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- PDB-5ahi: Crystal structure of salmonalla enterica HisA mutant D7N with ProFAR -

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Basic information

Entry
Database: PDB / ID: 5ahi
TitleCrystal structure of salmonalla enterica HisA mutant D7N with ProFAR
Components1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENE AMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE
KeywordsISOMERASE / HISA / HISTIDINE BIOSYNTHESIS
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 / 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
Chem-GUO / PHOSPHATE ION / 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: 1.999 Å
AuthorsSoderholm, A. / Guo, X. / Newton, M.S. / Evans, G.B. / Nasvall, J. / Patrick, W.M. / Selmer, M.
CitationJournal: To be Published
Title: Structure and Mechanism of Hisa from Salmonella Enterica
Authors: Soderholm, A. / Guo, X. / Newton, M.S. / Evans, G.B. / Nasvall, J. / Patrick, W.M. / Selmer, M.
History
DepositionFeb 6, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENE AMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9315
Polymers27,1311
Non-polymers8004
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.593, 85.593, 121.310
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-2083-

HOH

21A-2091-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENE AMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE / PHOSPHORIBOSYLFORMIMINO-5-AMINOIMIDAZOLE CARBOXAMIDE RIBOTIDE ISOMERASE / HISA


Mass: 27130.943 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA (bacteria) / Plasmid: PEXP5-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: P10372, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase

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Non-polymers , 5 types, 110 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-GUO / [(2R,3S,4R,5R)-5-[4-aminocarbonyl-5-[(E)-[[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]amino]methylideneamino]imidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate


Mass: 577.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N5O15P2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsGUO: PARTLY OBSERVED LIGAND PROFAR

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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: 2.38 Å3/Da / Density % sol: 48.39 % / Description: NONE
Crystal growpH: 7
Details: 0.2M LITHIUM SULFATE, 30% W/V PEG 8K, 0.1M SODIUM ACETATE PH4.5, PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 27, 2014 / Details: PT COATED MIRRORS
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2→46.94 Å / Num. obs: 17983 / % possible obs: 97.5 % / Observed criterion σ(I): 2.94 / Redundancy: 8.5 % / Biso Wilson estimate: 26.84 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 13.8
Reflection shellResolution: 2→2.12 Å / Redundancy: 8.01 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.94 / % possible all: 79.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE WILD TYPE S. ENTERICA HISA

Resolution: 1.999→46.942 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 24.02 / Stereochemistry target values: ML
Details: RESIDUES 17-24, 174, 178-179 AND 245- 253 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2471 934 5.1 %
Rwork0.1938 --
obs0.1965 18195 98.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.57 Å2
Refinement stepCycle: LAST / Resolution: 1.999→46.942 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 25 106 1864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091812
X-RAY DIFFRACTIONf_angle_d1.1372462
X-RAY DIFFRACTIONf_dihedral_angle_d14.792673
X-RAY DIFFRACTIONf_chiral_restr0.045293
X-RAY DIFFRACTIONf_plane_restr0.006316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.999-2.10440.31691490.27512353X-RAY DIFFRACTION98
2.1044-2.23630.2961380.25062433X-RAY DIFFRACTION100
2.2363-2.40890.26961390.22122437X-RAY DIFFRACTION100
2.4089-2.65130.25711220.2262470X-RAY DIFFRACTION100
2.6513-3.03490.26521460.20342435X-RAY DIFFRACTION99
3.0349-3.82340.24251180.1692515X-RAY DIFFRACTION99
3.8234-46.95520.19961220.1632618X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1861-0.0825-0.06090.36620.2456-0.07670.1763-0.1611-0.4087-0.3537-0.00080.72670.0594-0.22430.00490.22380.0178-0.02680.2567-0.01630.30966.696931.7747-8.1434
20.00450.0321-0.07650.01720.02950.0358-0.1441-0.15030.9975-0.41330.2863-0.30980.02540.047600.57530.0173-0.08640.50470.06620.88154.64640.9688-8.0503
30.8640.76380.23011.3564-0.2530.8597-0.01730.09950.3523-0.15040.02310.2495-0.103-0.032400.2256-0.0021-0.00950.20520.00910.23535.718227.083-12.5507
40.3685-0.02580.19890.1699-0.14190.3153-0.034-0.2077-0.07160.0133-0.13880.25170.0971-0.4505-0.00020.2309-0.00770.00980.2954-0.07730.226-1.787216.6896-9.3655
50.13350.13770.1808-0.10630.15910.528-0.1566-0.0522-0.44220.06430.12090.00250.1170.0717-0.00030.2237-0.01560.05880.2022-0.01850.2455-1.538213.33170.1553
60.81910.3015-0.28090.33870.23470.1828-0.05040.34810.3190.10410.12030.4074-0.110.19510.01440.24430.0144-0.00010.223-0.00070.2467-1.509126.848914.093
70.4067-0.03190.16330.3192-0.17860.2634-0.0849-0.1248-0.1456-0.09210.07110.0820.04190.03900.20780.01710.04470.2040.01110.21344.62816.54438.6463
8-0.0076-0.00730.0407-0.0176-0.094-0.05871.02330.1250.08880.24560.20330.3992-0.5663-0.746200.72270.23140.19420.41470.04090.620311.248433.94838.9083
91.0835-0.5427-0.51050.7461-0.29430.63870.0225-0.3247-0.05840.32390.0009-0.008-0.25640.33120.0290.2974-0.0612-0.02550.2675-0.00490.185416.003424.34288.8458
100.63560.54140.46710.52480.18120.34660.1762-0.0841-0.10230.1352-0.23350.1437-0.11090.0894-0.00670.2141-0.03570.03540.17680.01620.241219.422432.0353-2.0752
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:14)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 15:29)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 30:81)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 82:99)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 100:127)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 128:151)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 152:174)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 175:184)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 185:219)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 220:244)

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