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- PDB-4x5h: ecDHFR complexed with folate and NADP+ at 500 MPa -

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Basic information

Entry
Database: PDB / ID: 4x5h
TitleecDHFR complexed with folate and NADP+ at 500 MPa
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity ...methotrexate binding / dihydrofolic acid binding / 10-formyltetrahydrofolate biosynthetic process / response to methotrexate / NADP+ binding / folic acid biosynthetic process / folic acid binding / dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / NADPH binding / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / response to xenobiotic stimulus / response to antibiotic / 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
BETA-MERCAPTOETHANOL / FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsYamada, H. / Watanabe, N. / Nagae, T.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2018
Title: High-pressure protein crystal structure analysis of Escherichia coli dihydrofolate reductase complexed with folate and NADP.
Authors: Nagae, T. / Yamada, H. / Watanabe, N.
History
DepositionDec 5, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 3, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn_type.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)19,5654
Polymers18,3021
Non-polymers1,2633
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.182, 58.636, 38.284
Angle α, β, γ (deg.)90.00, 106.78, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-372-

HOH

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Components

#1: Protein Dihydrofolate reductase


Mass: 18301.619 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0ABQ4, 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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG 6000, imidazole, calcium chloride

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.75 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 18, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.75 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 12674 / % possible obs: 98.5 % / Redundancy: 4.2 % / Net I/σ(I): 27

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data scaling
RefinementResolution: 1.9→36.68 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.649 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.157 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22222 597 4.9 %RANDOM
Rwork0.16018 ---
obs0.16317 11688 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.661 Å2
Baniso -1Baniso -2Baniso -3
1-0.76 Å20 Å20.32 Å2
2---0.06 Å20 Å2
3----0.68 Å2
Refinement stepCycle: 1 / Resolution: 1.9→36.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 81 130 1479
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191389
X-RAY DIFFRACTIONr_bond_other_d0.0010.021248
X-RAY DIFFRACTIONr_angle_refined_deg2.0072.0131899
X-RAY DIFFRACTIONr_angle_other_deg0.8653.0012871
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3285158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72824.06364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.03615211
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.455159
X-RAY DIFFRACTIONr_chiral_restr0.1140.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211547
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02328
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4432.218638
X-RAY DIFFRACTIONr_mcbond_other2.4282.213636
X-RAY DIFFRACTIONr_mcangle_it3.5683.308794
X-RAY DIFFRACTIONr_mcangle_other3.5713.308794
X-RAY DIFFRACTIONr_scbond_it3.9832.919751
X-RAY DIFFRACTIONr_scbond_other3.9812.92752
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3064.1961106
X-RAY DIFFRACTIONr_long_range_B_refined8.60520.9481737
X-RAY DIFFRACTIONr_long_range_B_other8.61120.8651717
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 40 -
Rwork0.209 866 -
obs--99.89 %

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