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- PDB-1k9v: Structural evidence for ammonia tunelling across the (beta-alpha)... -

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Basic information

Entry
Database: PDB / ID: 1k9v
TitleStructural evidence for ammonia tunelling across the (beta-alpha)8-barrel of the imidazole glycerol phosphate synthase bienzyme complex
ComponentsAmidotransferase hisH
KeywordsTRANSFERASE / glutaminase / imidazole glycerol phosphate synthase / (beta-alpha)8-barrel / ammonia tunnel
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / glutaminase / histidine biosynthetic process / glutaminase activity / glutamine metabolic process / lyase activity / cytoplasm
Similarity search - Function
Imidazole glycerol phosphate synthase, subunit H / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETIC ACID / Imidazole glycerol phosphate synthase subunit HisH
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDouangamath, A. / Walker, M. / Beismann-Driemeyer, S. / Vega-Fernandez, M.C. / Sterner, R. / Wilmanns, M.
CitationJournal: 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.
History
DepositionOct 31, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 20, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
F: Amidotransferase hisH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,1912
Polymers23,1311
Non-polymers601
Water1,17165
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.008, 35.837, 42.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Amidotransferase hisH


Mass: 23130.564 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9X0C8, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 65 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG 200, sodium acetate, DTT, calcium chloride, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.91 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 25, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 32978 / Num. obs: 32780 / % possible obs: 99.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 49.6 Å2 / Rmerge(I) obs: 0.042 / Net I/σ(I): 31.7
Reflection shellResolution: 2.4→2.44 Å / Rmerge(I) obs: 0.215 / Mean I/σ(I) obs: 6.3 / % possible all: 97.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: His H from the complex structure HisH-HisF

Resolution: 2.4→15 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 427 5.67 %random
Rwork0.224 ---
all0.224 7530 --
obs0.224 7530 --
Displacement parametersBiso mean: 42.6 Å2
Baniso -1Baniso -2Baniso -3
1-10.871 Å20 Å20 Å2
2---10.32 Å20 Å2
3----0.552 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1574 0 0 69 1643
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.236
X-RAY DIFFRACTIONc_bond_d0.006

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