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- PDB-5g2i: S. enterica HisA mutant Dup13-15(VVR) -

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Basic information

Entry
Database: PDB / ID: 5g2i
TitleS. enterica HisA mutant Dup13-15(VVR)
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
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: 1.601 Å
AuthorsGuo, X. / Soderholm, A. / Newton, M. / Nasvall, J. / Duarte, F. / 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 8, 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 1.3Aug 23, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector / _diffrn_detector.type
Revision 2.0Jan 10, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp_atom ...atom_site / 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_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _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_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_residues.PDB_ins_code / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
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)27,7004
Polymers27,4871
Non-polymers2133
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.610, 86.610, 121.290
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-2046-

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: 27487.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: [DUP13-15(VVR)] / 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(DE3)
References: UniProt: A0A630AQ07, UniProt: P10372*PLUS, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.4 Å3/Da / Density % sol: 48.5 % / Description: NONE
Crystal growpH: 5.5 / Details: 0.1 M HEPES PH 7.5 0.8 M NAH2PO4 0.8 M KH2PO4

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9797 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 35940 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 21 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 42
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 21.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5G1T

5g1t


Resolution: 1.601→47.182 Å / SU ML: 0.14 / σ(F): 1.99 / Phase error: 19.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 1797 5 %
Rwork0.1834 --
obs0.1846 35934 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.601→47.182 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1730 0 11 124 1865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061863
X-RAY DIFFRACTIONf_angle_d1.0612564
X-RAY DIFFRACTIONf_dihedral_angle_d12.064696
X-RAY DIFFRACTIONf_chiral_restr0.04312
X-RAY DIFFRACTIONf_plane_restr0.005331
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6011-1.64440.26921340.21132547X-RAY DIFFRACTION100
1.6444-1.69280.22671370.19032608X-RAY DIFFRACTION100
1.6928-1.74750.19011350.1812564X-RAY DIFFRACTION100
1.7475-1.80990.20771360.17572590X-RAY DIFFRACTION100
1.8099-1.88240.22111370.19182604X-RAY DIFFRACTION100
1.8824-1.96810.25591330.2162530X-RAY DIFFRACTION98
1.9681-2.07180.20371370.18242601X-RAY DIFFRACTION100
2.0718-2.20160.20141380.17542606X-RAY DIFFRACTION100
2.2016-2.37160.2051360.18412601X-RAY DIFFRACTION99
2.3716-2.61030.21681400.17962653X-RAY DIFFRACTION100
2.6103-2.98790.23731400.1932669X-RAY DIFFRACTION100
2.9879-3.76420.19621430.17632703X-RAY DIFFRACTION100
3.7642-47.20230.18551510.17782861X-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)
17.2228-1.6533-2.55593.55431.06754.2291-0.33780.0084-0.24570.10610.1216-0.5290.46580.29680.20420.14990.0091-0.00340.12420.01540.219536.288142.875552.1058
27.2107-0.06961.16885.8928-1.7858.9129-0.4539-0.5644-1.40670.3645-0.4711-1.40950.55670.54090.91920.56340.08490.04190.35530.09380.816837.871533.469953.2882
33.20331.8284-0.03251.769-0.12371.6577-0.16850.1787-0.246-0.10350.0509-0.09010.23480.00290.10920.1854-0.01870.00810.1069-0.00630.138728.630545.346747.8801
42.7094-1.3292-0.55742.2243-0.06544.1203-0.04880.0914-0.215-0.1780.2176-1.8397-0.05220.6058-0.06240.14920.03940.06230.2615-0.01020.657347.520546.700749.2788
53.9328-0.58230.46433.1317-0.11273.98140.00710.0614-0.056-0.3513-0.0166-0.23260.02050.1529-0.00040.1747-0.01680.03120.13270.00370.148235.949851.97146.9572
68.1257-0.24714.84624.46351.53777.3083-0.1570.05960.0658-0.0360.0451-0.3905-0.1951.12850.12040.1159-0.01460.00990.30.050.142945.846658.122550.1491
72.3597-0.50980.97961.88890.30563.4594-0.20480.01450.34960.10410.1-0.1035-0.08410.06430.12650.1450.0055-0.03260.1350.01040.179445.813159.284461.2811
83.76721.1794-0.4027.0612-2.14194.6403-0.11350.1050.28820.11320.066-0.0714-0.3635-0.24540.07720.1855-0.0243-0.05470.16560.02970.168240.493562.525858.6864
95.9659-0.1631-2.04253.1290.47854.6962-0.2496-0.2134-0.34940.69450.3881-0.01530.5062-0.0116-0.1150.2770.0661-0.00980.19390.00440.152842.842747.116675.4155
101.5695-2.46130.864.0562-1.27660.526-0.322-0.23330.27650.27750.3016-0.3513-0.0188-0.09350.01730.1580.0311-0.03660.1632-0.05460.204644.097355.676473.3625
114.21191.0709-0.05075.9598-0.29083.51680.0729-0.05870.0330.0160.02310.57410.1736-0.3432-0.11380.1318-0.027-0.01490.16780.01530.114636.534655.991266.7597
122.7212.9155-3.01793.3803-3.15373.40970.2115-0.1029-0.78380.417-0.2384-0.23521.0277-0.4551-0.02780.3573-0.0266-0.04630.31650.02060.299228.713549.047475.2004
131.45770.47480.48463.58121.41752.49870.0371-0.1921-0.0710.08060.05860.00760.3018-0.3347-0.10950.1907-0.0253-0.03360.19520.01750.108129.026251.99668.883
143.66963.8357-1.06744.26030.13776.07790.2976-0.68320.48570.4682-0.28130.61750.2322-0.6647-0.06830.2316-0.08430.0030.3583-0.04710.208122.640250.163267.7005
152.1131.674-0.34688.92284.32093.14320.1099-0.0453-0.1750.35970.0693-0.67390.2922-0.0487-0.1510.1904-0.0459-0.07170.17770.03660.241228.823739.863758.3851
164.4835-1.47220.35232.12412.72285.82330.1249-0.53740.27250.5983-0.2110.07430.0042-0.32810.12330.19-0.08460.00680.191-0.03150.176418.213744.694358.199
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 30:48)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 49:64)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 65:82)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 83:96)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 97:115)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 116:128)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 129:145)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 146:160)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 161:174)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 182:189)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 190:210)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 211:220)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 221:232)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 233:244)

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