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- PDB-5l6u: S. ENTERICA HISA MUTANT - D10G, DUP13-15, Q24L, G102A -

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Basic information

Entry
Database: PDB / ID: 5l6u
TitleS. ENTERICA HISA MUTANT - D10G, DUP13-15, Q24L, G102A
Components1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
KeywordsISOMERASE / HisA / protein evolution / IAD model / TrpF
Function / homology
Function and homology information


1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity / L-histidine biosynthetic process / L-tryptophan biosynthetic process / cytoplasm
Similarity search - Function
HisA, bacterial-type / HisA/PriA, bacterial-type / Histidine biosynthesis, HisA-like / Histidine biosynthesis protein / Histidine biosynthesis protein / Ribulose-phosphate binding barrel / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase / 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Similarity search - Component
Biological speciesSalmonella enterica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGuo, X. / Soderholm, A. / Selmer, M.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural and functional innovations in the real-time evolution of new ( beta alpha )8 barrel enzymes.
Authors: Newton, M.S. / Guo, X. / Soderholm, A. / Nasvall, J. / Lundstrom, P. / Andersson, D.I. / Selmer, M. / Patrick, W.M.
History
DepositionMay 31, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Sep 8, 2021Group: Advisory / Database references / Structure summary
Category: database_2 / entity ...database_2 / entity / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_unobs_or_zero_occ_residues.PDB_ins_code / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_ref_seq_dif.details
Revision 1.5Jan 10, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7934
Polymers27,5051
Non-polymers2883
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area600 Å2
ΔGint-43 kcal/mol
Surface area10450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.940, 85.940, 120.960
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-411-

HOH

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Components

#1: Protein 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase / Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase


Mass: 27504.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CYS241 is partially modified to CME / Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: hisA, SeHA_C2302 / Plasmid: pEXP5-CT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B4T9N8, UniProt: P10372*PLUS, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 4.8
Details: 0.2M ammonium sulfate, 0.1M sodium acetate, pH4.8, 25% w/v PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.97628 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 1.6→74.426 Å / Num. obs: 35410 / % possible obs: 99.8 % / Redundancy: 38.4 % / Biso Wilson estimate: 30.4 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.084 / Net I/σ(I): 37
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 39 % / Rmerge(I) obs: 1.62 / Mean I/σ(I) obs: 2.77 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5g1t

5g1t


Resolution: 1.6→74.426 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 17.24
RfactorNum. reflection% reflection
Rfree0.189 1769 5 %
Rwork0.155 --
obs0.1567 35398 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.6→74.426 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1755 0 15 114 1884
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061937
X-RAY DIFFRACTIONf_angle_d1.0352655
X-RAY DIFFRACTIONf_dihedral_angle_d11.876705
X-RAY DIFFRACTIONf_chiral_restr0.039315
X-RAY DIFFRACTIONf_plane_restr0.004347
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.64330.25351310.19392498X-RAY DIFFRACTION99
1.6433-1.69160.2081340.16572536X-RAY DIFFRACTION100
1.6916-1.74630.22231330.15782537X-RAY DIFFRACTION100
1.7463-1.80870.24481330.15022534X-RAY DIFFRACTION100
1.8087-1.88110.22581350.14432554X-RAY DIFFRACTION100
1.8811-1.96670.19981340.1352547X-RAY DIFFRACTION100
1.9667-2.07040.19381350.13562558X-RAY DIFFRACTION100
2.0704-2.20010.18811350.13682577X-RAY DIFFRACTION100
2.2001-2.370.16171360.14242577X-RAY DIFFRACTION100
2.37-2.60850.20141370.15772608X-RAY DIFFRACTION100
2.6085-2.9860.20011370.16982610X-RAY DIFFRACTION100
2.986-3.7620.16211410.15952662X-RAY DIFFRACTION100
3.762-74.50680.18731480.15762831X-RAY DIFFRACTION100

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