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- PDB-5g1t: S. enterica HisA mutant dup13-15, D10G -

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Basic information

Entry
Database: PDB / ID: 5g1t
TitleS. enterica HisA mutant dup13-15, D10G
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 / 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
PHOSPHATE ION / 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: 1.7 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
DepositionMar 30, 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 1.3Jan 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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

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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)27,9344
Polymers27,5051
Non-polymers4283
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)87.220, 87.220, 121.860
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-2014-

HOH

21A-2052-

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: 27505.465 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M HEPES, PH 7.5, 0.8M NAH2PO4 AND 0.8M KH2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorDate: Oct 5, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 30762 / % possible obs: 99.9 % / Observed criterion σ(I): 5.4 / Redundancy: 10.7 % / Biso Wilson estimate: 21.32 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 30.7
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 11 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 5.4 / % possible all: 100

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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 4GJ1

4gj1


Resolution: 1.7→28.549 Å / SU ML: 0.16 / σ(F): 2 / Phase error: 18.26 / Stereochemistry target values: ML / Details: RESIDUES 15C-23, 175-182, 244-256 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.1996 1539 5 %
Rwork0.1715 --
obs0.1729 30762 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.19 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1724 0 25 147 1896
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071902
X-RAY DIFFRACTIONf_angle_d1.0572621
X-RAY DIFFRACTIONf_dihedral_angle_d12.765724
X-RAY DIFFRACTIONf_chiral_restr0.045316
X-RAY DIFFRACTIONf_plane_restr0.005335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6999-1.75480.27281360.21612583X-RAY DIFFRACTION100
1.7548-1.81750.20941380.19422622X-RAY DIFFRACTION100
1.8175-1.89030.21911380.18332607X-RAY DIFFRACTION100
1.8903-1.97630.20451370.17842616X-RAY DIFFRACTION100
1.9763-2.08040.21361380.17452613X-RAY DIFFRACTION100
2.0804-2.21070.21181380.17272620X-RAY DIFFRACTION100
2.2107-2.38140.18921390.17132639X-RAY DIFFRACTION100
2.3814-2.62090.21881390.17342654X-RAY DIFFRACTION100
2.6209-2.99970.1911420.18882682X-RAY DIFFRACTION100
2.9997-3.7780.19441420.16852709X-RAY DIFFRACTION100
3.778-28.55350.18641520.1542878X-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)
17.006-2.8762-3.57416.56912.75697.1094-0.3551-0.1769-0.08480.10650.1908-0.59660.36560.53590.16690.11370.0072-0.01330.13170.01410.194635.952843.228852.7781
25.7005-1.0511.99245.861-3.92112.9184-0.2779-0.6837-1.18950.68770.1396-0.85650.4310.15780.15970.51730.0853-0.02890.360.08440.558936.575735.90950.6337
35.06180.74190.53543.59820.6322.73310.04290.1161-0.206-0.02630.0099-0.54950.17590.29910.00050.12730.0026-0.00520.10460.01330.173535.594846.504750.5736
47.6771-2.3584-1.19464.20630.26333.7346-0.00810.18980.1398-0.61870.1008-0.63530.10950.4269-0.05940.2038-0.00290.07140.1599-0.01680.193138.126151.135244.3881
57.96516.3413-0.74817.55641.63372.1517-0.38020.0869-0.1980.12230.2148-0.61060.17860.81330.00450.1390.0275-0.07750.38850.03180.211545.901454.766155.3831
68.0326-0.40653.76447.97954.1815.52610.0810.1909-0.1895-0.0128-0.3155-0.4244-0.33440.83430.17950.13-0.0356-0.03620.22550.07510.143342.639458.446449.8629
78.90164.60716.06596.67563.00266.4897-0.14580.11820.28680.16280.08630.07580.12440.03670.0660.13180.0225-0.01540.1276-0.00130.139546.929655.557463.0719
84.9126-3.1290.37964.0093-3.26934.6226-0.3997-0.03171.32730.21150.1567-0.4081-0.58830.15610.14650.2242-0.0184-0.07180.134-0.00360.319347.563264.922362.6327
97.0520.12435.47416.85532.024.7928-0.05980.62310.1377-0.013-0.1146-0.4236-1.23490.44460.04420.2714-0.0828-0.03550.22410.08890.271142.780266.496154.8654
101.3665-1.63031.96846.7216-6.4427.7755-0.1507-0.02380.01570.27620.24650.0503-0.2025-0.31320.00620.1829-0.0167-0.03860.19070.01730.181439.620654.392665.1966
115.32272.8091-2.0862.841-2.90585.35-0.3705-0.684-0.20220.74320.4496-0.04360.83950.27860.02410.37150.13690.00990.32980.03150.181442.243448.558978.4443
126.961-5.3572.14044.3008-2.24422.6672-0.3754-0.22930.23670.2850.4152-0.5002-0.0429-0.0312-0.06960.1484-0.0153-0.00760.1769-0.04440.212844.915353.466273.4508
135.90640.60910.25567.7011-1.97955.31610.0604-0.13030.15540.02230.17320.31560.1398-0.2805-0.21020.118-0.0105-0.02260.1303-0.00170.106637.4557.278567.2139
147.37630.24991.14275.53475.52575.6051-0.0575-0.4966-0.52530.53970.1548-0.0240.7816-0.6996-0.27520.29020.0123-0.01070.35250.02810.224929.95952.5674.787
159.10470.6756-2.74735.8303-5.10298.0185-0.1889-0.7240.18770.05280.0158-0.335-0.11590.24370.1710.15560.0446-0.00910.2182-0.0520.154330.870961.665674.1328
164.69623.04412.2939.33474.3753.33950.2308-0.272-0.19290.6218-0.0875-0.22250.4148-0.145-0.14030.2293-0.0211-0.02730.18540.01060.109730.092948.694465.5536
175.44524.93453.55947.97247.18066.81390.606-1.12220.26451.1125-1.03740.72950.6426-0.64850.54730.2934-0.10320.07290.3979-0.04450.246521.105746.255568.0995
188.2870.89350.08064.98574.97155.05970.1364-0.25480.5643-0.2502-0.2423-0.0319-0.2999-0.53370.21770.1915-0.0016-0.02020.1861-0.03310.21427.444151.098163.1298
197.22740.3116-4.45632.94073.1246.5446-0.1753-0.4659-0.15380.3652-0.0105-0.41690.4610.26120.12930.17-0.0485-0.04280.1313-0.00430.15725.854937.93456.5299
202.4865-0.20221.13992.35062.96269.83430.1146-0.69340.31290.7193-0.07170.4346-0.1718-0.5506-0.0280.2365-0.04860.03420.252-0.0470.273217.070346.444260.4049
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:14)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 15:33)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 34:58)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 59:76)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 77:85)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 86:99)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 100:107)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 108:117)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 118:121)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 122:131)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 132:143)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 144:159)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 160:177)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 186:190)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 191:196)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 197:207)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 208:218)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 219:224)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 225:236)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 237:247)

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