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- PDB-5a5w: Crystal structure of Salmonella enterica HisA D7N D176A with ProFAR -

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Basic information

Entry
Database: PDB / ID: 5a5w
TitleCrystal structure of Salmonella enterica HisA D7N D176A with ProFAR
Components1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
KeywordsISOMERASE / HISTIDINE BIOSYNTHESIS / PROFAR
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
Chem-GUO / 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: 1.6 Å
AuthorsSoderholm, A. / Guo, X. / Newton, M.S. / Evans, G.B. / Nasvall, J. / Patrick, W.M. / Selmer, M.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Two-Step Ligand Binding in a Beta/Alpha8 Barrel Enzyme -Substrate-Bound Structures Shed New Light on the Catalytic Cycle of Hisa
Authors: Soderholm, A. / Guo, X. / Newton, M.S. / Evans, G.B. / Nasvall, J. / Patrick, W.M. / Selmer, M.
History
DepositionJun 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2015Group: Database references
Revision 1.2Jan 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_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 DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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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)27,6642
Polymers27,0871
Non-polymers5771
Water3,765209
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.607, 46.607, 197.949
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: 27086.934 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, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical ChemComp-GUO / [(2R,3S,4R,5R)-5-[4-aminocarbonyl-5-[(E)-[[(2R,3R,4S,5R)-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]amino]methylideneamino]imidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate


Mass: 577.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H25N5O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 209 / 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: 1.53 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 9 / Details: 0.1 M BICINE PH9.0, 20 % W/V PEG 6000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97625
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 28, 2015
Details: KIRKPATRICK BAEZ BIMORPH MIRROR PAIR FOR HORIZONTAL AND VERTICAL FOCUSSING
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.6→40.36 Å / Num. obs: 63157 / % possible obs: 99.5 % / Observed criterion σ(I): 3.5 / Redundancy: 3.1 % / Biso Wilson estimate: 24.75 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 20.69
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 3.18 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.5 / % possible all: 99.7

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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: 1.6→40.363 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 18.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 1632 4.8 %
Rwork0.1662 --
obs0.1679 34069 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.08 Å2
Refinement stepCycle: LAST / Resolution: 1.6→40.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 37 209 2080
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071963
X-RAY DIFFRACTIONf_angle_d1.1982690
X-RAY DIFFRACTIONf_dihedral_angle_d14.116769
X-RAY DIFFRACTIONf_chiral_restr0.054318
X-RAY DIFFRACTIONf_plane_restr0.006352
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6004-1.64750.25241420.21032613X-RAY DIFFRACTION100
1.6475-1.70070.21881450.18982618X-RAY DIFFRACTION100
1.7007-1.76150.23071490.19212643X-RAY DIFFRACTION100
1.7615-1.8320.24241260.17872676X-RAY DIFFRACTION100
1.832-1.91540.21521350.18292666X-RAY DIFFRACTION100
1.9154-2.01640.20641250.18472700X-RAY DIFFRACTION100
2.0164-2.14270.2191360.18162674X-RAY DIFFRACTION100
2.1427-2.30810.22241430.17152679X-RAY DIFFRACTION100
2.3081-2.54040.1832940.17152752X-RAY DIFFRACTION100
2.5404-2.90790.2031340.18062755X-RAY DIFFRACTION100
2.9079-3.66330.21481460.16712728X-RAY DIFFRACTION100
3.6633-40.37570.17731570.14242933X-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)
14.10571.00950.70524.28080.51181.8303-0.03360.13510.1596-0.3221-0.04490.0565-0.12530.09020.07140.2612-0.0423-0.03050.16990.01340.099525.47928.49686.8295
23.18284.3513-2.53426.9384-2.25313.464-0.26980.41770.3175-1.06040.03740.18620.0687-0.16150.11160.7357-0.1368-0.14750.26420.15650.06724.95789.1893-0.997
33.32392.52890.78616.48740.86832.77370.0135-0.0197-0.0266-0.2408-0.0930.27110.3041-0.48210.10730.2161-0.089-0.03510.2208-0.02270.167218.70860.71079.3038
46.73683.38781.12342.48162.19353.9276-0.0799-0.05170.8759-0.4603-0.29770.9838-0.2975-0.88890.30530.2370.0217-0.0770.3828-0.08560.377713.28111.454412.5845
54.54980.22620.5411.87230.53.85240.0091-0.38980.18430.3292-0.10520.5140.2349-0.61260.14280.2002-0.0630.00870.322-0.05160.171918.10527.180119.001
63.99581.07350.73992.7321-3.51957.13680.0242-1.26371.14210.4387-0.68850.8551-0.5591-0.94160.38960.2578-0.02410.09610.6961-0.22660.414213.32114.368226.054
75.13993.9011-1.32695.5336-2.54911.5160.2666-0.4290.27840.3079-0.33820.37330.0338-0.63450.06610.2083-0.09940.03970.3966-0.13420.226119.05829.403923.1227
85.6065-0.082-1.81733.4231-1.93041.75330.0583-0.61030.30670.7846-0.2285-0.0005-0.3083-0.6011-0.50940.4066-0.14180.10990.6224-0.22570.232522.037615.111532.2503
92.59011.0368-3.93083.6031-0.53566.99330.0935-0.42570.13720.1289-0.19810.0138-0.00120.18510.11030.2077-0.0868-0.02740.30550.00280.145431.46929.938922.0648
102.20030.11050.70138.45762.7221.07580.01060.9117-0.239-0.26350.0662-1.0764-0.68111.3928-0.12060.2493-0.2295-0.0370.6345-0.00080.326545.755915.287220.0174
113.0799-0.08041.75771.256-0.05827.8455-0.0169-0.55080.38910.2947-0.1795-0.0583-0.40340.15960.13650.2427-0.0842-0.0190.2997-0.05270.200533.290414.254925.4847
121.1703-0.0249-1.22942.7922.06037.42360.1027-0.0585-0.0947-0.11840.0863-0.3328-0.00250.3047-0.22070.1944-0.0618-0.00840.24990.01260.179935.46985.647713.4145
133.6171.21741.64123.16450.16567.78320.2347-0.2197-0.51430.1661-0.0375-0.66910.50920.3793-0.16980.2068-0.0068-0.05260.17860.03590.274536.6936-1.364818.0388
143.8802-4.17092.79574.5732-2.52644.643-0.00940.7085-0.4235-0.88080.1984-0.37610.05010.5768-0.22330.413-0.06740.05610.2929-0.08120.27129.7574-3.13761.3
157.3671-1.5232-1.17318.33992.72451.81610.21520.1588-1.5862-0.2891-0.1812-0.3061.31390.04070.02040.5115-0.0546-0.02510.1961-0.01480.439628.3977-12.27979.0557
161.5121-0.7115-3.28130.33691.54417.1296-0.8308-0.1426-2.43731.6290.3796-0.93022.64210.53160.25440.72390.0988-0.03630.3649-0.03810.993532.942-13.503116.3415
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:22)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 23:29)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 30:54)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 55:72)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 73:84)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 85:90)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 91:106)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 107:119)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 120:133)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 134:139)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 140:166)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 167:182)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 183:228)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 229:233)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 234:241)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 242:246)

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