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- PDB-4p68: Electrostatics of Active Site Microenvironments for E. coli DHFR -

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Basic information

Entry
Database: PDB / ID: 4p68
TitleElectrostatics of Active Site Microenvironments for E. coli DHFR
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / electrostatics / catalysis / DHFR
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
ACETATE ION / METHOTREXATE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.26 Å
AuthorsLiu, C.T. / Layfield, J.P. / Stewart III, R.J. / French, J.B. / Hanoian, P. / Asbury, J.B. / Hammes-Schiffer, S. / Benkovic, S.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM092946 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM056207 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2014
Title: Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase.
Authors: Liu, C.T. / Layfield, J.P. / Stewart, R.J. / French, J.B. / Hanoian, P. / Asbury, J.B. / Hammes-Schiffer, S. / Benkovic, S.J.
History
DepositionMar 22, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Structure summary
Revision 1.2Oct 1, 2014Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.4Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 27, 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_struct_conn_angle / refine_hist / struct_conn
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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)19,3827
Polymers17,9861
Non-polymers1,3966
Water70339
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.132, 42.650, 98.586
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Dihydrofolate reductase


Mass: 17986.205 Da / Num. of mol.: 1 / Mutation: L54(XCN), C85A, C152S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: folA, ECs0051, LF82_0721 / Production host: Escherichia coli (E. coli) / References: UniProt: C3TR70, dihydrofolate reductase

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Non-polymers , 5 types, 45 molecules

#2: Chemical ChemComp-MTX / METHOTREXATE


Mass: 454.439 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / 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: 1.99 Å3/Da / Density % sol: 38.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM calcium acetate, 34% Peg 400, 100 mM Hepes, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 9, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.26→49.29 Å / Num. obs: 6821 / % possible obs: 95.9 % / Redundancy: 5.1 % / Net I/σ(I): 15.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
ADSCdata collection
HKL-2000data scaling
REFMAC5.5.0110refinement
PDB_EXTRACT3.14data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.26→25 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 7.664 / SU ML: 0.191 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.51 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2506 320 4.7 %RANDOM
Rwork0.1911 6501 --
obs0.194 6821 95.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 73.82 Å2 / Biso mean: 25.54 Å2 / Biso min: 12.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.78 Å20 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 2.26→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1234 0 91 39 1364
Biso mean--34.09 37.84 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221361
X-RAY DIFFRACTIONr_bond_other_d0.0050.02877
X-RAY DIFFRACTIONr_angle_refined_deg1.5932.0151856
X-RAY DIFFRACTIONr_angle_other_deg1.1073.0192131
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.795156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.28223.92956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.32915194
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.783157
X-RAY DIFFRACTIONr_chiral_restr0.0990.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211480
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02270
X-RAY DIFFRACTIONr_mcbond_it0.8631.5807
X-RAY DIFFRACTIONr_mcbond_other0.1481.5321
X-RAY DIFFRACTIONr_mcangle_it1.62321288
X-RAY DIFFRACTIONr_scbond_it2.213554
X-RAY DIFFRACTIONr_scangle_it3.6584.5568
LS refinement shellResolution: 2.26→2.32 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.266 12 -
Rwork0.221 426 -
all-438 -
obs--88.13 %

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