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- PDB-2cff: Crystal Structure Of N-((5'-Phosphoribosyl)-Formimino)-5- Aminoim... -

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Basic information

Entry
Database: PDB / ID: 2cff
TitleCrystal Structure Of N-((5'-Phosphoribosyl)-Formimino)-5- Aminoimidazol-4-Carboxamid Ribonucleotid Isomerase mutant D127V (Ec 3. 1.3.15, Hisa)
Components1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE
KeywordsISOMERASE / HISTIDINE BIOSYNTHESIS / THERMOPHILIC PROTEIN / AMINO-ACID 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 / 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
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.5 Å
AuthorsHe, C. / Kuper, J. / Sterner, R. / Wilmmans, M.
CitationJournal: To be Published
Title: Crystal Structure of N-((5'-Phosphoribosyl)- Formimino)-5-Aminoimidazol-4-Carboxamid Ribonucleotid Isomerase Mutant D127V (Ec 3.1.3.15, Hisa)
Authors: He, C. / Kuper, J. / Sterner, R. / Wilmmans, M.
History
DepositionFeb 20, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Mar 29, 2017Group: Source and taxonomy
Revision 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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: 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)54,2233
Polymers54,1052
Non-polymers1181
Water1,26170
1
A: 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,1702
Polymers27,0521
Non-polymers1181
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE


Theoretical massNumber of molelcules
Total (without water)27,0521
Polymers27,0521
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)48.710, 47.080, 105.250
Angle α, β, γ (deg.)90.00, 98.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO) METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE / HISA / PHOSPHORIBOSYLFORMIMINO-5-AMINOIMIDAZOLE CARBOXAMIDE RIBOTIDE ISOMERASE


Mass: 27052.311 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: Q9X0C7, 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase
#2: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 127 TO VAL ENGINEERED RESIDUE IN CHAIN B, ASP 127 TO VAL

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 8.5
Details: 0.1M TRIS PH8.5, 27% PEG 4000, 4.5% MPD, 0.2M MGCL2, pH 8.50

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.813
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.813 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 18703 / % possible obs: 90.3 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.5→50 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.89 / SU B: 24.974 / SU ML: 0.269 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.373 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflection
Rfree0.283 770 5.02 %
Rwork0.2 --
obs-15393 92.4 %
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 38.07 Å2
Baniso -1Baniso -2Baniso -3
1-3.411 Å20 Å20.242 Å2
2---1.867 Å20 Å2
3----1.476 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3795 0 8 70 3873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223854
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3871.9945186
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7525480
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52124.39164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.44915755
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6061526
X-RAY DIFFRACTIONr_chiral_restr0.0880.2606
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022784
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2210.21809
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.22587
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.2198
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4691.52469
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.81423849
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.19731541
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.9694.51337
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: 10.92→50 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.17 9
Rwork0.173 162
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)
13.31130.3129-0.83892.8575-0.31682.7304-0.12250.0447-0.04120.1784-0.081-0.17630.21010.18870.2036-0.25120.0373-0.0647-0.02650.0143-0.0603-10.0215.27-38.286
23.317-0.3581-0.95885.4556-0.03353.00550.01010.2859-0.01320.1801-0.1220.31990.0938-0.14650.112-0.2934-0.00380.0759-0.06160.0164-0.047812.316-4.442-14.679
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 241
2X-RAY DIFFRACTION2B1 - 241

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