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- PDB-1jvn: CRYSTAL STRUCTURE OF IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE: A TUN... -

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Basic information

Entry
Database: PDB / ID: 1jvn
TitleCRYSTAL STRUCTURE OF IMIDAZOLE GLYCEROL PHOSPHATE SYNTHASE: A TUNNEL THROUGH A (BETA/ALPHA)8 BARREL JOINS TWO ACTIVE SITES
ComponentsBIFUNCTIONAL HISTIDINE BIOSYNTHESIS PROTEIN HISHF
KeywordsTRANSFERASE / substrate channeling / amidotransferase / TIM-barrel as a substrate tunnel
Function / homology
Function and homology information


imidazole glycerol-phosphate synthase / imidazoleglycerol-phosphate synthase activity / oxo-acid-lyase 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 class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Ribulose-phosphate binding barrel ...Imidazole glycerol phosphate synthase HisHF / 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. / 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 / MAD / Resolution: 2.1 Å
AuthorsChaudhuri, B.N. / Smith, J.L. / Davisson, V.J. / Myers, R.S. / Lange, S.C. / Chittur, S.V.
CitationJournal: Structure / Year: 2001
Title: Crystal structure of imidazole glycerol phosphate synthase: a tunnel through a (beta/alpha)8 barrel joins two active sites.
Authors: Chaudhuri, B.N. / Lange, S.C. / Myers, R.S. / Chittur, S.V. / Davisson, V.J. / Smith, J.L.
History
DepositionAug 30, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BIFUNCTIONAL HISTIDINE BIOSYNTHESIS PROTEIN HISHF
B: BIFUNCTIONAL HISTIDINE BIOSYNTHESIS PROTEIN HISHF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,90210
Polymers123,1292
Non-polymers7748
Water7,422412
1
A: BIFUNCTIONAL HISTIDINE BIOSYNTHESIS PROTEIN HISHF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9115
Polymers61,5641
Non-polymers3474
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BIFUNCTIONAL HISTIDINE BIOSYNTHESIS PROTEIN HISHF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9915
Polymers61,5641
Non-polymers4274
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)98.370, 112.173, 116.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121
DetailsMonomer in solution

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Components

#1: Protein BIFUNCTIONAL HISTIDINE BIOSYNTHESIS PROTEIN HISHF / E.C.2.4.2.- / IMIDAZOLE GLYCEROPHOSPHATE SYNTHASE / GLUTAMINE AMIDOTRANSFERASE:CYCLASE / HIS7P / CYCLASE HIS7 / ...IMIDAZOLE GLYCEROPHOSPHATE SYNTHASE / GLUTAMINE AMIDOTRANSFERASE:CYCLASE / HIS7P / CYCLASE HIS7 / AMIDOTRANSFERASE HIS7


Mass: 61564.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PROTEIN RESIDUE 143, NUMBER 83, IS CYS COVALENTLY MODIFIED BY ACIVICIN
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: HIS7 / Plasmid: PHIS7-T7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): BL21(DE3)
References: UniProt: P33734, Transferases; Glycosyltransferases; Pentosyltransferases
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-POP / PYROPHOSPHATE 2- / Pyrophosphate


Mass: 175.959 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O7P2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.61 Å3/Da / Density % sol: 52.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 28 % PEG MME 5000, 0.2 M Ammonium sulfate, 0.1 M MES buffer, pH 6.5, VAPOR DIFFUSION, HANGING DROP at 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / PH range low: 7 / PH range high: 6.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
122-28 %PEG5000 MME1reservoir
20.1 MMES1reservoirpH6.5-7.0
30.2 Mammonium sulfate1reservoir
410 mg/mlprotein1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 17-ID11
SYNCHROTRONAPS 14-BM-D20.9796, 0.9795, 0.9537
Detector
TypeIDDetectorDateDetails
MARRESEARCH1CCDNov 5, 2001Si(111) double-crystal
ADSC QUANTUM 42CCDNov 17, 2001bent cylindrical Si-mirror (Rh coating), Si(111) double-crystal
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
30.97951
40.95371
ReflectionResolution: 2.1→100 Å / Num. obs: 73741 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 14.3 % / Biso Wilson estimate: 21.3 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 7.3
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 2 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 100 Å / % possible obs: 100 %
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.1→75.21 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1768716.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: CNS dictionary
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3686 5 %RANDOM
Rwork0.224 ---
obs0.224 73662 97.6 %-
all-73662 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.9268 Å2 / ksol: 0.363298 e/Å3
Displacement parametersBiso mean: 31.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.96 Å20 Å20 Å2
2---5.22 Å20 Å2
3---1.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.1→75.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8370 0 36 412 8818
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it1.21.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.872.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 497 4.9 %
Rwork0.28 9720 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REPMOD.PARAMPROTEIN_MOD.TOP
X-RAY DIFFRACTION2CIS_PEPTIDE.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER.PARAMPOP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5POP.PARAM
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 31.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.305 / % reflection Rfree: 4.9 % / Rfactor Rwork: 0.28

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