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- PDB-2oip: Crystal Structure of the S290G Active Site Mutant of TS-DHFR from... -

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Basic information

Entry
Database: PDB / ID: 2oip
TitleCrystal Structure of the S290G Active Site Mutant of TS-DHFR from Cryptosporidium hominis
ComponentsChain A, crystal structure of Dhfr
KeywordsTRANSFERASE / OXIDOREDUCTASE / BIFUNCTIONAL ENZYME
Function / homology
Function and homology information


Thymidylate Synthase; Chain A / Thymidylate synthase/dCMP hydroxymethylase domain / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
10-PROPARGYL-5,8-DIDEAZAFOLIC ACID / METHOTREXATE / Chem-NDP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / :
Similarity search - Component
Biological speciesCryptosporidium hominis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsMartucci, W.E. / Vargo, M.A.
CitationJournal: Biochemistry / Year: 2007
Title: Nonconserved residues Ala287 and Ser290 of the Cryptosporidium hominis thymidylate synthase domain facilitate its rapid rate of catalysis
Authors: Doan, L.T. / Martucci, W.E. / Vargo, M.A. / Atreya, C.E. / Anderson, K.S.
History
DepositionJan 11, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: database_PDB_caveat / pdbx_entry_details ...database_PDB_caveat / pdbx_entry_details / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chain A, crystal structure of Dhfr
B: Chain A, crystal structure of Dhfr
C: Chain A, crystal structure of Dhfr
D: Chain A, crystal structure of Dhfr
E: Chain A, crystal structure of Dhfr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)309,99925
Polymers300,0715
Non-polymers9,92820
Water7,278404
1
A: Chain A, crystal structure of Dhfr
B: Chain A, crystal structure of Dhfr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,99910
Polymers120,0282
Non-polymers3,9718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16300 Å2
ΔGint-54 kcal/mol
Surface area38440 Å2
MethodPISA
2
C: Chain A, crystal structure of Dhfr
D: Chain A, crystal structure of Dhfr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,99910
Polymers120,0282
Non-polymers3,9718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16280 Å2
ΔGint-58 kcal/mol
Surface area38530 Å2
MethodPISA
3
E: Chain A, crystal structure of Dhfr
hetero molecules

E: Chain A, crystal structure of Dhfr
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,99910
Polymers120,0282
Non-polymers3,9718
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_457-x-1,y,-z+21
Unit cell
Length a, b, c (Å)215.026, 116.204, 216.601
Angle α, β, γ (deg.)90.00, 94.27, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is the dimer present in the asymmetric unit, either with monomers A+B or C+D. The second half of the dimer formed by monomer E lies across the crystallographic axis.

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Components

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Protein , 1 types, 5 molecules ABCDE

#1: Protein
Chain A, crystal structure of Dhfr


Mass: 60014.219 Da / Num. of mol.: 5 / Mutation: S290G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptosporidium hominis (eukaryote) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5CGA3, thymidylate synthase, dihydrofolate reductase

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Non-polymers , 5 types, 424 molecules

#2: Chemical
ChemComp-UMP / 2'-DEOXYURIDINE 5'-MONOPHOSPHATE / DUMP


Mass: 308.182 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C9H13N2O8P
#3: Chemical
ChemComp-CB3 / 10-PROPARGYL-5,8-DIDEAZAFOLIC ACID


Mass: 477.469 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C24H23N5O6
#4: Chemical
ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C20H22N8O5
#5: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 404 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationN

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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: 4.49 Å3/Da / Density % sol: 72.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1mM ammonium sulfate, 0.3M lithium sulfate, 0.1M Tris, 10% PEG 6000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 9, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 130177 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 65 Å2 / Rmerge(I) obs: 0.117 / Χ2: 1.234 / Net I/σ(I): 13.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.9 / Num. unique all: 12987 / Χ2: 1.252 / % possible all: 99.6

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Phasing

Phasing dmFOM : 0.783 / FOM centric: 0.676 / Reflection: 131011 / Reflection centric: 4636
Phasing dm shell
Resolution (Å)FOM acentricFOM centricReflection acentricReflection centric
8.12-49.750.8930.7734461435
5.78-8.120.8640.7488637499
4.73-5.780.8810.73811195506
4.1-4.730.8770.74613232499
3.67-4.10.7970.66415074500
3.35-3.670.7940.69216635496
3.11-3.350.7570.6618100480
2.91-3.110.7340.62619510468
2.74-2.910.720.56112541296

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLOMONphasing
CNS1.1refinement
PDB_EXTRACT2data extraction
CBASSdata collection
HKL-2000data reduction
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1QZF

1qzf


Resolution: 2.8→50 Å / FOM work R set: 0.78 / Isotropic thermal model: group / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 6550 -random
Rwork0.222 ---
all0.222 130114 --
obs0.222 123564 99.2 %-
Displacement parametersBiso mean: 66.525 Å2
Baniso -1Baniso -2Baniso -3
1--12.8 Å20 Å2-8.79 Å2
2--2.05 Å20 Å2
3---10.75 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20847 0 680 404 21931
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d2.23
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.012
RfactorNum. reflection% reflection
Rfree0.392 1075 -
Rwork0.353 --
obs-20413 98.7 %

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