE / AMMONIA CHANNEL / LYASE-TRANSFERASE complex
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / glutaminase / L-histidine biosynthetic process / glutaminase activity / lyase activity / cytoplasm
Similarity search - Function
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 ...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
PHOSPHATE ION / 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: 2.4 Å
AuthorsWalker, M. / Beismann-Driemeyer, S. / Sterner, R. / Wilmanns, M.
Citation
Journal: Structure / Year: 2002
Title: Structural Evidence for Ammonia Tunneling Across the (Beta Alpha)(8) Barrel of the Imidazole Glycerol Phosphate Synthase Bienzyme Complex.
Authors: Douangamath, A. / Walker, M. / Beismann-Driemeyer, S. / Vega-Fernandez, M.C. / Sterner, R. / Wilmanns, M.
#1: Journal: J.Biol.Chem. / Year: 2001
Title: Imidazole Glycerol Phosphate Synthase from Thermotoga Maritima
Authors: Beismann-Driemeyer, S. / Sterner, R.
History
DepositionNov 12, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 10, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 12, 2017Group: Advisory / Atomic model / Derived calculations
Category: atom_site / pdbx_struct_sheet_hbond ...atom_site / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.auth_seq_id ..._atom_site.auth_atom_id / _atom_site.auth_seq_id / _atom_site.label_atom_id / _atom_site.label_seq_id / _atom_site.type_symbol / _struct_conf.pdbx_PDB_helix_id / _struct_sheet.id / _struct_sheet.number_strands / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_comp_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_comp_id / _struct_site_gen.label_seq_id / _struct_site_gen.pdbx_num_res / _struct_site_gen.site_id
Revision 2.1Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.2Dec 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "EA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 10-STRANDED BARREL THIS IS REPRESENTED BY A 11-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HISF PROTEIN
B: AMIDOTRANSFERASE HISH
C: HISF PROTEIN
D: AMIDOTRANSFERASE HISH
E: HISF PROTEIN
F: AMIDOTRANSFERASE HISH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,22012
Polymers152,6506
Non-polymers5706
Water8,269459
1
A: HISF PROTEIN
B: AMIDOTRANSFERASE HISH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0734
Polymers50,8832
Non-polymers1902
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: HISF PROTEIN
D: AMIDOTRANSFERASE HISH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1685
Polymers50,8832
Non-polymers2853
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: HISF PROTEIN
F: AMIDOTRANSFERASE HISH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9783
Polymers50,8832
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)74.000, 91.900, 131.000
Angle α, β, γ (deg.)90.00, 105.90, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICALLY RELEVANT UNITS ARE THE FOLLOWING HETERODIMERS:HISF/HISH CHAIN A/CHAIN B , HISF/HISH CHAIN C/CHAIN D, HISF/HISHCHAIN E/ CHAIN F. THERE ARE SIGNIFICANT CONFORMATIONAL DIFFERENCESIN THE THREE HETERO-DIMERS, HENCE THEY CANNOT BE RELATED BYUNIQUE SETS OF NCS OPERATORS.

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Components

#1: Protein HISF PROTEIN


Mass: 27752.887 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: RBSIISPHI-THISH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 / Variant (production host): W3110 DELTA-TRPEA2 / References: UniProt: Q9X0C6
#2: Protein AMIDOTRANSFERASE HISH


Mass: 23130.564 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Plasmid: RBSIISPHI-THISH / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 / Variant (production host): W3110 DELTA-TRPEA2 / References: UniProt: Q9X0C8
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growpH: 8
Details: PROTEIN SOLUTION: 10 MM TRIS (PH 8.0), 1 MM DTT, 1 MM EDTA, 28.8 MG/ML PROTEIN COMPLEX. PRECIPITATE SOLUTION: 15 %[W/V] PEG-8000, 0.9 M AMMONIUM NITRATE, 0.1 M HEPES/HCL (PH 8.5), 10 MM DTT, 5% [V/V] MPD
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mMTris-NaOH1droppH8.0
2150 mM1dropNaCl
31 mMEDTA1drop
45 mMdithiothreitol1drop
512.5 mg/mlprotein1drop
60.1 Msodium acetate1reservoirpH5.0
710 mMdithiothreitol1reservoir
815 mM1reservoirCaCl2
930 %(v/v)PEG2001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.88
DetectorType: X-RAY RESEARCH / Detector: CCD / Details: BENT MIRROR
RadiationMonochromator: TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.88 Å / Relative weight: 1
ReflectionResolution: 2.37→30 Å / Num. obs: 65356 / % possible obs: 96.7 % / Redundancy: 2.9 % / Biso Wilson estimate: 46.2 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 28
Reflection shellResolution: 2.37→2.45 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 4.5 / % possible all: 78.8
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
% possible obs: 78.8 % / Num. unique obs: 5485

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1THF

1thf


Resolution: 2.4→30 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.29 3327 5.1 %RANDOM
Rwork0.226 ---
obs0.226 65356 97.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 59.6192 Å2 / ksol: 0.320971 e/Å3
Displacement parametersBiso mean: 58.4 Å2
Baniso -1Baniso -2Baniso -3
1-22.48 Å20 Å27.36 Å2
2---9.16 Å20 Å2
3----13.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.35 Å
Luzzati d res low-6 Å
Luzzati sigma a0.47 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10643 0 30 459 11132
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it9.631.5
X-RAY DIFFRACTIONc_mcangle_it9.732
X-RAY DIFFRACTIONc_scbond_it13.342
X-RAY DIFFRACTIONc_scangle_it13.922.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 529 5.2 %
Rwork0.311 9566 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1ION.PARAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3PROTEIN_REP.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.29
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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