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- PDB-1qo2: Crystal structure of N-((5'-phosphoribosyl)-formimino)-5-aminoimi... -

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Basic information

Entry
Database: PDB / ID: 1qo2
TitleCrystal structure of N-((5'-phosphoribosyl)-formimino)-5-aminoimidazol-4-carboxamid ribonucleotid isomerase (EC 3.1.3.15, HisA)
Components1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
KeywordsISOMERASE / HISTIDINE BIOSYNTHESIS / THERMOPHILIC PROTEIN
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 / 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
1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase
Similarity search - Component
Biological speciesTHERMOTOGA MARITIMA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.85 Å
AuthorsWilmanns, M. / Lang, D. / Thoma, R. / Sterner, R.
Citation
Journal: Science / Year: 2000
Title: Structural Evidence for Evolution of the Beta/Alpha-Barrel Scaffold by Repeated Gene Duplication and Fusion
Authors: Lang, D. / Thoma, R. / Henn-Sax, M. / Sterner, R. / Wilmanns, M.
#1: Journal: FEBS Lett. / Year: 1999
Title: Efficient Expression, Purification and Crystallisation of Two Hyperthermostable Enzymes of Histidine Biosynthesis
Authors: Thoma, R. / Obmolova, G. / Lang, D.A. / Schwander, M. / Jenoe, P. / Sterner, R. / Wilmanns, M.
History
DepositionNov 1, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status ...pdbx_database_proc / pdbx_database_status / refine / struct_conn
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description

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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


Theoretical massNumber of molelcules
Total (without water)54,4182
Polymers54,4182
Non-polymers00
Water9,854547
1
A: 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase


Theoretical massNumber of molelcules
Total (without water)27,2091
Polymers27,2091
Non-polymers00
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)27,2091
Polymers27,2091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)46.780, 73.160, 62.700
Angle α, β, γ (deg.)90.00, 97.42, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.9992, -0.01298, -0.03791), (-0.03851, 0.05016, 0.998), (-0.01105, 0.99866, -0.05062)
Vector: 16.28184, -4.59496, 5.49976)

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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: 27208.951 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: M1, M17 AND M236 ARE SELENOMETHIONINE SUBSTITUTED / Source: (gene. exp.) THERMOTOGA MARITIMA (bacteria) / Cellular location: CYTOPLASM / Gene: THISA / Plasmid: PDMI, 1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): W3110 TRPEA2 / References: UniProt: Q9X0C7, D-lyxose ketol-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.82 Å3/Da / Density % sol: 31.86 %
Crystal growpH: 5.6
Details: SEE THOMA ET AL. (1999) FEBS LETTERS 454, 1-6., pH 5.60
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.2 / Method: vapor diffusion, hanging drop / Details: Thoma, R., (1999) FEBS Lett., 454, 1.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 mg/mlprotein1drop
210 mMBis-Tris1drop
31 mMdithiothreitol1drop
41 mMEDTA1drop
529-35 %(w/v)PEG40001reservoir
60.1 Mcitrate1reservoir
7200 mM1reservoirNH4Ac
83 %(v/v)MPD1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.97893, 0.97929, 0.98089
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1998 / Details: RHODIUM COATED PRE-MIRROR FOCUSSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978931
20.979291
30.980891
ReflectionResolution: 1.85→39.841 Å / Num. obs: 34932 / % possible obs: 97.4 % / Observed criterion σ(I): 0 / Redundancy: 3.51 % / Biso Wilson estimate: 27.24 Å2 / Rsym value: 0.041 / Net I/σ(I): 17
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 1.95 % / Mean I/σ(I) obs: 2.53 / Rsym value: 0.269 / % possible all: 91.9
Reflection
*PLUS
Redundancy: 5.8 % / Rmerge(I) obs: 0.048
Reflection shell
*PLUS
Rmerge(I) obs: 0.304

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.9phasing
SHARPphasing
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.85→8 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1707 5 %RANDOM
Rwork0.188 ---
obs0.188 34472 97.4 %-
Solvent computationSolvent model: CNS DEFAULT, ANISOTROPIC B FACTORS
Displacement parametersBiso mean: 20.81 Å2
Baniso -1Baniso -2Baniso -3
1--2.878 Å20 Å2-3.646 Å2
2--5.037 Å20 Å2
3----2.159 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.21 Å
Luzzati d res low-8 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.85→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3798 0 0 547 4345
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.31
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.649
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.7889
X-RAY DIFFRACTIONc_mcangle_it1.29312
X-RAY DIFFRACTIONc_scbond_it1.28212
X-RAY DIFFRACTIONc_scangle_it1.98715
LS refinement shellResolution: 1.85→1.87 Å / Total num. of bins used: 34
RfactorNum. reflection% reflection
Rfree0.365 58 5 %
Rwork0.306 855 -
obs--78.64 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0047
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.31
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.649

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