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- PDB-1qd1: THE CRYSTAL STRUCTURE OF THE FORMIMINOTRANSFERASE DOMAIN OF FORMI... -

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Basic information

Entry
Database: PDB / ID: 1qd1
TitleTHE CRYSTAL STRUCTURE OF THE FORMIMINOTRANSFERASE DOMAIN OF FORMIMINOTRANSFERASE-CYCLODEAMINASE.
ComponentsFORMIMINOTRANSFERASE-CYCLODEAMINASE
KeywordsTRANSFERASE / FUNCTIONAL DIMER / ALPHA-BETA-BETA-ALPHA SANDWICH / ELECTROSTATICALLY CHARGED SUBSTRATE TUNNEL
Function / homology
Function and homology information


glutamate formimidoyltransferase / formimidoyltetrahydrofolate cyclodeaminase / glutamate formimidoyltransferase activity / formimidoyltetrahydrofolate cyclodeaminase activity / L-histidine catabolic process / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate / tetrahydrofolate interconversion / folic acid binding / centriole / Golgi apparatus
Similarity search - Function
Formiminotransferase, C-terminal subdomain / Formiminotransferase-cyclodeaminase; Chain B, domain 1 / Formiminotransferase, N-terminal subdomain / Formiminotransferase catalytic domain / Formiminotransferase, N-terminal subdomain / Formiminotransferase, C-terminal subdomain / Formiminotransferase catalytic domain superfamily / Formiminotransferase, N-terminal subdomain superfamily / Formiminotransferase, C-terminal subdomain superfamily / Formiminotransferase domain ...Formiminotransferase, C-terminal subdomain / Formiminotransferase-cyclodeaminase; Chain B, domain 1 / Formiminotransferase, N-terminal subdomain / Formiminotransferase catalytic domain / Formiminotransferase, N-terminal subdomain / Formiminotransferase, C-terminal subdomain / Formiminotransferase catalytic domain superfamily / Formiminotransferase, N-terminal subdomain superfamily / Formiminotransferase, C-terminal subdomain superfamily / Formiminotransferase domain / Formiminotransferase domain, N-terminal subdomain / Formiminotransferase domain / Formiminotransferase domain, N-terminal subdomain / Cyclodeaminase/cyclohydrolase / Formimidoyltransferase-cyclodeaminase-like superfamily / Formiminotransferase-cyclodeaminase / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-FON / Formimidoyltransferase-cyclodeaminase
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsKohls, D. / Sulea, T. / Purisima, E. / MacKenzie, R.E. / Vrielink, A.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: The crystal structure of the formiminotransferase domain of formiminotransferase-cyclodeaminase: implications for substrate channeling in a bifunctional enzyme.
Authors: Kohls, D. / Sulea, T. / Purisima, E.O. / MacKenzie, R.E. / Vrielink, A.
History
DepositionJul 8, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FORMIMINOTRANSFERASE-CYCLODEAMINASE
B: FORMIMINOTRANSFERASE-CYCLODEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,8896
Polymers71,7582
Non-polymers1,1314
Water13,890771
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.31, 103.84, 122.77
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 FORMIMINOTRANSFERASE-CYCLODEAMINASE


Mass: 35878.910 Da / Num. of mol.: 2 / Fragment: FORMIMINOTRANSFERASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Organ: liver / Plasmid: pBke-Cm1 / Production host: Escherichia coli (E. coli)
References: UniProt: P53603, glutamate formimidoyltransferase
#2: Chemical ChemComp-FON / N-{[4-({[(6R)-2-amino-5-formyl-4-oxo-1,4,5,6,7,8-hexahydropteridin-6-yl]methyl}amino)phenyl]carbonyl}-L-glutamic acid / [6R]-5-FORMYL-5,6,7,8-TETRAHYDROFOLATE / 6R-FOLINIC ACID


Mass: 473.439 Da / Num. of mol.: 2 / Fragment: FOLINIC ACID / Mutation: PRODUCT ANALOGUE OF THE NATURAL SUBSTRATE / Source method: obtained synthetically / Formula: C20H23N7O7
#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.: 771 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.85 Å3/Da / Density % sol: 56.92 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8
Details: sodium citrate, glycerol, tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
18 mg/mlprotein1drop
21 Msodium citrate1reservoir
3100 mMTris-HCl1reservoir
415 %(v/v)glycerol1reservoir
52 mMfolinic acid1reservoir

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1901
2831
Diffraction source
SourceSiteBeamlineTypeIDWavelength
ROTATING ANODERIGAKU RU20011.5418
SYNCHROTRONNSLS X8C21.072
Detector
TypeIDDetectorDate
MARRESEARCH1IMAGE PLATEFeb 9, 1998
MARRESEARCH2IMAGE PLATEAug 25, 1998
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.0721
ReflectionResolution: 1.7→50 Å / Num. all: 89972 / Num. obs: 436554 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.85 % / Biso Wilson estimate: 20.92 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.5
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.186 / Num. unique all: 8547 / % possible all: 95.1
Reflection
*PLUS
Num. obs: 89972 / Num. measured all: 436554
Reflection shell
*PLUS
% possible obs: 95.1 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.7→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: no NCS restraints imposed Parameter and topology files for the ligands, folinic acid and glycerol were obtained from the Heteroatom compound database (Upsala, Sweden). The stereochemistry ...Details: no NCS restraints imposed Parameter and topology files for the ligands, folinic acid and glycerol were obtained from the Heteroatom compound database (Upsala, Sweden). The stereochemistry for folinic acid was manually altered from 6S to 6R.
RfactorNum. reflection% reflection
Rfree0.213 8996 -
Rwork0.191 --
all-89891 -
obs-89891 100 %
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5000 0 80 771 5851
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005026
X-RAY DIFFRACTIONc_angle_deg1.24521
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 22.21 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.25

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