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- PDB-5abt: S.enterica HisA mutant D7N, G102A, V106M, D176A -

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Basic information

Entry
Database: PDB / ID: 5abt
TitleS.enterica HisA mutant D7N, G102A, V106M, D176A
Components1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENE AMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE
KeywordsISOMERASE / 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 / 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 / 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: 1.65 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 8, 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
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENE AMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7102
Polymers27,1331
Non-polymers5771
Water4,071226
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.555, 46.555, 196.378
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) METHYLIDENE AMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE / PHOSPHORIBOSYLFORMIMINO-5-AMINOIMIDAZOLE CARBOXAMIDE RIBOTIDE ISOMERASE / HISA


Mass: 27133.023 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SALMONELLA ENTERICA (bacteria) / Plasmid: PEXP5-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: V7IJE3, UniProt: P10372*PLUS, 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.: 226 / 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: 8.5 / Details: MORPHEUS SCREEN H9, pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 112168 / % possible obs: 97.8 % / Observed criterion σ(I): 2.05 / Redundancy: 2.55 % / Biso Wilson estimate: 19.33 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.64
Reflection shellResolution: 1.65→1.75 Å / Redundancy: 2.56 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.05 / % possible all: 97.4

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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 5A5W

5a5w


Resolution: 1.65→40.318 Å / SU ML: 0.14 / σ(F): 1.34 / Phase error: 17.27 / Stereochemistry target values: ML
Details: RESIDUES 247-253 ARE DISORDERED. K246 IS REPLACED BY ALANINE DUE TO POOR DENSITY
RfactorNum. reflection% reflection
Rfree0.1874 1464 4.8 %
Rwork0.1645 --
obs0.1656 30686 99.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 25.77 Å2
Refinement stepCycle: LAST / Resolution: 1.65→40.318 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1841 0 37 226 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091968
X-RAY DIFFRACTIONf_angle_d1.442693
X-RAY DIFFRACTIONf_dihedral_angle_d14.79772
X-RAY DIFFRACTIONf_chiral_restr0.062321
X-RAY DIFFRACTIONf_plane_restr0.006350
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6498-1.70880.21011760.19142781X-RAY DIFFRACTION99
1.7088-1.77720.25171370.17792840X-RAY DIFFRACTION99
1.7772-1.85810.20821340.17172893X-RAY DIFFRACTION99
1.8581-1.9560.19641560.17072856X-RAY DIFFRACTION99
1.956-2.07860.21961350.17022861X-RAY DIFFRACTION99
2.0786-2.23910.20181520.16992933X-RAY DIFFRACTION99
2.2391-2.46440.19881110.16642950X-RAY DIFFRACTION100
2.4644-2.82090.1771300.17462942X-RAY DIFFRACTION100
2.8209-3.55370.1881590.17283006X-RAY DIFFRACTION100
3.5537-40.32980.16241740.14463160X-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)
16.79645.8222-4.70456.817-7.05048.33080.0182-0.0751-0.20740.35240.29540.408-0.2545-0.3699-0.29390.13490.00780.02160.19090.07320.1942-12.59817.2877-19.4843
24.9881-2.3007-0.57613.0710.89742.9663-0.03260.29460.2336-0.16620.0036-0.1222-0.11840.13720.00840.1152-0.03230.02220.17580.04010.13330.740623.6191-28.5125
32.4363-1.68380.35431.1637-0.10092.991-0.4070.67510.0487-0.26210.2046-0.12860.04530.29290.20580.2449-0.07960.0060.34730.07120.2063-2.780222.4904-34.158
43.385-0.31541.67182.6910.11953.3422-0.08760.26850.2188-0.09910.1160.2587-0.1855-0.3755-0.00250.12750.0331-0.06310.26110.03960.2374-15.709125.8382-28.3038
56.65873.26611.2384.38130.72132.25170.0979-0.17150.28590.1580.01440.2716-0.2537-0.32420.14810.07520.0351-0.0080.15750.02790.1486-9.003123.9985-20.2387
65.51071.20221.25643.2973-0.06633.1832-0.207-0.09140.7134-0.03280.07960.0727-0.5827-0.19420.0810.23280.0491-0.03370.1657-0.0090.1896-6.605734.2317-20.0583
73.69822.2094-0.43814.67620.91923.0509-0.0104-0.36190.24280.42210.03450.2104-0.2346-0.28320.04530.17560.0637-0.01140.2096-0.00460.1293-7.37428.7372-12.6313
89.7491-1.9936-2.65797.7233-4.02574.1882-0.4728-0.93860.96140.57330.0847-0.0209-0.9091-0.0187-0.16780.33550.1548-0.01250.2738-0.11560.1962-7.970635.2111-8.5883
94.9542-0.72410.83173.6336-0.2713.1436-0.0707-0.3224-0.14550.14040.14460.0792-0.1794-0.0953-0.03890.15760.0521-0.01730.2083-0.02280.108-2.634225.7323-9.3872
104.6048-0.3851-2.38114.0291.8392.1007-0.0629-0.83180.20970.33380.0813-0.0865-0.42980.0006-0.05380.30640.1116-0.04530.4493-0.08930.15710.358728.46-0.377
115.556-6.5907-5.46138.25646.4746.272-0.1799-0.3334-0.07030.32510.07320.07390.0744-0.06590.10440.14060.0607-0.00780.28140.03450.1469-0.767518.7605-9.7071
122.7453-1.1742.61159.5802-1.95552.56690.23130.1212-0.332-0.5614-0.0108-0.63120.67130.9182-0.05730.23780.1215-0.03230.37660.01930.282612.73537.9842-13.1685
131.1369-0.62360.53951.5939-0.89955.2597-0.16-0.3724-0.0250.23240.1422-0.170.01750.21340.04540.15890.0484-0.040.2660.01620.1595.461618.5499-7.3168
142.17190.07410.40640.96950.26924.76110.0288-0.159-0.28690.01440.15290.00050.1995-0.0192-0.06410.11520.02040.00590.15930.03920.1727-0.60211.254-19.1553
153.1164-0.081-0.43773.1449-2.41512.086-0.2005-0.6361-1.0674-0.04380.25560.22180.81180.082-0.13010.27460.03660.02410.22980.16570.4466-0.70394.2498-12.0063
161.8735-0.53490.10691.2143-0.48254.08370.0642-0.3983-0.67710.14670.18660.16270.2883-0.1231-0.15270.1661-0.0020.00370.22860.13450.2658-5.59347.9576-12.8596
172.1804-0.14671.26563.4522-1.48247.23360.0318-0.1328-0.57780.22390.17330.24170.3223-0.34620.09540.1061-0.02990.01460.18020.07240.2322-9.448910.2079-19.1585
185.03331.44524.46517.4791.59853.9657-0.13640.4997-0.7228-0.19080.1010.06040.381-0.2916-0.15750.1336-0.0222-0.04310.2017-0.02210.2317-13.178612.1541-30.3439
197.28510.46522.62014.52381.25486.05190.0227-0.2127-0.9585-0.22410.44261.35490.5703-0.7756-0.19480.1491-0.1317-0.03110.41520.11540.4633-19.87828.4837-23.4364
203.3543-3.41680.85465.6869-4.60946.63070.00550.70860.8919-0.75990.63521.92830.2287-1.3043-0.49240.3945-0.1332-0.03610.32980.09190.4766-18.33694.7013-16.241
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:6)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 7:23)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 24:27)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 28:40)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 41:54)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 55:72)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 73:85)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 86:94)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 95:106)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 107:119)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 120:132)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 133:139)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 140:166)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 167:184)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 185:189)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 190:213)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 214:229)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 230:235)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 236:241)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 242:246)

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