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- PDB-5fda: The high resolution structure of apo form dihydrofolate reductase... -

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Basic information

Entry
Database: PDB / ID: 5fda
TitleThe high resolution structure of apo form dihydrofolate reductase from Yersinia pestis at 1.55 A
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center For Structural Genomics Of Infectious Diseases / CSGID / Dihydrofolate Reductase / Yersinia pestis
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 / metal ion binding / cytosol
Similarity search - Function
Dihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / Dihydrofolate reductase / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Dihydrofolate reductase
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.549 Å
AuthorsChang, C. / Maltseva, N. / Kim, Y. / Makowska-Grzyska, M. / Mulligan, R. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: structure of dihydrofolate reductase from Yersinia pestis complex with
Authors: Chang, C. / Maltseva, N. / Kim, Y. / Makowska-Grzyska, M. / Mulligan, R. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 15, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2018Group: Database references / Derived calculations / Category: citation_author / pdbx_struct_oper_list
Item: _citation_author.name / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 15, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7854
Polymers18,6791
Non-polymers1063
Water3,369187
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area560 Å2
ΔGint-26 kcal/mol
Surface area8900 Å2
2
A: Dihydrofolate reductase
hetero molecules

A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5718
Polymers37,3582
Non-polymers2136
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area2460 Å2
ΔGint-32 kcal/mol
Surface area15970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.265, 79.201, 64.321
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-201-

CL

21A-202-

CL

31A-203-

CL

41A-304-

HOH

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Components

#1: Protein Dihydrofolate reductase


Mass: 18678.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: folA, AK38_2080 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: A0A0B6NYF5, UniProt: A0A3N4BLI0*PLUS, dihydrofolate reductase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.12 Å3/Da / Density % sol: 42.11 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.5 / Details: 0.1 M Sodium Acetate, 3.0 M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.549→50 Å / Num. obs: 22728 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 12.97 Å2 / Rmerge(I) obs: 0.046 / Rpim(I) all: 0.018 / Rrim(I) all: 0.05 / Χ2: 0.957 / Net I/av σ(I): 42.923 / Net I/σ(I): 16 / Num. measured all: 166938
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.55-1.583.90.68810850.7330.3910.7960.87398
1.58-1.614.70.60911400.8160.3130.6870.91299.7
1.61-1.645.80.59410890.8640.2680.6530.916100
1.64-1.676.70.49911430.9120.2070.5410.94100
1.67-1.717.50.44411040.9410.1720.4770.941100
1.71-1.757.90.35911240.9690.1360.3840.939100
1.75-1.797.90.28911340.9730.1090.3090.968100
1.79-1.847.90.20511370.9810.0770.2190.974100
1.84-1.897.90.15711300.9880.0590.1680.974100
1.89-1.957.90.11211080.9920.0420.120.903100
1.95-2.027.90.08811250.9940.0330.0940.903100
2.02-2.17.90.06911340.9960.0260.0740.843100
2.1-2.280.05911500.9960.0220.0630.893100
2.2-2.327.90.04511340.9970.0170.0480.827100
2.32-2.4680.03911310.9970.0150.0420.776100
2.46-2.657.90.03611420.9980.0140.0390.828100
2.65-2.927.90.03411560.9980.0130.0370.984100
2.92-3.347.90.03711500.9980.0140.041.43199.9
3.34-4.217.70.02911760.9980.0110.0321.186100
4.21-507.30.02812360.9970.0110.031.04699.7

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
MOLREPphasing
Cootmodel building
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q1H

3q1h


Resolution: 1.549→47.96 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1942 1113 5 %
Rwork0.1568 --
obs0.1587 22259 97.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.549→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1272 0 3 187 1462
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091365
X-RAY DIFFRACTIONf_angle_d0.9731861
X-RAY DIFFRACTIONf_dihedral_angle_d18.538816
X-RAY DIFFRACTIONf_chiral_restr0.063197
X-RAY DIFFRACTIONf_plane_restr0.006249
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5486-1.61910.27531200.19552187X-RAY DIFFRACTION83
1.6191-1.70450.23851250.1632669X-RAY DIFFRACTION100
1.7045-1.81130.21021420.14662662X-RAY DIFFRACTION100
1.8113-1.95110.18591370.1392693X-RAY DIFFRACTION100
1.9511-2.14750.16141420.13352694X-RAY DIFFRACTION100
2.1475-2.45820.19851520.14342682X-RAY DIFFRACTION100
2.4582-3.0970.21031620.16762712X-RAY DIFFRACTION100
3.097-47.98260.1761330.16572847X-RAY DIFFRACTION100

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