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

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Basic information

Entry
Database: PDB / ID: 5ahf
TitleCrystal structure of Salmonella enterica HisA D7N with ProFAR
Components
KeywordsISOMERASE / HISA / 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
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: 2.201 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
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

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Assembly

Deposited unit
A:
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8924
Polymers27,1311
Non-polymers7623
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.698, 86.698, 121.861
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-2043-

HOH

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Components

#1: Protein / HISA / PHOSPHORIBOSYLFORMIMINO-5-AMINOIMIDAZOLE CARBOXAMIDE RIBOTIDE ISOMER


Mass: 27130.943 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: P10372, 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: 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
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 47.01 %
Description: AS SEARCH MODEL THE WILD TYPE S. ENTERICA HISA WAS USED.
Crystal growpH: 7
Details: 0.2 M AMMONIUM ACETATE, 0.1 M NA ACETATE AND 20% PEG4000 PH5.15, pH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8729
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 12, 2014 / Details: PT COATED SI MIRRORS
RadiationMonochromator: SILICON 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.2→47.31 Å / Num. obs: 25987 / % possible obs: 100 % / Observed criterion σ(I): 1.8 / Redundancy: 10 % / Biso Wilson estimate: 38.34 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 14.09
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 9.66 % / Rmerge(I) obs: 1.25 / Mean I/σ(I) obs: 1.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.201→47.312 Å / SU ML: 0.27 / σ(F): 1.37 / Phase error: 22.67 / Stereochemistry target values: ML / Details: RESIDUES 17-24, 175-18, 245-253 ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.218 1310 5 %
Rwork0.1697 --
obs0.1722 25987 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.71 Å2
Refinement stepCycle: LAST / Resolution: 2.201→47.312 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1718 0 49 52 1819
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081848
X-RAY DIFFRACTIONf_angle_d1.1412521
X-RAY DIFFRACTIONf_dihedral_angle_d15.101724
X-RAY DIFFRACTIONf_chiral_restr0.041303
X-RAY DIFFRACTIONf_plane_restr0.005323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2007-2.28880.32281470.2632705X-RAY DIFFRACTION100
2.2888-2.39290.28671420.22432774X-RAY DIFFRACTION100
2.3929-2.51910.22371460.20912730X-RAY DIFFRACTION100
2.5191-2.67690.26671480.20722751X-RAY DIFFRACTION100
2.6769-2.88360.29351470.19982741X-RAY DIFFRACTION100
2.8836-3.17370.2121430.18522743X-RAY DIFFRACTION100
3.1737-3.63280.24251440.16592745X-RAY DIFFRACTION100
3.6328-4.57640.17921400.13212747X-RAY DIFFRACTION100
4.5764-47.32280.17621530.14652741X-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)
10.0577-0.0084-0.0510.04810.04990.0825-0.1080.0560.1771-0.07750.06970.0927-0.1452-0.1113-00.28390.022-0.00220.2580.04590.3136.456832.3298-8.8511
20.01450.0013-0.01530.00960.00650.0172-0.2018-0.24440.14950.1079-0.09740.00890.01740.190300.79340.0164-0.09120.6594-0.08461.32964.590941.699-6.5942
30.04350.1624-0.06210.6663-0.12620.30.00940.10320.3425-0.15730.03880.1196-0.1723-0.0322-00.3158-0.0068-0.00070.32690.0310.34565.837228.5836-13.3042
40.3922-0.22490.10570.1948-0.17970.3809-0.07060.0656-0.03020.00820.03340.1010.0559-0.0898-00.271-0.01530.02380.2571-0.00580.25610.107916.1493-4.242
50.0603-0.00850.02720.07860.00370.01460.1277-0.01240.29010.1564-0.03820.25870.0989-0.0682-00.47360.02110.03140.3795-0.05470.38290.797327.221515.6195
60.19040.0436-0.04610.08170.05560.0641-0.1596-0.10890.0072-0.14010.13530.534-0.10190.043200.37280.01830.01090.30890.00310.3421-0.59918.891511.2346
70.1677-0.04680.10420.0496-0.03530.0569-0.0816-0.13130.29540.21540.2643-0.5178-0.17320.295200.3691-0.01920.0040.3167-0.0250.36577.777522.83516.6685
80.02040.0499-0.03510.0951-0.08170.05290.041-0.2680.01530.1852-0.123-0.1998-0.11350.2303-00.3847-0.02-0.00680.35470.01910.325916.407624.44089.1293
90.15320.10940.06590.0907-0.00870.11890.0844-0.0833-0.01720.204-0.1498-0.0601-0.22830.214700.3604-0.04710.0090.31870.03410.36520.101332.1946-2.1367
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:14)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 15:28)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 29:72)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 73:128)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 129:144)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 145:163)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 164:183)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 184:219)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 220:244)

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