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- PDB-5g5i: S. enterica HisA mutant D10G -

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Basic information

Entry
Database: PDB / ID: 5g5i
TitleS. enterica HisA mutant D10G
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
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: 2.001 Å
AuthorsGuo, X. / Soderholm, A. / Newton, M. / 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
DepositionMay 25, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 19, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Jan 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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)27,5024
Polymers27,0741
Non-polymers4283
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.880, 85.880, 121.350
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-2068-

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: 27073.891 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica (bacteria) / Gene: hisA, EA588_15715 / Plasmid: PEXP5-CT / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: A0A5T2G6F4, UniProt: P10372*PLUS, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 7.5
Details: 0.1M HEPES, PH7.5; 0.8M SODIUM DIHYDROGEN PHOSPHATE; 0.8M POTASSIUM DIHYDROGEN PHOSPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.91637
DetectorDetector: CCD / Date: Mar 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91637 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 18463 / % possible obs: 99.9 % / Observed criterion σ(I): 3.35 / Redundancy: 11.7 % / Biso Wilson estimate: 25.42 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 17.82
Reflection shellResolution: 2→2.12 Å / Redundancy: 11.8 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 3.35 / % possible all: 99.4

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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 5G1T

5g1t


Resolution: 2.001→47.015 Å / SU ML: 0.18 / σ(F): 2 / Phase error: 19.22 / Stereochemistry target values: ML / Details: RESIDUES 16-23, 176-183, 245-256 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.21 923 5 %
Rwork0.1708 --
obs0.1728 18458 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31 Å2
Refinement stepCycle: LAST / Resolution: 2.001→47.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1709 0 25 81 1815
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081812
X-RAY DIFFRACTIONf_angle_d1.0732472
X-RAY DIFFRACTIONf_dihedral_angle_d13.588663
X-RAY DIFFRACTIONf_chiral_restr0.042292
X-RAY DIFFRACTIONf_plane_restr0.004316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.001-2.10640.27121270.19752419X-RAY DIFFRACTION100
2.1064-2.23840.22421280.18072443X-RAY DIFFRACTION100
2.2384-2.41120.2121300.17622469X-RAY DIFFRACTION100
2.4112-2.65390.22041310.18132481X-RAY DIFFRACTION100
2.6539-3.03780.20811310.17542484X-RAY DIFFRACTION100
3.0378-3.82710.20431330.16292541X-RAY DIFFRACTION100
3.8271-47.02750.19591430.16182698X-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)
14.4269-0.62260.67272.4287-0.66922.9744-0.30270.02690.1494-0.10420.26760.4164-0.3667-0.4595-0.09810.22750.00330.00630.19070.00890.20537.546831.6302-8.0431
22.8418-3.384-1.47744.0541.50143.76220.2520.00831.3566-0.11030.2476-0.2726-0.6820.0713-0.24170.45090.0799-0.13580.4255-0.17221.49324.893442.2652-7.1164
33.0811.5033-1.30562.0533-0.12052.7384-0.19590.13270.3799-0.10340.13160.0555-0.3832-0.0699-0.05570.2931-0.03510.00270.18220.01040.211512.802730.4192-12.7588
45.61121.98191.35780.888-0.20212.79740.0143-0.3990.1980.15360.54551.016-0.5811-0.6206-0.09380.19590.09370.04660.3233-0.00350.6016-4.990630.1605-7.5811
53.4876-0.3563-0.67463.11770.13913.530.07890.19820.1725-0.1996-0.03481.31480.0257-1.0849-0.12050.26790.0204-0.11120.38210.05510.5245-4.708926.2259-14.0009
62.80840.5295-1.13592.2672-0.13453.2316-0.03020.2706-0.036-0.35210.09990.2021-0.1447-0.06830.02830.2696-0.0112-0.00660.19210.01740.17757.019722.8995-13.6492
78.5736-0.4324-4.23464.0527-1.03578.2981-0.12260.4437-0.2531-0.0458-0.0690.3977-0.1911-1.35370.08460.2083-0.0154-0.02190.3417-0.05490.248-4.546916.1218-9.6274
82.41950.1034-2.41041.6946-0.75154.5534-0.1794-0.0509-0.42190.0719-0.07690.2351-0.0903-0.06680.08220.1660.01450.01730.15470.00050.202-1.41116.9224-1.5581
92.9464-0.13-0.74843.61440.50293.7286-0.26810.1721-0.3151-0.22070.28420.09470.33610.14830.12820.2159-0.00770.04790.2022-0.00360.21771.298812.7213-0.9905
103.7070.28041.01723.7188-1.67888.6443-0.6678-0.7495-0.05251.68550.50630.2815-0.26550.19-0.09150.54360.09560.03480.3506-0.08180.3921.922728.429819.4498
112.5772-0.5776-0.72922.85670.80382.0083-0.2462-0.1673-0.03210.23950.27820.222-0.08070.09770.01650.20520.01740.03130.19920.0490.2245-0.579820.937212.2793
122.66451.7408-1.11284.575-0.92732.54410.0578-0.1116-0.33090.2282-0.1699-0.6518-0.02960.32670.10530.20350.0460.03650.2027-0.0050.17037.482716.77153.9357
134.70.71070.40215.67432.01627.3520.2066-0.32361.47120.10890.2459-0.5027-0.60340.219-0.13570.4079-0.0490.05280.3097-0.0340.43846.218131.84210.8355
144.44721.0941-1.15338.8542-1.76534.72580.1188-0.61160.49780.69720.02830.4231-0.63810.37580.07990.31980.00470.0030.32950.00570.219813.581521.256914.2984
152.30470.8308-0.70012.6618-0.92923.4632-0.1263-0.2568-0.0829-0.03160.1619-0.0866-0.19690.02830.11510.21040.01530.03220.18470.00480.135111.912818.07156.946
164.007-0.5221-0.92353.1324-0.78073.0540.4457-0.91590.31880.4834-0.3119-0.132-0.50850.9802-0.04670.3385-0.12760.02960.3533-0.03540.231418.966433.91935.3843
172.34792.0791-2.27492.1677-3.53199.33310.1548-0.1067-0.54040.3773-0.4326-1.0251-0.48180.9612-0.11490.1999-0.0505-0.06840.35810.05870.368320.243222.32017.1915
183.87120.90060.74197.9118-4.14385.04460.021-0.39080.55540.1831-0.00390.0606-0.436-0.2508-0.06750.2253-0.04150.04820.1537-0.02280.279613.394232.8614-1.5038
192.75190.60370.65623.7963-0.98963.41330.02980.01760.16410.1687-0.172-0.096-0.26580.1839-0.070.2314-0.09280.01470.1911-0.0170.184820.927335.3022-4.5704
203.36250.4841-3.78833.83823.48858.60270.3615-0.6667-0.74980.65770.0631-0.98710.46080.96020.42560.3696-0.0341-0.09850.29060.11080.357425.981426.51881.4843
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:14)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 15:27)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 28:49)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 50:55)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 56:65)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 66:82)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 83:93)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 94:112)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 113:129)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 130:135)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 136:162)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 163:170)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 171:175)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 184:193)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 194:202)
16X-RAY DIFFRACTION16(CHAIN A AND RESID 203:214)
17X-RAY DIFFRACTION17(CHAIN A AND RESID 215:220)
18X-RAY DIFFRACTION18(CHAIN A AND RESID 221:228)
19X-RAY DIFFRACTION19(CHAIN A AND RESID 229:240)
20X-RAY DIFFRACTION20(CHAIN A AND RESID 241:244)

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