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- PDB-5ac7: S. enterica HisA with mutations D7N, D10G, dup13-15 -

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Basic information

Entry
Database: PDB / ID: 5ac7
TitleS. enterica HisA with mutations D7N, D10G, dup13-15
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: 1.904 Å
AuthorsNewton, M. / Guo, X. / Soderholm, A. / 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
DepositionAug 12, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 28, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references
Revision 1.2Apr 26, 2017Group: Database references
Revision 1.3May 10, 2017Group: Database references
Revision 1.4Jan 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
B: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3528
Polymers54,8572
Non-polymers4956
Water4,197233
1
A: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7365
Polymers27,4281
Non-polymers3074
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6173
Polymers27,4281
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.999, 61.999, 607.094
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-2023-

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: 27428.363 Da / Num. of mol.: 2 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 233 / 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: 3.29 Å3/Da / Density % sol: 62.61 % / Description: NONE
Crystal growpH: 5.5 / Details: 2.0 M AMMONIUM SULFATE; 0.1 M BIS-TRIS PH5.5

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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 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 56836 / % possible obs: 99.8 % / Observed criterion σ(I): 1.71 / Redundancy: 37.6 % / Biso Wilson estimate: 31.77 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 30
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 37.8 % / Rmerge(I) obs: 0.86 / Mean I/σ(I) obs: 1.71 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5AHF

5ahf


Resolution: 1.904→49.106 Å / SU ML: 0.18 / σ(F): 1.34 / Phase error: 19.94 / Stereochemistry target values: ML
Details: RESIDUES 244-252 ARE DISORDERED FOR BOTH CHAINA AND CHAINB
RfactorNum. reflection% reflection
Rfree0.2138 2868 5.1 %
Rwork0.1855 --
obs0.187 56576 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.94 Å2
Refinement stepCycle: LAST / Resolution: 1.904→49.106 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 28 233 3955
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073803
X-RAY DIFFRACTIONf_angle_d1.1025174
X-RAY DIFFRACTIONf_dihedral_angle_d12.7091384
X-RAY DIFFRACTIONf_chiral_restr0.045609
X-RAY DIFFRACTIONf_plane_restr0.005671
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9043-1.93710.30011480.25872583X-RAY DIFFRACTION97
1.9371-1.97230.27111370.22852558X-RAY DIFFRACTION100
1.9723-2.01030.23281180.20922628X-RAY DIFFRACTION100
2.0103-2.05130.23691420.2012623X-RAY DIFFRACTION100
2.0513-2.09590.24561510.18762597X-RAY DIFFRACTION100
2.0959-2.14470.24391290.19642656X-RAY DIFFRACTION100
2.1447-2.19830.23391490.19862605X-RAY DIFFRACTION100
2.1983-2.25770.21871410.19212622X-RAY DIFFRACTION100
2.2577-2.32420.2421550.19162612X-RAY DIFFRACTION100
2.3242-2.39920.20881320.19292685X-RAY DIFFRACTION100
2.3992-2.48490.24511710.18782638X-RAY DIFFRACTION100
2.4849-2.58440.25451440.20772663X-RAY DIFFRACTION100
2.5844-2.7020.23661310.20182671X-RAY DIFFRACTION100
2.702-2.84450.22391340.21092680X-RAY DIFFRACTION100
2.8445-3.02270.21971390.2192681X-RAY DIFFRACTION100
3.0227-3.2560.23011370.21342753X-RAY DIFFRACTION100
3.256-3.58360.24071490.19932729X-RAY DIFFRACTION100
3.5836-4.10190.19111340.16092794X-RAY DIFFRACTION100
4.1019-5.16710.18031510.14332861X-RAY DIFFRACTION100
5.1671-49.12190.17231760.16723069X-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)
14.38243.45795.68175.59812.99018.33630.0868-0.7640.3040.1781-0.19870.0621-0.1104-0.460.12630.24480.00370.0330.1110.03830.178716.1817-20.4618-39.6277
22.8803-2.28251.94497.4514-6.07659.37880.41590.0407-0.39120.4869-0.17070.95070.45560.7456-0.2690.32990.05030.07680.3688-0.10140.42036.3935-22.8166-30.5379
39.41343.8275-7.01294.0041-2.70139.34250.4003-0.25960.24480.3479-0.31850.819-0.5158-0.5324-0.18270.28630.06050.07190.348-0.01110.41839.8639-15.102-40.5489
48.08632.9346-0.00718.0748-0.50762.55920.197-0.1090.12560.304-0.16650.1641-0.0285-0.292-0.03540.26930.01560.0090.20740.00310.147718.1967-20.4603-42.4426
56.38042.5816-2.11649.1884-3.62987.73040.18470.0956-0.1336-0.1870.21740.95790.1525-0.977-0.27390.2316-0.0048-0.05170.3669-0.00960.29358.4081-27.7447-47.4153
64.88332.6091-0.23989.3431-2.36615.82990.09750.1836-0.3341-0.02630.12690.24430.4329-0.5309-0.21970.1790.0022-0.01670.18020.0040.169716.504-32.6354-45.1116
79.98850.0179-1.34197.22421.33712.45590.2327-0.3433-0.49980.2956-0.13160.46720.6599-0.761-0.12030.3699-0.0233-0.02510.31450.01480.283516.6475-43.5885-35.3196
83.62830.15290.76740.50060.90926.8362-0.2262-0.1184-0.24560.24810.12360.1330.43360.18390.10980.34530.03880.00330.13470.00910.226321.5662-37.2082-38.0118
96.12340.59334.32247.79160.75583.2041-0.3994-0.87370.30681.96720.11331.2824-0.3193-1.05310.16190.65760.17670.08990.39620.00780.388119.2951-33.0038-15.2103
106.3656-5.1899-2.24974.83881.41527.22180.482-0.2636-0.85832.2869-0.62871.9337-1.2166-1.77040.12270.80940.02070.29420.87280.11770.746310.2768-34.1253-21.0889
113.5596-1.80380.95165.2537-1.05417.9496-0.1106-0.1231-0.12270.2120.13930.1551-0.06490.0594-0.05670.23690.0189-0.03330.1094-0.00090.205724.1129-38.6866-29.5086
127.8877-5.0818-2.81633.32261.73771.53240.42060.0362-0.2560.1333-0.39560.3204-0.3565-0.2852-0.010.41860.063-0.03680.24340.0040.403820.5903-21.2577-22.9087
137.0013-5.0623.06353.6163-2.16997.1878-0.3252-0.07170.27510.25180.008-0.1442-0.30360.25010.30850.3196-0.0367-0.05930.15550.02010.281330.3791-30.9072-27.6896
149.0513-5.25680.12183.9918-2.13594.5612-0.2928-0.2180.30430.72890.2168-0.3096-0.54220.0680.04870.4326-0.0498-0.07230.2218-0.02390.295926.5693-14.1273-27.5343
156.26161.03711.76134.5139-1.81766.1776-0.02840.13660.4280.357-0.185-0.3308-0.4390.01620.1820.283-0.019-0.00730.1161-0.04380.231524.8927-14.8696-34.0555
163.74093.9107-3.8814.4066-5.40799.8034-0.0607-0.00190.3935-0.8603-0.4093-1.9272-0.91021.09920.29530.4346-0.06140.05070.28680.04450.517833.4983-14.0932-35.6362
173.05012.27283.14682.65563.01043.80730.0502-0.19440.4307-0.0047-0.5790.81051.0798-0.22170.37610.5709-0.08160.07090.1918-0.01090.30115.1232-12.9288-8.0237
184.8336-0.2014-0.94245.4025-0.42550.21580.56650.74440.09260.16790.04220.58720.0140.233-0.07560.925-0.0860.3619-0.0254-0.1960.52422.1502-18.4596-20.2392
191.95042.77190.14753.81180.30175.0198-0.69050.3461-0.6455-0.4779-0.0065-0.07410.83680.53460.54950.81850.02060.2070.2871-0.03570.57015.5345-21.3464-9.0283
207.5754.21932.81728.00421.76168.0682-0.0791-0.2211-0.1255-0.6129-0.13890.3840.7253-0.64060.16050.4874-0.07180.03360.21220.01460.21330.9947-13.7095-7.0117
216.97754.66454.38513.72593.62053.675-0.20860.36020.1746-0.26790.17830.4890.4072-0.0248-0.0370.5417-0.12280.0220.23550.03030.3448-4.5609-15.9722-0.867
226.2277-2.53372.72818.4497-4.25058.99750.14780.0485-0.4852-0.0910.40021.14530.6787-1.0588-0.47470.3882-0.09350.00270.28550.05620.3447-8.5268-7.5819-6.4598
239.6448-1.2146-0.70462.38360.10737.0734-0.04540.4341-0.4097-0.50350.34480.89410.4476-0.9305-0.32040.3339-0.0361-0.05840.31310.0610.4085-12.9518-0.1916-16.5255
248.8993-0.4943-5.44283.62372.25984.43580.13130.1785-0.182-0.3034-0.13750.4198-0.6675-0.9239-0.19770.37050.0455-0.03270.36540.07060.25-8.16431.0412-8.6155
253.44652.0653-2.5933.9638-4.8815.98750.26830.8438-0.6503-1.0228-0.1657-0.00811.28520.06430.09540.51040.071-0.02820.2854-0.03780.30942.1797-0.8943-29.7139
264.1247-5.7426-0.03988.1588-0.82814.55310.49421.0961-0.4363-1.5493-1.77390.84242.70751.04070.98661.74410.1009-0.1970.8907-0.12970.7925-3.3169-7.5172-31.1217
273.16260.67540.40171.827-0.07115.64290.0994-0.0095-0.0207-0.0404-0.06440.08220.0173-0.05-0.05670.31270.013-0.03330.1160.00330.1929-2.92054.5212-17.9999
283.8678-4.81-0.25386.0002-0.153.21090.13940.1264-0.6251-1.1113-0.19660.42730.16870.34110.06330.54360.1307-0.04310.2922-0.02110.332412.0606-6.0854-22.1657
294.137-1.9401-0.54066.7927-4.29815.2652-0.02310.0968-0.01280.1198-0.1465-0.1878-0.16220.06180.17510.3166-0.004-0.05430.1707-0.02590.20036.21826.068-16.241
302.5638-2.3191.11232.7926-3.09037.543-0.04290.1438-0.0705-0.9173-0.4596-1.22970.46811.03950.42460.36090.03260.04210.33180.07350.403318.7486-4.4898-13.9725
317.9223-0.7934-1.4259.0212.40717.5882-0.4987-0.0676-0.235-0.08010.03140.18830.3638-0.02190.4440.2143-0.0069-0.00130.18520.01810.145111.0393-4.3123-11.6459
325.97042.9049-0.6556.11930.73274.1074-0.1604-1.3643-0.848-0.043-0.6968-0.75570.2870.98420.32570.42240.1580.06920.50730.22950.454618.4579-8.8689-6.1768
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:10)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 11:20)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 21:37)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 38:52)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 53:71)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 72:101)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 102:116)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 117:130)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 131:139)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 140:148)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 149:171)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 172:186)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 187:202)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 203:214)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 215:239)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 240:244)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 1:10)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 11:19)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 20:37)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 38:57)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 58:74)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 75:101)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 102:116)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 117:128)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 129:142)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 143:150)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 151:172)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 173:186)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 187:202)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 203:216)
31X-RAY DIFFRACTION31(CHAIN B AND RESID 217:227)
32X-RAY DIFFRACTION32(CHAIN B AND RESID 228:244)

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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