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- PDB-1m9n: CRYSTAL STRUCTURE OF THE HOMODIMERIC BIFUNCTIONAL TRANSFORMYLASE ... -

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Basic information

Entry
Database: PDB / ID: 1m9n
TitleCRYSTAL STRUCTURE OF THE HOMODIMERIC BIFUNCTIONAL TRANSFORMYLASE AND CYCLOHYDROLASE ENZYME AVIAN ATIC IN COMPLEX WITH AICAR AND XMP AT 1.93 ANGSTROMS.
ComponentsAICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE
Keywordstransferase / hydrolase / HOMODIMER / 2 FUNCTIONAL DOMAINS / IMPCH DOMAIN = ALPHA/BETA/ALPHA / AICAR TFASE = 2 ALPHA/BETA/ALPHA DOMAINS / 1 ALPHA + BETA DOMAIN
Function / homology
Function and homology information


De novo synthesis of IMP / phosphoribosylaminoimidazolecarboxamide formyltransferase / phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase / IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process / protein homodimerization activity / cytosol
Similarity search - Function
Helix Hairpins - #440 / AICAR transformylase, insert domain superfamily / AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily ...Helix Hairpins - #440 / AICAR transformylase, insert domain superfamily / AICAR transformylase, duplication domain / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain profile. / MGS-like domain / Cytidine Deaminase; domain 2 / Cytidine deaminase-like / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / : / XANTHOSINE-5'-MONOPHOSPHATE / Bifunctional purine biosynthesis protein ATIC
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsWolan, D.W. / Greasly, S.E. / Beardsley, G.P. / Wilson, I.A.
CitationJournal: Biochemistry / Year: 2002
Title: Structural Insights into the Avian AICAR Transformylase Mechanism.
Authors: Wolan, D.W. / Greasly, S.E. / Beardsley, G.P. / Wilson, I.A.
History
DepositionJul 29, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 12OTHER REFINEMENT REMARKS Reported B value is prior to incorporation of tensors with TLSANL. Tensors ...OTHER REFINEMENT REMARKS Reported B value is prior to incorporation of tensors with TLSANL. Tensors have been added to the B value for the publication.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE
B: AICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,8238
Polymers133,3382
Non-polymers1,4856
Water9,206511
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14540 Å2
ΔGint-69 kcal/mol
Surface area43180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.480, 107.880, 103.860
Angle α, β, γ (deg.)90.00, 91.20, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBoth monomers of the biologically significant avian ATIC homodimer are located within the asymmetric unit.

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Components

#1: Protein AICAR TRANSFORMYLASE-IMP CYCLOHYDROLASE / BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH [INCLUDES PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE ...BIFUNCTIONAL PURINE BIOSYNTHESIS PROTEIN PURH [INCLUDES PHOSPHORIBOSYLAMINOIMIDAZOLECARBOXAMIDE FORMYLTRANSFERASE (AICAR TRANSFORMYLASE) AND IMP CYCLOHYDROLASE (INOSINICASE / IMP SYNTHETASE / ATIC)]


Mass: 66669.086 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: PURH / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P31335, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-AMZ / AMINOIMIDAZOLE 4-CARBOXAMIDE RIBONUCLEOTIDE / AICAR


Mass: 338.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15N4O8P
#4: Chemical ChemComp-XMP / XANTHOSINE-5'-MONOPHOSPHATE / 5-MONOPHOSPHATE-9-BETA-D-RIBOFURANOSYL XANTHINE


Mass: 365.213 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N4O9P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 511 / 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: 2.37 Å3/Da / Density % sol: 48.16 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: PEG 8000, imidazole, DTT, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
214 %(w/v)PEG80001reservoir
30.2 Mimidazole1reservoirpH7.2
45 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 16, 1999
Details: bent conical Si-mirror (Rh coating); bent cylindrical Ge(111) monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.93→30 Å / Num. all: 92862 / Num. obs: 91184 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 33.5 Å2 / Rsym value: 0.044 / Net I/σ(I): 25.3
Reflection shellResolution: 1.93→1.96 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.4 / Num. unique all: 4619 / Rsym value: 0.419 / % possible all: 99.6
Reflection
*PLUS
Lowest resolution: 30 Å / Rmerge(I) obs: 0.044
Reflection shell
*PLUS
% possible obs: 99.6 % / Num. unique obs: 4619 / Rmerge(I) obs: 0.419

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1G8M

1g8m


Resolution: 1.93→29.24 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.934 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24397 8292 10 %RANDOM
Rwork0.2057 ---
all0.20955 91184 --
obs0.20955 74522 90.84 %-
Solvent computationShrinkage radii: 0.8 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.949 Å2
Baniso -1Baniso -2Baniso -3
1-4.67 Å20 Å2-0.56 Å2
2---1.02 Å20 Å2
3----3.67 Å2
Refinement stepCycle: LAST / Resolution: 1.93→29.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9020 0 94 511 9625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0219286
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.96912610
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.61931178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.011151638
X-RAY DIFFRACTIONr_chiral_restr0.0920.21457
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026920
X-RAY DIFFRACTIONr_nbd_refined0.2340.34657
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.5837
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.57
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1960.331
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2620.57
X-RAY DIFFRACTIONr_mcbond_it0.5191.55898
X-RAY DIFFRACTIONr_mcangle_it0.91329494
X-RAY DIFFRACTIONr_scbond_it1.56333388
X-RAY DIFFRACTIONr_scangle_it2.4924.53116
LS refinement shellResolution: 1.933→1.983 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.339 502
Rwork0.294 4809
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)
12.08420.67520.80411.9851-0.00783.3285-0.00240.3931-0.3357-0.83440.10790.09041.0826-0.1866-0.10561.1945-0.1021-0.01570.3563-0.01480.369920.4179-10.9055-14.1307
21.21440.1476-0.34311.2880.12461.666-0.0506-0.26860.05620.0307-0.0045-0.03230.20040.09610.05520.03420.02430.00970.3710.01290.400726.84044.542739.8818
31.2241.0726-0.44222.4173-1.29283.0261-0.07510.17780.1799-0.52570.0149-0.03610.26940.14040.06010.62590.03880.02070.30880.02810.334829.32188.3283-10.9353
41.13210.08330.2081.4581-0.68411.79940.0114-0.2204-0.0923-0.09940.00010.1880.4038-0.2576-0.01150.4564-0.0932-0.00340.31550.00810.357214.3076-19.060335.8324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA4 - 20024 - 220
2X-RAY DIFFRACTION2AA201 - 593221 - 613
3X-RAY DIFFRACTION3BB4 - 20024 - 220
4X-RAY DIFFRACTION4BB201 - 593221 - 613
Refinement
*PLUS
Lowest resolution: 29.2 Å / % reflection Rfree: 10 % / Rfactor Rfree: 0.244 / Rfactor Rwork: 0.206
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.009
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.3
LS refinement shell
*PLUS
Highest resolution: 1.93 Å / Lowest resolution: 1.98 Å

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