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- PDB-5ac6: S.enterica HisA mutant D10G, dup13-15, Q24L, G102A -

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Basic information

Entry
Database: PDB / ID: 5ac6
TitleS.enterica HisA mutant D10G, dup13-15, Q24L, 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 / L-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
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: 1.993 Å
AuthorsGuo, X. / Soderholm, A. / Newton, M. / Nasvall, J. / Andersson, D. / Patrick, W. / Selmer, M.
CitationJournal: To be Published
Title: The Protein Structures, Functions and Dynamics of Adaptive Evolution
Authors: Newton, M. / Guo, X. / Soderholm, A. / Nasvall, J. / Andersson, D. / Patrick, W. / Selmer, M.
History
DepositionAug 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...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 / 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 / _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)27,6223
Polymers27,4291
Non-polymers1922
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.239, 85.239, 119.986
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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: 27429.389 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(DE3)
References: UniProt: A0A630AQ07, UniProt: P10372*PLUS, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 5.5
Details: 0.2 M SODIUM CHLORIDE, 0.1 M BIS-TRIS PH5.5, 25% W/V PEG 3350

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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 18, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 18270 / % possible obs: 99.9 % / Observed criterion σ(I): 1.3 / Redundancy: 23.8 % / Biso Wilson estimate: 22.87 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10.9
Reflection shellResolution: 1.99→2.04 Å / Redundancy: 19.2 % / Rmerge(I) obs: 0.92 / Mean I/σ(I) obs: 1.3 / % possible all: 98.9

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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 5AHF

5ahf


Resolution: 1.993→46.557 Å / SU ML: 0.23 / σ(F): 1.34 / Phase error: 22.91 / Stereochemistry target values: ML / Details: RESIDUES 16-21 AND 245-256 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2437 929 5.1 %
Rwork0.1928 --
obs0.1953 18219 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.13 Å2
Refinement stepCycle: LAST / Resolution: 1.993→46.557 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1782 0 10 96 1888
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011870
X-RAY DIFFRACTIONf_angle_d1.262555
X-RAY DIFFRACTIONf_dihedral_angle_d13.697679
X-RAY DIFFRACTIONf_chiral_restr0.062306
X-RAY DIFFRACTIONf_plane_restr0.004332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9926-2.09760.31011260.26882389X-RAY DIFFRACTION99
2.0976-2.2290.29761400.23842408X-RAY DIFFRACTION100
2.229-2.40110.24681120.21142442X-RAY DIFFRACTION100
2.4011-2.64270.32661350.21012435X-RAY DIFFRACTION100
2.6427-3.02510.25691340.20262461X-RAY DIFFRACTION100
3.0251-3.8110.23141540.17672475X-RAY DIFFRACTION100
3.811-46.56950.17651280.162680X-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)
16.1597-1.78936.71381.6397-2.08938.6886-0.59640.14510.25410.01330.26090.1328-0.6577-0.21660.44630.2228-0.02370.01840.17130.03580.24927.405231.2976-7.9107
24.0227-4.03785.29669.7584-5.1716.97810.00371.9806-1.36021.6275-0.80190.5467-0.0806-0.50150.67580.7595-0.02890.16930.8913-0.29230.80012.760238.9833-1.003
38.9582-2.6419-2.15235.95695.68355.62860.30590.27261.9945-0.33870.35430.9172-0.5022-0.5047-0.63940.3196-0.0505-0.01550.41370.14810.81395.95639.5685-13.3396
44.24090.54870.80681.08870.93130.9266-0.26010.07130.1263-0.11620.1367-0.0273-0.21040.07040.1180.2696-0.03220.03820.16070.00760.18914.192528.826-12.1986
52.0648-0.57511.2035.24323.18283.23820.0052-0.46830.01850.43090.20681.20140.2434-1.2057-0.11590.25520.02240.0050.44410.08530.4751-5.964428.0107-9.6837
68.3407-2.2029-0.57574.30021.02672.89810.04670.2755-0.0276-0.3805-0.02170.254-0.2147-0.0098-0.03770.2396-0.0232-0.01460.14920.02190.16815.611723.2403-14.3531
72.14241.3017-2.69764.3532-1.91889.352-0.04870.2147-0.116-0.0707-0.05740.2857-0.1999-0.46870.10940.20340.00750.01240.204-0.02980.1939-1.477216.333-9.6586
86.306-2.1811-1.08454.30381.05693.8223-0.2181-0.0338-0.44580.03810.14130.14540.19690.03830.07230.19460.00180.03720.14040.01940.175-0.941613.48630.1253
93.1429-1.56684.06385.7369-2.16285.2725-0.356-0.51990.32290.74670.26380.2159-0.4168-0.17170.08380.35280.0641-0.00310.3541-0.03850.28592.039226.541917.3752
106.0141-2.8334-3.11647.72494.74764.2135-0.064-0.0779-0.03440.08170.09710.3539-0.0543-0.127-0.02320.16850.01610.03090.20220.06470.2266-1.536820.897111.2262
116.75872.69350.2291.9127-0.81244.5923-0.04-0.16750.6707-0.14910.0423-0.1475-0.77910.129-0.01390.27570.00340.03490.2143-0.00850.21396.860523.26756.1044
124.8029-2.57691.44954.4034-5.93459.32920.06451.03940.06591.39180.07990.4445-1.4345-1.7259-0.21390.74270.12880.17460.55540.02730.536113.9432.562410.9473
133.5974-1.3221-0.49848.8886-4.40422.5746-0.1983-0.60520.20430.55560.3415-0.112-0.56580.1395-0.1030.23420.0286-0.00310.2605-0.0020.161612.490918.54710.8203
145.4312-0.937-2.53937.0674-1.3775.20190.8504-0.65550.29631.0094-0.5190.0795-0.60430.653-0.31150.4376-0.14380.05170.309-0.05490.209319.062334.29835.0066
153.83161.2948-0.30065.7053-4.34353.48860.1262-0.2812-0.03110.4088-0.00320.0972-0.33840.1092-0.10910.2123-0.01970.02540.187-0.03420.17716.981430.5110.3709
167.36044.752-4.56075.1448-5.10665.08160.1866-0.4576-0.70420.5096-0.4629-0.6917-0.12720.94910.35840.2713-0.0443-0.01670.26690.04970.279725.497828.6152-1.8193
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:14)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 15:25)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 26:30)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 31:48)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 49:61)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 62:82)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 83:99)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 100:128)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 129:140)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 141:161)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 162:178)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 179:185)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 186:202)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 203:213)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 214:235)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 236:244)

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