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- PDB-6j22: Crystal structure of Bi-functional enzyme -

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Basic information

Entry
Database: PDB / ID: 6j22
TitleCrystal structure of Bi-functional enzyme
ComponentsHistidine biosynthesis bifunctional protein HisIE
KeywordsHYDROLASE / Bi-functional enzyme
Function / homology
Function and homology information


phosphoribosyl-AMP cyclohydrolase / phosphoribosyl-AMP cyclohydrolase activity / phosphoribosyl-ATP diphosphatase / phosphoribosyl-ATP diphosphatase activity / histidine biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Histidine biosynthesis bifunctional protein HisIE / Phosphoribosyl-AMP cyclohydrolase domain / Phosphoribosyl-AMP cyclohydrolase domain superfamily / Phosphoribosyl-AMP cyclohydrolase / Phosphoribosyl-ATP pyrophosphohydrolase / Phosphoribosyl-ATP pyrophosphohydrolase-like / Phosphoribosyl-ATP pyrophosphohydrolase
Similarity search - Domain/homology
Histidine biosynthesis bifunctional protein HisIE
Similarity search - Component
Biological speciesShigella flexneri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.2 Å
AuthorsZhang, H. / Shang, G. / Wang, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structural analysis of Shigella flexneri bi-functional enzyme HisIE in histidine biosynthesis.
Authors: Wang, Y. / Zhang, F. / Nie, Y. / Shang, G. / Zhang, H.
History
DepositionDec 30, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 1, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Histidine biosynthesis bifunctional protein HisIE
B: Histidine biosynthesis bifunctional protein HisIE


Theoretical massNumber of molelcules
Total (without water)45,6182
Polymers45,6182
Non-polymers00
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6470 Å2
ΔGint-57 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.711, 45.195, 65.800
Angle α, β, γ (deg.)90.00, 112.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Histidine biosynthesis bifunctional protein HisIE


Mass: 22808.814 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella flexneri (bacteria) / Gene: hisI, hisIE, SF2088, S2209 / Production host: Escherichia coli (E. coli)
References: UniProt: P37793, phosphoribosyl-AMP cyclohydrolase, phosphoribosyl-ATP diphosphatase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate, pH 4.6, 1.8 M ammonium sulfate, 1% 1,2-butanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / % possible obs: 93.6 % / Redundancy: 3.9 % / Net I/σ(I): 17.9
Reflection shellResolution: 2.199→2.256 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.2→50 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.899 / SU B: 6.177 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.267 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25764 1193 5.2 %RANDOM
Rwork0.19563 ---
obs0.19891 21889 97.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.516 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.14 Å2
2---0.58 Å2-0 Å2
3---0.12 Å2
Refinement stepCycle: 1 / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3049 0 0 198 3247
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0193102
X-RAY DIFFRACTIONr_bond_other_d0.0020.022872
X-RAY DIFFRACTIONr_angle_refined_deg1.7211.9624202
X-RAY DIFFRACTIONr_angle_other_deg1.03336672
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9225381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44325.102147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98515554
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.2361516
X-RAY DIFFRACTIONr_chiral_restr0.10.2485
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023420
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02596
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.4333.6111536
X-RAY DIFFRACTIONr_mcbond_other3.4253.611535
X-RAY DIFFRACTIONr_mcangle_it5.5385.3951913
X-RAY DIFFRACTIONr_mcangle_other5.5375.3951914
X-RAY DIFFRACTIONr_scbond_it3.54.0271566
X-RAY DIFFRACTIONr_scbond_other3.4994.0261567
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5135.872290
X-RAY DIFFRACTIONr_long_range_B_refined9.09243.213665
X-RAY DIFFRACTIONr_long_range_B_other9.08842.9473607
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.199→2.256 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 105 -
Rwork0.226 1550 -
obs--95.06 %

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