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- PDB-3q1h: Crystal Structure of Dihydrofolate Reductase from Yersinia pestis -

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Basic information

Entry
Database: PDB / ID: 3q1h
TitleCrystal Structure of Dihydrofolate Reductase from Yersinia pestis
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / alpha beta fold / cytosol
Function / homology
Function and homology information


dihydrofolate metabolic process / folic acid metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / 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 / Dihydrofolate reductase
Similarity search - Component
Biological speciesYersinia pestis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsMaltseva, 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: Crystal Structure of Dihydrofolate Reductase from Yersinia pestis
Authors: 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 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5433
Polymers18,3511
Non-polymers1922
Water2,936163
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.477, 79.152, 64.685
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-298-

HOH

21A-318-

HOH

31A-319-

HOH

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Components

#1: Protein Dihydrofolate reductase / Dihydrofolate reductase type I


Mass: 18350.652 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: folA, y3688, YPO0486, YP_3693 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): KRXpGro7
References: UniProt: Q7CG83, UniProt: A0A3N4BLI0*PLUS, dihydrofolate reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2M Lithium Sulfate, 0.1M Bis-Tris pH5.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 15, 2010 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 14518 / Num. obs: 14518 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 18.1 Å2 / Rsym value: 0.07 / Net I/σ(I): 12.6
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.88 / Num. unique all: 640 / Rsym value: 0.393 / % possible all: 89

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
BALBESphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDBID 1DDS

1dds


Resolution: 1.804→33.759 Å / SU ML: 0.18 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2 730 5.04 %random
Rwork0.166 ---
all0.167 14493 --
obs0.167 14493 98.94 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.421 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 21.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.471 Å20 Å20 Å2
2--0.1235 Å20 Å2
3---1.3475 Å2
Refinement stepCycle: LAST / Resolution: 1.804→33.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1276 0 10 163 1449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071362
X-RAY DIFFRACTIONf_angle_d1.0571854
X-RAY DIFFRACTIONf_dihedral_angle_d12.934499
X-RAY DIFFRACTIONf_chiral_restr0.079194
X-RAY DIFFRACTIONf_plane_restr0.004246
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.8039-1.94320.2291500.19442579272995
1.9432-2.13870.23641630.1627222885100
2.1387-2.44810.21631340.164127622896100
2.4481-3.08410.22531440.173227952939100
3.0841-33.76460.16231390.158329053044100
Refinement TLS params.Method: refined / Origin x: 15.8425 Å / Origin y: -12.2798 Å / Origin z: 13.0938 Å
111213212223313233
T0.0666 Å2-0.0052 Å20.0004 Å2-0.0725 Å2-0.0016 Å2--0.0476 Å2
L0.2296 °20.2034 °2-0.0271 °2-0.7127 °20.1526 °2--0.1208 °2
S-0.0277 Å °0.0599 Å °0.0016 Å °-0.0576 Å °0.035 Å °0.0359 Å °0.005 Å °-0.0435 Å °-0.0043 Å °
Refinement TLS groupSelection details: chain A

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