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- PDB-4ptj: Ensemble model for Escherichia coli dihydrofolate reductase at 277K -

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Basic information

Entry
Database: PDB / ID: 4ptj
TitleEnsemble model for Escherichia coli dihydrofolate reductase at 277K
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD
Function / homologyDihydrofolate Reductase, subunit A / Dihydrofolate Reductase, subunit A / 3-Layer(aba) Sandwich / Alpha Beta / FOLIC ACID / : / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsKeedy, D.A. / van den Bedem, H. / Sivak, D.A. / Petsko, G.A. / Ringe, D. / Wilson, M.A. / Fraser, J.S.
CitationJournal: Structure / Year: 2014
Title: Crystal Cryocooling Distorts Conformational Heterogeneity in a Model Michaelis Complex of DHFR.
Authors: Keedy, D.A. / van den Bedem, H. / Sivak, D.A. / Petsko, G.A. / Ringe, D. / Wilson, M.A. / Fraser, J.S.
History
DepositionMar 10, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 14, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Database references
Revision 1.2Nov 12, 2014Group: Non-polymer description / Structure summary
Revision 1.3Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)19,3465
Polymers18,0511
Non-polymers1,2954
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.299, 45.521, 98.711
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Number of models125

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Components

#1: Protein Dihydrofolate reductase


Mass: 18051.338 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / DH10B / Gene: folA, ECDH10B_0049 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B1XC49, dihydrofolate reductase
#2: Chemical ChemComp-FOL / FOLIC ACID


Mass: 441.397 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H19N7O6
#3: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.13 Å3/Da / Density % sol: 42.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 17% PEG 400, 20 mM imidazole pH 7.0, 125 mM MnCl2 , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 25, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.05→49.4 Å / Num. all: 71782 / Num. obs: 71782 / % possible obs: 98.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 9.9 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 40.8
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 5.2 / Num. unique all: 6984 / % possible all: 97.2

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXmodel building
PHENIX1.8.4-1496refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RX2

1rx2


Resolution: 1.05→49.4 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: Ensemble refinement as implemented in PHENIX
RfactorNum. reflection% reflectionSelection details
Rfree0.1655 3666 -RANDOM
Rwork0.1359 ---
all0.1374 71709 --
obs0.1374 71709 98.24 %-
Refinement stepCycle: LAST / Resolution: 1.05→49.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 82 89 1441
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_deg1.508
X-RAY DIFFRACTIONf_dihedral_angle_d9.05
LS refinement shellResolution: 1.0503→1.0641 Å
RfactorNum. reflection% reflection
Rfree0.2237 135 -
Rwork0.1871 --
obs-2633 95 %

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