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- PDB-5ahe: Crystal structure of Salmonella enterica HisA -

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Basic information

Entry
Database: PDB / ID: 5ahe
TitleCrystal structure of Salmonella enterica HisA
Components1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
KeywordsISOMERASE / HISTIDINE BIOSYNTHESIS
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: 1.7 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
DepositionFeb 5, 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 / pdbx_struct_conn_angle / pdbx_struct_mod_residue / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_mod_residue.details / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ref_seq_dif.pdbx_seq_db_accession_code / _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)27,9388
Polymers27,2081
Non-polymers7307
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.769, 86.769, 121.530
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

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Components

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Protein , 1 types, 1 molecules A

#1: Protein 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase / Phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase


Mass: 27208.045 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 122 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / 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: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.38 Å3/Da / Density % sol: 49.5 %
Crystal growpH: 5.5
Details: PROTEIN WAS CRYSTALLIZED IN 0.1 M HEPES PH 7.5, 0.8 M NAH2PO4 AND 0.8 M KH2PO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH CHESS / Detector: CCD / Date: Apr 18, 2013 / Details: PT COATED SI MIRRORS
RadiationMonochromator: SILICON 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 1.7→47.25 Å / Num. obs: 30376 / % possible obs: 100 % / Observed criterion σ(I): 2.82 / Redundancy: 19.1 % / Biso Wilson estimate: 21.08 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 21.81
Reflection shellResolution: 1.7→1.75 Å / Redundancy: 19.1 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 2.82 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: A MUTANT SALMONELLA ENTERICA HISA WAS USED, WHICH IN TURN HAD BEEN SOLVED USING 4GJ1 AS SEARCH MODEL.

4gj1


Resolution: 1.7→47.25 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 18.42 / Stereochemistry target values: ML
Details: RESIDUES 17-23, 175-180 AND 245- -253 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.2062 1520 5 %
Rwork0.1742 --
obs0.1758 30375 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.94 Å2
Refinement stepCycle: LAST / Resolution: 1.7→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1732 0 43 115 1890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081902
X-RAY DIFFRACTIONf_angle_d1.1052610
X-RAY DIFFRACTIONf_dihedral_angle_d12.651714
X-RAY DIFFRACTIONf_chiral_restr0.052312
X-RAY DIFFRACTIONf_plane_restr0.006332
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7001-1.75490.26941340.22812554X-RAY DIFFRACTION100
1.7549-1.81770.27881360.20752579X-RAY DIFFRACTION100
1.8177-1.89040.23621350.19082568X-RAY DIFFRACTION100
1.8904-1.97650.23821360.1752578X-RAY DIFFRACTION100
1.9765-2.08070.21551370.17382584X-RAY DIFFRACTION100
2.0807-2.2110.19261360.17362586X-RAY DIFFRACTION100
2.211-2.38180.20091330.17142609X-RAY DIFFRACTION100
2.3818-2.62140.18921380.17322630X-RAY DIFFRACTION100
2.6214-3.00070.21941390.18632635X-RAY DIFFRACTION100
3.0007-3.78030.20161490.17032682X-RAY DIFFRACTION100
3.7803-47.26780.18831470.16122850X-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)
10.53260.4411-0.08840.4796-0.00490.4179-0.1713-0.11450.07830.10630.0360.1466-0.2165-0.0831-0.04170.15240.0338-0.01430.1296-0.01330.16296.226334.009-7.9228
20.89750.4390.34261.5286-0.07740.3778-0.0590.01810.1405-0.12520.0480.1862-0.1425-0.01620.00090.14630.0048-0.01310.1280.01020.14916.778728.7103-12.7555
30.1244-0.1301-0.13230.3843-0.1790.3484-0.09630.008-0.1014-0.0693-0.04940.0398-0.0926-0.3434-0.02580.1380.00210.00380.2084-0.03050.1494-1.288517.1521-10.019
40.4766-0.3173-0.01340.1835-0.13270.3241-0.11810.009-0.17580.00590.14170.03040.0062-0.0194-0.00020.1486-0.00020.030.1266-0.00950.1697-1.136414.1292-0.0825
50.57240.10220.00320.45220.11030.014-0.2320.00090.11470.52420.32720.08030.02570.22140.02170.27770.0785-0.0010.201-0.00340.13681.444627.278715.8443
60.58550.0762-0.0790.90290.38040.613-0.1287-0.096-0.12020.03330.19760.1403-0.00060.1060.11790.14510.01690.02520.13290.03080.1562.276919.89.389
70.05280.0435-0.01730.0391-0.00440.02310.1521-0.15440.4672-0.1024-0.202-0.0101-0.26390.175200.2932-0.00580.010.3129-0.00670.303114.540726.924414.2051
80.2915-0.1084-0.30950.4216-0.41170.40670.0585-0.1612-0.04440.1202-0.0738-0.0455-0.08640.23650.02490.165-0.02340.00110.18480.00710.110916.832324.48737.9689
90.26280.04230.20080.2530.1040.23010.0478-0.235-0.01180.1359-0.0072-0.0184-0.10740.07410.00350.1596-0.03620.00040.15420.02010.143920.470531.9936-1.9662
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:24)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 25:81)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 82:98)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 99:128)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 129:144)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 145:174)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 181:188)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 189:219)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 220:244)

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