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- PDB-6cw7: E. coli DHFR product complex with (6S)-5,6,7,8-TETRAHYDROFOLATE -

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Basic information

Entry
Database: PDB / ID: 6cw7
TitleE. coli DHFR product complex with (6S)-5,6,7,8-TETRAHYDROFOLATE
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / DHFR / dihydrofolate reductase / tetrahydrofolate / complex
Function / homology
Function and homology information


dihydrofolate metabolic process / dihydrofolate reductase / dihydrofolate reductase activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding / 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
(6S)-5,6,7,8-TETRAHYDROFOLATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli O6:H1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.03 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: Commun Biol / Year: 2018
Title: The crystal structure of a tetrahydrofolate-bound dihydrofolate reductase reveals the origin of slow product release.
Authors: Cao, H. / Gao, M. / Zhou, H. / Skolnick, J.
History
DepositionMar 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 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 4, 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

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Assembly

Deposited unit
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4979
Polymers18,8481
Non-polymers6498
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.861, 51.529, 77.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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 O6:H1 (strain CFT073 / ATCC 700928 / UPEC) (bacteria)
Strain: CFT073 / ATCC 700928 / UPEC / Gene: folA, c0058 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABQ5, dihydrofolate reductase
#2: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N7O6
#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 205 / 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: 33.22 %
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
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Dec 8, 2017 / 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: 1.03→31.057 Å / Num. obs: 65916 / % possible obs: 97.3 % / Redundancy: 6.354 % / Biso Wilson estimate: 10.76 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 12.57
Reflection shellResolution: 1.03→1.09 Å / Redundancy: 3.06 % / Rmerge(I) obs: 1.019 / Mean I/σ(I) obs: 1.01 / % possible all: 84.2

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DFR

7dfr


Resolution: 1.03→31.06 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.73
RfactorNum. reflection% reflection
Rfree0.206 1995 3.03 %
Rwork0.186 --
obs0.186 65896 97.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 16.39 Å2
Refinement stepCycle: LAST / Resolution: 1.03→31.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 39 205 1541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081511
X-RAY DIFFRACTIONf_angle_d1.3872071
X-RAY DIFFRACTIONf_dihedral_angle_d13.331553
X-RAY DIFFRACTIONf_chiral_restr0.074214
X-RAY DIFFRACTIONf_plane_restr0.007277
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0322-1.0580.37261050.37493331X-RAY DIFFRACTION72
1.058-1.08660.31751320.31874281X-RAY DIFFRACTION92
1.0866-1.11860.27671430.27574565X-RAY DIFFRACTION99
1.1186-1.15470.2451440.24024618X-RAY DIFFRACTION100
1.1547-1.1960.26191450.22264648X-RAY DIFFRACTION100
1.196-1.24390.2271450.20824624X-RAY DIFFRACTION100
1.2439-1.30050.19691460.20324648X-RAY DIFFRACTION100
1.3005-1.36910.20861460.1954677X-RAY DIFFRACTION100
1.3691-1.45480.22891460.19174659X-RAY DIFFRACTION100
1.4548-1.56720.20471450.17934693X-RAY DIFFRACTION100
1.5672-1.72480.20491480.17624708X-RAY DIFFRACTION100
1.7248-1.97440.22951470.17394726X-RAY DIFFRACTION100
1.9744-2.48740.1681500.17024770X-RAY DIFFRACTION100
2.4874-31.07110.18651530.16494953X-RAY DIFFRACTION99

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