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- PDB-5g2w: S. enterica HisA mutant D10G, G102A -

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Basic information

Entry
Database: PDB / ID: 5g2w
TitleS. enterica HisA mutant D10G, 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 / 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: 2.099 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 14, 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 2.0Jan 10, 2024Group: Atomic model / Data collection ...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_struct_mod_residue / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif / 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.pdbx_ec / _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_struct_mod_residue.details / _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_seq_db_accession_code / _struct_ref_seq_dif.pdbx_seq_db_seq_num / _struct_ref_seq_dif.seq_num / _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)methylideneamino] imidazole-4-carboxamide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3563
Polymers27,1641
Non-polymers1922
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.960, 85.960, 121.550
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-189-

GLU

21A-2048-

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: 27164.033 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.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 5.15
Details: 0.2M AMMONIUM ACETATE, 0.1M SODIUM ACETATE, PH 5.15, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9763
DetectorType: ADSC CCD / Detector: 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: 2.1→50 Å / Num. obs: 16100 / % possible obs: 99.8 % / Observed criterion σ(I): 5.26 / Redundancy: 17.2 % / Biso Wilson estimate: 29.72 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 29.22
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 17.6 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 5.26 / % possible all: 99.4

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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: 2.099→47.079 Å / SU ML: 0.2 / σ(F): 1.36 / Phase error: 19.6 / Stereochemistry target values: ML / Details: RESIDUES 15-25, 175-182, 245-256 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2202 805 5 %
Rwork0.1676 --
obs0.1702 16099 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.71 Å2
Refinement stepCycle: LAST / Resolution: 2.099→47.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 10 52 1742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091812
X-RAY DIFFRACTIONf_angle_d1.0732475
X-RAY DIFFRACTIONf_dihedral_angle_d13.536654
X-RAY DIFFRACTIONf_chiral_restr0.046293
X-RAY DIFFRACTIONf_plane_restr0.005320
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0994-2.23090.2431290.18792458X-RAY DIFFRACTION100
2.2309-2.40320.25631320.19282502X-RAY DIFFRACTION100
2.4032-2.6450.22291320.17972507X-RAY DIFFRACTION100
2.645-3.02770.23581320.17132515X-RAY DIFFRACTION100
3.0277-3.81430.19721360.15492575X-RAY DIFFRACTION100
3.8143-47.09040.21591440.16132737X-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)
18.6085-4.0894.76038.916-0.58344.2248-0.54310.38131.1034-0.512-0.0170.559-0.6118-0.67690.63030.3888-0.0055-0.02790.44180.09470.5337.131134.2634-9.7286
22.0388-1.6378-0.51754.23271.86810.98190.40030.2030.2616-0.1826-0.0943-0.2468-0.30310.1088-0.27250.3372-0.07550.03520.25050.06080.207512.968932.8815-15.755
34.02581.1183-0.2265.0173-0.60363.27250.01520.04830.2483-0.23280.07750.6153-0.047-0.5151-0.06760.27420.0092-0.02380.22560.02540.23133.136827.31-11.7764
45.83353.9691-6.44793.6751-3.1998.3070.04290.35660.16580.12350.13520.1691-0.1212-0.4119-0.2490.24950.0131-0.00380.19920.00840.20063.93621.0483-10.1229
58.8561-3.2478-4.50457.00751.34672.5112-0.23610.1217-0.1586-0.2507-0.01570.69080.0618-0.96990.270.2713-0.01890.00280.3344-0.05030.2363-0.473516.5459-12.3049
65.7698-1.5645-4.046.72391.26673.6318-0.3241-0.0993-0.42440.15150.18180.42420.2539-0.17160.18360.2107-0.00180.00250.21430.00220.1956-3.157814.11250.5637
70.71391.80541.87334.06514.31054.4462-0.22090.03670.02940.15340.1826-0.05340.25490.1570.09670.2625-0.0090.03070.2655-0.00820.29093.20218.24451.9185
82.9761-0.3984.7426.39661.92029.6775-0.3402-0.4360.26691.45040.20140.06070.1511-0.88510.24060.53130.07820.0470.36940.00940.35290.308626.36616.6184
94.26722.5480.68297.1871-6.46468.6922-0.15660.37280.5628-0.53370.9348-0.9603-0.59070.3588-0.3610.4056-0.05330.16350.3010.09580.5329-6.450431.7429.7259
105.1307-5.566-5.39916.05525.57386.0661-0.3467-0.6886-0.57420.87540.15220.57170.15870.46660.16070.35510.02520.07950.31720.06090.30390.338818.555613.7492
116.36012.54511.2355.79550.2484.3921-0.0946-0.21660.20290.01180.04630.0009-0.20820.15160.08910.1950.06020.04420.22530.02520.22616.783419.01238.1812
126.75073.9087-2.64847.1314-1.78158.3983-0.0038-0.48420.45870.75860.11710.3906-0.4372-0.2381-0.04940.27220.058-0.04270.2830.00850.213213.14217.428613.1989
137.79254.9035-4.14264.2858-4.36724.8430.3163-0.60640.24070.4616-0.4601-0.4106-0.41560.58320.16410.3096-0.0381-0.03110.2920.00580.224417.164328.80885.5347
146.4471-3.03524.79917.1053-4.86924.89710.1968-0.1944-0.35780.2971-0.1806-0.076-0.35960.617-0.08760.2092-0.0398-0.00520.25870.02570.253216.53922.82944.5984
158.7774-0.91234.48622.3491-2.87144.9169-0.0205-0.54660.23960.5222-0.01420.5167-0.6054-0.0719-0.05060.2574-0.060.05960.18490.0180.232916.724337.085-4.1807
162.17750.6675-0.40232.8185-3.99117.5159-0.0121-0.6005-0.23780.74650.2978-0.6464-0.08620.5793-0.17490.2814-0.0244-0.02650.32360.05210.361525.782929.0442-0.4985
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:30)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 31:37)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 38:68)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 69:85)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 86:97)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 98:118)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 119:131)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 132:143)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 144:148)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 149:157)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 158:186)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 187:196)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 197:216)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 217:223)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 224:236)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 237:247)

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