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- PDB-1lrt: CRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INO... -

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Basic information

Entry
Database: PDB / ID: 1lrt
TitleCRYSTAL STRUCTURE OF TERNARY COMPLEX OF TRITRICHOMONAS FOETUS INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE: STRUCTURAL CHARACTERIZATION OF NAD+ SITE IN MICROBIAL ENZYME
ComponentsINOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / ternary complex / alpha-beta barrel / flexible loop / flap
Function / homology
Function and homology information


IMP dehydrogenase activity / IMP dehydrogenase / GMP biosynthetic process / nucleotide binding / protein-containing complex / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. ...IMP dehydrogenase / GMP reductase domain / Inosine-5'-monophosphate dehydrogenase / IMP dehydrogenase / GMP reductase, conserved site / IMP dehydrogenase / GMP reductase signature. / IMP dehydrogenase/GMP reductase / IMP dehydrogenase / GMP reductase domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
INOSINIC ACID / : / Chem-TAD / Inosine-5'-monophosphate dehydrogenase
Similarity search - Component
Biological speciesTritrichomonas foetus (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGan, L. / Petsko, G.A. / Hedstrom, L.
CitationJournal: Biochemistry / Year: 2003
Title: Crystal structure of a ternary complex of Tritrichomonas foetus inosine 5'-monophosphate dehydrogenase: NAD+ orients the active site loop for catalysis
Authors: Gan, L. / Petsko, G.A. / Hedstrom, L.
History
DepositionMay 15, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Remark 999SEQUENCE AUTHOR STATES THE WILD TYPE T. FOETUS IMPDH CONSISTS OF 503 RESIDUES, HOWEVER THEIR ...SEQUENCE AUTHOR STATES THE WILD TYPE T. FOETUS IMPDH CONSISTS OF 503 RESIDUES, HOWEVER THEIR PROTEIN WAS A MUTANT OFIMPDH. RESIDUES 101-226 IN THE SUBDOMAIN WERE DELETED BECAUSE IT IS NOT REQUIRED FOR IMPDH ACTIVITY. ACCORDING TO THE AUTHORS THE SUBDOMAIN WAS DELETED IN THIS CONSTRUCT TO FACILITATE CRYSTALLIZATION AND THERE IS NO EXOGENOUS LINKER BETWEEN THE RESIDUES 100 AND 227. AUTHOR ALSO STATES ALTHOUGH RESIDUE 279 IS GLU IN SWISS DATABANK, BOTH SEQUENCING RESULT AND ELECTRON DENSITY OF THE STRUCTURE SHOW RESIDUE 279 AS ASP IN THEIR PROTEIN. THE AUTHOR SUGGEST A CONSERVED MUTATION OCCURS AFTER THE CDNA OF THE ENZYME GENE IS TRANSFORMED INTO E. COLI.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
B: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
C: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
D: INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,06530
Polymers164,7964
Non-polymers6,27026
Water9,782543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22910 Å2
ΔGint-68 kcal/mol
Surface area50250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.144, 112.369, 161.997
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 6 molecules ABCD

#1: Protein
INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE / INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE / IMP DEHYDROGENASE / IMPDH / IMPD


Mass: 41198.891 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Tritrichomonas foetus (eukaryote) / Gene: IMPDH / Plasmid: pKK233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): H712 / References: UniProt: P50097, IMP dehydrogenase
#2: Sugar ChemComp-BOG / octyl beta-D-glucopyranoside / Octyl glucoside


Type: D-saccharide / Mass: 292.369 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C14H28O6 / Comment: detergent*YM
IdentifierTypeProgram
b-octylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 567 molecules

#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-IMP / INOSINIC ACID / Inosinic acid


Mass: 348.206 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N4O8P
#5: Chemical
ChemComp-TAD / BETA-METHYLENE-THIAZOLE-4-CARBOXYAMIDE-ADENINE DINUCLEOTIDE


Mass: 667.480 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H27N7O13P2S
#6: Chemical
ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 543 / 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: 2.72 Å3/Da / Density % sol: 54 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.25
Details: PEG 10,000, MES, glycerol, potassium chloride, beta-octylglucoside, pH 6.25, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12 mg/mlprotein1drop
250 mMTris-HCl1droppH7.5
35 %glycerol1drop
440 mMIMP1drop
53.5 mMbeta-methylene-TAD1drop
61 mMdithiothreitol1drop
710 %PEG100001reservoir
8100 mMMES1reservoirpH6.25
9120 mM1reservoirKCl
1020 %glycerol1reservoir
112 %(w/v)beta-octylglucoside1reservoir
121 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: Mar 5, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 87015 / Num. obs: 82096 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.1 % / Biso Wilson estimate: 19.3 Å2 / Rmerge(I) obs: 0.089 / Rsym value: 0.089 / Net I/σ(I): 12.2
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 3.4 / Num. unique all: 8087 / Rsym value: 0.398 / % possible all: 91.3
Reflection
*PLUS
Num. obs: 87015 / % possible obs: 96.8 % / Num. measured all: 356029
Reflection shell
*PLUS
% possible obs: 91.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AK5

1ak5


Resolution: 2.2→29.86 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 392538.27 / Data cutoff high rms absF: 392538.27 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 8229 10 %RANDOM
Rwork0.212 ---
all0.218 81977 --
obs0.218 81977 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.6917 Å2 / ksol: 0.421356 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--4.2 Å20 Å2
3----4.65 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10291 0 404 543 11238
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it2.092
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection obs% reflection obs (%)
2.2-2.210.31431379.80.2832110550.003122183
2.21-2.230.26971240.25031218
2.23-2.250.26041430.26551300
2.25-2.260.28771560.24881376
2.26-2.280.31181340.25271366
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4IMP.PARIMP.TOP
X-RAY DIFFRACTION5TAD.PARTAD.TOP
X-RAY DIFFRACTION6BOG.PARBOG.TOP
X-RAY DIFFRACTION7TRIS.PARTRIS.TOP
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. reflection obs: 71997 / Num. reflection Rfree: 8033 / Rfactor Rwork: 0.218
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.27
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03

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