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- PDB-4axk: CRYSTAL STRUCTURE OF subHisA from the thermophile Corynebacterium... -

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Basic information

Entry
Database: PDB / ID: 4axk
TitleCRYSTAL STRUCTURE OF subHisA from the thermophile Corynebacterium efficiens
Components1-(5-PHOSPHORIBOSYL)-5-((5'-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO)IMIDAZOLE-4-CARBOXAMIDE ISOMERASE
KeywordsISOMERASE / (BETA-ALPHA)8-BARREL / METABOLISM / EVOLUTION OF SUBSTRATE SPECIFICITY / 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 / phosphoribosylanthranilate isomerase activity / histidine biosynthetic process / tryptophan biosynthetic process / cytoplasm
Similarity search - Function
HisA/PriA, Actinobacteria / 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
Similarity search - Component
Biological speciesCORYNEBACTERIUM EFFICIENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsNoda-Garcia, L. / Camacho-Zarco, A.R. / Medina-Ruiz, S. / Verduzco-Castro, E.A. / Gaytan, P. / Carrillo-Tripp, M. / Fulop, V. / Barona-Gomez, F.
CitationJournal: Mol.Biol.Evol. / Year: 2013
Title: Evolution of Substrate Specificity in a Recipient'S Enzyme Following Horizontal Gene Transfer.
Authors: Noda-Garcia, L. / Camacho-Zarco, A.R. / Medina-Ruiz, S. / Gaytan, P. / Carrillo-Tripp, M. / Fulop, V. / Barona-Gomez, F.
History
DepositionJun 13, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: 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. THE SHEETS PRESENTED AS "BA" 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

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)54,2574
Polymers54,0732
Non-polymers1842
Water1,49583
1
A: 1-(5-PHOSPHORIBOSYL)-5-((5'-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO)IMIDAZOLE-4-CARBOXAMIDE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1282
Polymers27,0361
Non-polymers921
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)27,1282
Polymers27,0361
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.460, 78.840, 92.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 1-(5-PHOSPHORIBOSYL)-5-((5'-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO)IMIDAZOLE-4-CARBOXAMIDE ISOMERASE / PHOSPHORIBOSYL ISOMERASE\ / SUBHISA


Mass: 27036.264 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CORYNEBACTERIUM EFFICIENS (bacteria) / Plasmid: PET22-CEFF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: C8NPV3, UniProt: Q8FNZ7*PLUS, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.3 Å3/Da / Density % sol: 45 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M BIS-TRIS PH 7.5, 25% V/W PEG-3350, 0.2 M MGCL2,30% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.25→56 Å / Num. obs: 24561 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 7.1 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.2
Reflection shellResolution: 2.25→2.37 Å / Redundancy: 6.6 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VEP

2vep


Resolution: 2.25→55.64 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.889 / SU B: 9.538 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.351 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES A1, A22-28, A143-146, B1, B140-149 ARE DISORDERED AND NOT MODELED, RESIDUES A247, B247-250 ARE PART ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES A1, A22-28, A143-146, B1, B140-149 ARE DISORDERED AND NOT MODELED, RESIDUES A247, B247-250 ARE PART OF THE C-TERMINAL HIS-TAG LINKER AND VISIBLE AND MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.30263 957 3.9 %RANDOM
Rwork0.23556 ---
obs0.23813 23607 99.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.141 Å2
Baniso -1Baniso -2Baniso -3
1-1.13 Å20 Å20 Å2
2---2.15 Å20 Å2
3---1.03 Å2
Refinement stepCycle: LAST / Resolution: 2.25→55.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 12 83 3721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223685
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9624996
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0015469
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.7624.535172
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.78415621
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9671530
X-RAY DIFFRACTIONr_chiral_restr0.120.2583
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022772
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8911.52334
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.63423726
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.20431351
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6524.51270
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.25→2.308 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 60 -
Rwork0.338 1567 -
obs--92.08 %

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