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- PDB-6mth: E. coli DHFR complex modeled with three ligand states -

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Basic information

Entry
Database: PDB / ID: 6mth
TitleE. coli DHFR complex modeled with three ligand states
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / complex
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
DIHYDROFOLIC ACID / (6S)-5,6,7,8-TETRAHYDROFOLATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsCao, H. / Rodrigues, J. / Benach, J. / Frommelt, A. / Morisco, L. / Koss, J. / Shakhnovich, E. / Skolnick, J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM118039 United States
CitationJournal: Struct Dyn. / Year: 2019
Title: Time-resolved x-ray crystallography capture of a slow reaction tetrahydrofolate intermediate.
Authors: Cao, H. / Skolnick, J.
History
DepositionOct 19, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
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_alt_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,38611
Polymers18,8481
Non-polymers1,53810
Water3,603200
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.050, 51.666, 79.014
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: 18848.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: folA, tmrA, b0048, JW0047 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ4, dihydrofolate reductase

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Non-polymers , 5 types, 210 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H23N7O6
#5: Chemical ChemComp-DHF / DIHYDROFOLIC ACID


Mass: 443.413 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H21N7O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 200 / 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: 1.84 Å3/Da / Density % sol: 33.29 %
Description: rectangular blocks, with longest dimension of 0.3-0.8mm
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 mg/ml protein working stock was prepared from 2:1 v/v mixing of 30mg/ml protein in 20mM Tris pH 8, 1mM DTT and 50mM HEPES pH 7.3, 100mM NaCl. Then the working protein stock at 20 mg/ml is ...Details: 20 mg/ml protein working stock was prepared from 2:1 v/v mixing of 30mg/ml protein in 20mM Tris pH 8, 1mM DTT and 50mM HEPES pH 7.3, 100mM NaCl. Then the working protein stock at 20 mg/ml is mixed at 1:1 v/v ratio with reservoir solution of 0.1M MES pH 6.5, 30% PEG3350, 0.4M MgCl2
Temp details: room temperature 20-22 oC

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jul 10, 2018 / Details: Diamond(111)
RadiationMonochromator: Kohzu HLD-4 Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.21→31.27 Å / Num. obs: 56495 / % possible obs: 81.6 % / Redundancy: 5.823 % / Biso Wilson estimate: 14.04 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.1 / Rrim(I) all: 0.11 / Χ2: 0.888 / Net I/σ(I): 9.44
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.21-1.281.8962.1540.3915950.2052.89323.2
1.28-1.372.6751.6220.6642520.2222.02265
1.37-1.483.9521.0821.3156500.4941.24993.2
1.48-1.626.7990.6043.4756150.8740.655100
1.62-1.817.2370.3266.3450750.9670.351100
1.81-2.097.2650.13412.6745210.9940.145100
2.09-2.567.2540.07920.0538480.9960.085100
2.56-3.627.1530.0626.7330490.9970.065100
3.62-31.276.6720.05531.317720.9940.0699.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CW7

6cw7


Resolution: 1.35→31.27 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.85
RfactorNum. reflection% reflection
Rfree0.1902 3667 6.5 %
Rwork0.1672 --
obs0.1687 56412 95.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.18 Å2 / Biso mean: 21.23 Å2 / Biso min: 8.58 Å2
Refinement stepCycle: final / Resolution: 1.35→31.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1275 0 164 200 1639
Biso mean--27.48 32.54 -
Num. residues----159
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071505
X-RAY DIFFRACTIONf_angle_d1.3152061
X-RAY DIFFRACTIONf_chiral_restr0.07207
X-RAY DIFFRACTIONf_plane_restr0.006270
X-RAY DIFFRACTIONf_dihedral_angle_d13.084540
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 26

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.3501-1.36780.33241000.36211406150666
1.3678-1.38660.37781060.35421521162772
1.3866-1.40640.35361130.3391658177177
1.4064-1.42740.35631310.3231798192985
1.4274-1.44970.30961310.31691885201688
1.4497-1.47340.37571390.28842053219294
1.4734-1.49880.29051390.28642019215897
1.4988-1.52610.2881440.256921172261100
1.5261-1.55540.26351510.235921472298100
1.5554-1.58720.23531450.211821182263100
1.5872-1.62170.21791560.201421482304100
1.6217-1.65940.20921490.194420892238100
1.6594-1.70090.25851440.19721402284100
1.7009-1.74690.23041490.197421132262100
1.7469-1.79830.22111480.175321312279100
1.7983-1.85630.20481500.175721182268100
1.8563-1.92270.20521440.161321452289100
1.9227-1.99960.18681510.153121492300100
1.9996-2.09060.16831500.141720972247100
2.0906-2.20080.19231470.137621292276100
2.2008-2.33870.15321480.13821122260100
2.3387-2.51920.17331440.145721392283100
2.5192-2.77250.13651440.146521392283100
2.7725-3.17340.16051460.146221332279100
3.1734-3.99690.13631450.122221242269100
3.9969-31.27840.1761530.146421172270100

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