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- PDB-5g1y: S. enterica HisA mutant D10G, dup13-15,V14:2M, Q24L, G102 -

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Basic information

Entry
Database: PDB / ID: 5g1y
TitleS. enterica HisA mutant D10G, dup13-15,V14:2M, Q24L, G102
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 / histidine biosynthetic process / tryptophan biosynthetic process / cytoplasm
Similarity search - Function
HisA, bacterial-type / Histidine biosynthesis, HisA-like / HisA/PriA, bacterial-type / 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: 1.798 Å
AuthorsGuo, X. / Soderholm, A. / Newton, M. / Nasvall, J. / Andersson, D. / Patrick, W. / 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
DepositionApr 1, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3May 10, 2017Group: Database references
Revision 1.4Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_poly_seq_scheme / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity_name_com.name / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_seq_type / _pdbx_database_status.status_code_sf / _pdbx_poly_seq_scheme.pdb_ins_code / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_struct_mod_residue.details / _pdbx_unobs_or_zero_occ_residues.PDB_ins_code / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_db_accession / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.pdbx_db_accession / _struct_ref_seq_dif.db_mon_id / _struct_ref_seq_dif.details / _struct_ref_seq_dif.mon_id / _struct_ref_seq_dif.pdbx_auth_seq_num / _struct_ref_seq_dif.pdbx_pdb_ins_code / _struct_ref_seq_dif.pdbx_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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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)methylideneamino] imidazole-4-carboxamide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1017
Polymers27,5371
Non-polymers5646
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.012, 86.012, 122.179
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-2010-

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: 27536.584 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria)
Gene: hisA, AIY46_13150, AL463_17045, CQW68_13095, D3346_17640, D3Q81_15095, EAW95_14430, FJR52_10950, GCH85_22590, NCTC6385_02080, ND68_15100
Plasmid: PEXP5-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: A0A630AQ07, UniProt: P10372*PLUS, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.27 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growpH: 4.6
Details: 0.2M AMMONIUM SULPHATE, 0.1M NA ACETATE PH4.6, 25%W/V PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763
DetectorDetector: CCD / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 25362 / % possible obs: 99.5 % / Observed criterion σ(I): 2 / Redundancy: 13.3 % / Biso Wilson estimate: 22.15 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2 / % possible all: 93.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G1T

5g1t


Resolution: 1.798→47.236 Å / SU ML: 0.17 / σ(F): 1.35 / Phase error: 18.95 / Stereochemistry target values: ML
Details: RESIDUES 15B-23, 175-177, 181 AND 245-256 DISORDERED
RfactorNum. reflection% reflection
Rfree0.2101 1291 5.1 %
Rwork0.1663 --
obs0.1684 25335 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.8 Å2
Refinement stepCycle: LAST / Resolution: 1.798→47.236 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1743 0 33 105 1881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071887
X-RAY DIFFRACTIONf_angle_d1.0922580
X-RAY DIFFRACTIONf_dihedral_angle_d12.696694
X-RAY DIFFRACTIONf_chiral_restr0.046310
X-RAY DIFFRACTIONf_plane_restr0.004330
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.798-1.86990.24161230.24112502X-RAY DIFFRACTION95
1.8699-1.95510.28471440.19562620X-RAY DIFFRACTION100
1.9551-2.05810.22271580.17922601X-RAY DIFFRACTION100
2.0581-2.18710.22391560.1742638X-RAY DIFFRACTION100
2.1871-2.35590.20151460.16612648X-RAY DIFFRACTION100
2.3559-2.5930.23741520.16832659X-RAY DIFFRACTION100
2.593-2.96820.20981550.17032697X-RAY DIFFRACTION100
2.9682-3.73940.18291400.15372742X-RAY DIFFRACTION100
3.7394-47.25210.19421170.15422937X-RAY DIFFRACTION100
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)
19.2915-6.4637-6.48958.98275.07938.7348-0.166-0.10570.1315-0.21060.18-0.61620.25090.4732-0.02710.1232-0.0187-0.00130.11190.00150.1937-7.2851-31.6025-8.0137
22.00017.33632.82215.00011.17049.92620.2708-1.7616-1.04740.8822-0.2358-0.06330.73580.0577-0.00150.37810.12540.05990.38090.1150.5357-4.8909-39.6536-4.166
33.6204-3.94885.92364.3605-6.45579.6952-0.0711-0.0067-0.8819-0.15320.2946-0.63390.5098-0.033-0.21740.417-0.03440.02790.3335-0.06860.795-5.4198-41.4105-11.0684
46.41910.1736-0.65853.40810.80762.0903-0.1530.0549-0.1611-0.07260.101-0.25120.19710.02870.04680.177-0.01870.00530.08750.01290.1264-9.7733-29.4625-11.2285
58.2663-1.34095.34855.9352-1.19318.4051-0.17650.62020.1493-0.19650.1001-1.0014-0.13280.89730.12650.2252-0.04210.06690.2007-0.05710.2868-0.1094-25.4416-15.7683
65.0517-5.65882.33137.1189-3.95478.83260.5405-0.28790.0198-0.0990.0005-0.16640.3488-0.0196-0.49790.129-0.0301-0.00820.0935-0.03520.1305-8.1517-22.0595-9.6223
76.2637-0.20712.90368.62190.63157.9472-0.09360.19840.07490.0165-0.0024-0.3825-0.06020.71210.10010.1218-0.012-0.00710.1660.01760.10961.1824-16.8998-9.4591
87.4102-2.17122.24233.7838-0.44194.2659-0.1752-0.0210.27920.01470.1185-0.1072-0.1970.03820.06140.1458-0.0096-0.01290.1112-0.00640.11280.903-13.80980.3062
97.77160.2999-5.03028.0830.73733.3635-0.4336-0.8149-0.41641.26740.21280.11290.13360.59940.16230.3730.10780.02540.30920.03670.2163-2.5887-27.207618.064
108.4098-4.32992.13772.5946-0.67398.8142-0.07140.3237-0.18630.01220.06190.05280.23580.04920.05260.1626-0.0123-0.0150.1206-0.02230.1863.1413-25.823411.7414
114.3960.41850.80078.0611-0.20494.9472-0.0242-0.2580.12790.24130.1105-0.0460.125-0.1518-0.08490.1010.0217-0.0070.1383-0.02820.1627-5.0569-17.25317.8236
123.88350.7532.79843.47710.96664.51740.5101-0.1684-2.17171.6337-0.1-1.14851.9357-0.2723-0.45110.7491-0.0545-0.12560.4145-0.00060.7127-14.9087-30.250113.1996
132.7424-0.16980.35433.3594.40325.88150.1126-0.38190.03470.419-0.01620.00940.4092-0.2558-0.07680.1803-0.0133-0.02050.20290.00370.1272-12.9061-20.45099.5933
148.5874.84683.93915.59535.29235.09930.6339-0.96840.04641.1311-0.94390.51250.6786-0.87830.34940.3226-0.09810.08020.3646-0.01080.2564-22.1407-31.1796.5103
152.9321-0.0896-1.28437.18527.11558.1797-0.0145-0.1068-0.03830.18350.1915-0.15440.28880.1046-0.1930.135-0.0247-0.05190.12010.0330.1164-15.7227-32.3247-0.4033
167.6942-0.21660.10914.47284.37444.36980.1539-0.3410.31630.6072-0.33450.64840.3309-0.75460.21010.2112-0.05680.03090.1874-0.01610.2069-25.2332-29.8789-2.2056
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:13)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 14:23)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 24:30)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 31:55)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 56:72)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 73:81)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 82:99)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 100:128)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 129:139)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 140:154)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 155:174)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 175:187)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 188:206)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 207:216)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 217:233)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 234:244)

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