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- PDB-3ql0: Crystal structure of N23PP/S148A mutant of E. coli dihydrofolate ... -

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Basic information

Entry
Database: PDB / ID: 3ql0
TitleCrystal structure of N23PP/S148A mutant of E. coli dihydrofolate reductase
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP binding
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
FOLIC ACID / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Dihydrofolate reductase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBhabha, G. / Ekiert, D.C. / Wright, P.E. / Wilson, I.A.
CitationJournal: Science / Year: 2011
Title: A dynamic knockout reveals that conformational fluctuations influence the chemical step of enzyme catalysis.
Authors: Bhabha, G. / Lee, J. / Ekiert, D.C. / Gam, J. / Wilson, I.A. / Dyson, H.J. / Benkovic, S.J. / Wright, P.E.
History
DepositionFeb 2, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 12, 2014Group: Structure summary
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif / 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.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)19,3376
Polymers18,0831
Non-polymers1,2545
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.662, 79.662, 71.464
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-159-

ARG

21A-159-

ARG

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Components

#1: Protein Dihydrofolate reductase


Mass: 18083.469 Da / Num. of mol.: 1 / Mutation: N23PP, S148A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: UTI89 / UPEC / Gene: folA, UTI89_C0054 / Production host: Escherichia coli (E. coli) / References: UniProt: Q1RGF0, 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-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 3.62 Å3/Da / Density % sol: 66.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M calcium acetate, 0.1 M HEPES, 40% v/v PEG 400, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: double crystal monochromator and K-B pair of biomorph mirrors for vertical and horizontal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 35695 / Num. obs: 35547 / % possible obs: 99.6 %
Reflection shellResolution: 1.6→1.642 Å / % possible all: 97.6

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
XPREPdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→49.63 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.663 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24534 1639 5 %RANDOM
Rwork0.20849 ---
obs0.21029 31133 93.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.373 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20.14 Å2-0 Å2
2--0.28 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.6→49.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 83 199 1555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221457
X-RAY DIFFRACTIONr_bond_other_d0.0020.02970
X-RAY DIFFRACTIONr_angle_refined_deg1.5392.0281999
X-RAY DIFFRACTIONr_angle_other_deg0.88632361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3345168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.15323.7564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.26615224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2571510
X-RAY DIFFRACTIONr_chiral_restr0.0860.2208
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211596
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02277
X-RAY DIFFRACTIONr_mcbond_it0.5891.5844
X-RAY DIFFRACTIONr_mcbond_other0.171.5331
X-RAY DIFFRACTIONr_mcangle_it1.07521376
X-RAY DIFFRACTIONr_scbond_it1.8893613
X-RAY DIFFRACTIONr_scangle_it3.0824.5622
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 115 -
Rwork0.293 2320 -
obs--95.9 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.2157-0.3416-0.93240.96940.15131.46040.04740.11760.0281-0.0482-0.0109-0.00910.0278-0.0116-0.03650.02-0.00470.00320.02620.00180.0022-2.50536.25785.5608
24.6111-0.8265-0.31210.7455-0.22862.626-0.02680.2691-0.4275-0.00650.03440.16720.2903-0.1558-0.00770.0508-0.04650.0020.0912-0.01680.057-16.255830.78268.828
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 102
2X-RAY DIFFRACTION2A103 - 160

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