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- PDB-1vdr: DIHYDROFOLATE REDUCTASE -

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Basic information

Entry
Database: PDB / ID: 1vdr
TitleDIHYDROFOLATE REDUCTASE
ComponentsDIHYDROFOLATE REDUCTASE
KeywordsOXIDOREDUCTASE / DIHYDROFOLATE REDUCTASE / HALOPHILIC ENZYME
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / cytosol
Similarity search - Function
Dihydrofolate reductase / Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Dihydrofolate reductase HdrA
Similarity search - Component
Biological speciesHaloferax volcanii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsPieper, U. / Herzberg, O.
CitationJournal: Structure / Year: 1998
Title: Structural features of halophilicity derived from the crystal structure of dihydrofolate reductase from the Dead Sea halophilic archaeon, Haloferax volcanii.
Authors: Pieper, U. / Kapadia, G. / Mevarech, M. / Herzberg, O.
History
DepositionNov 30, 1997Processing site: BNL
Revision 1.0Feb 25, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHYDROFOLATE REDUCTASE
B: DIHYDROFOLATE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2815
Polymers35,9962
Non-polymers2853
Water1,44180
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.870, 59.450, 78.150
Angle α, β, γ (deg.)90.00, 95.80, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DIHYDROFOLATE REDUCTASE / DHFR


Mass: 17997.822 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: FORMERLY HALOBACTERIUM VOLCANII / Source: (natural) Haloferax volcanii (archaea) / References: UniProt: P15093, dihydrofolate reductase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.9
Details: HANGING DROP VAPOR DIFFUSION. THE RESERVOIR SOLUTION CONTAINED 2.4M PHOSPHATE BUFFER (PH 7.8-8.0), 0.25-0.5% PEG 1000 AND 2MM METHOTREXATE. THE DROPS CONTAINED EQUAL VOLUMES OF RESERVOIR ...Details: HANGING DROP VAPOR DIFFUSION. THE RESERVOIR SOLUTION CONTAINED 2.4M PHOSPHATE BUFFER (PH 7.8-8.0), 0.25-0.5% PEG 1000 AND 2MM METHOTREXATE. THE DROPS CONTAINED EQUAL VOLUMES OF RESERVOIR SOLUTION AND 10 MG/ML PROTEIN SOLUTION IN 0.1M PHOSPHATE BUFFER AT PH7.0., pH 7.9, vapor diffusion - hanging drop
PH range: 7.0-8.0
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.4 Mphosphate1reservoir
20.25-0.5 %PEG10001reservoir
32 mMmethotrexate1reservoir
410 mg/mlprotein1drop
50.1 Mphosphate1drop

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Jan 1, 1990 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 10496 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 18.2
Reflection shellResolution: 2.55→2.71 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 2.4 / % possible all: 89
Reflection shell
*PLUS
% possible obs: 88 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
XENGENdata reduction
XENGENdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SUPERPOSITION OF 7 MODELS: 4DFR, 5DFR, 6DFR, 7DFR, 8DFR, 3DFR, MODELED HV-DHFR

4dfr

5dfr

6dfr

7dfr

8dfr

3dfr


Resolution: 2.55→7 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2
Details: THE R-VALUE WITHOUT INCLUDING THE DATA THAT WAS RESERVED FOR THE FREE R CALCULATION THROUGHOUT IS 0.180.
RfactorNum. reflection% reflectionSelection details
Rfree0.3 794 10 %RANDOM
Rwork0.184 ---
obs0.184 7800 75 %-
Displacement parametersBiso mean: 26 Å2
Refinement stepCycle: LAST / Resolution: 2.55→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2406 0 15 80 2501
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.013
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.3
Solvent computation
*PLUS
Displacement parameters
*PLUS

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