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- PDB-5hi6: The high resolution structure of dihydrofolate reductase from Yer... -

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Basic information

Entry
Database: PDB / ID: 5hi6
TitleThe high resolution structure of dihydrofolate reductase from Yersinia pestis complex with methotrexate as closed form
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE / Structural Genomics / Center For Structural Genomics Of Infectious Diseases / CSGID / Dihydrofolate Reductase / Yersinia pestis
Function / homology
Function and homology information


dihydrofolate metabolic process / folic acid metabolic process / glycine biosynthetic process / dihydrofolate reductase / dihydrofolate reductase activity / tetrahydrofolate biosynthetic process / one-carbon metabolic process / NADP 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
: / METHOTREXATE / : / Dihydrofolate reductase
Similarity search - Component
Biological speciesYersinia pestis CO92 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.051 Å
AuthorsChang, C. / Maltseva, N. / Kim, Y. / Makowska-Grzyska, M. / Mulligan, R. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: The high resolution structure of dihydrofolate reductase from Yersinia pestis complex with methotrexate as closed form
Authors: Chang, C. / Maltseva, N. / Kim, Y. / Makowska-Grzyska, M. / Mulligan, R. / Papazisi, L. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2016Group: Database references / Structure summary
Revision 1.2Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 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_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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_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_asym_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_label_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / struct_ref
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2 / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dihydrofolate reductase
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4569
Polymers37,3582
Non-polymers1,0987
Water5,062281
1
A: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2134
Polymers18,6791
Non-polymers5343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2435
Polymers18,6791
Non-polymers5644
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.151, 60.623, 109.942
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, 2 molecules AB

#1: Protein Dihydrofolate reductase /


Mass: 18678.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pestis CO92 (bacteria) / Gene: folA, AK38_2080 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: A0A0B6NYF5, UniProt: A0A3N4BLI0*PLUS, dihydrofolate reductase

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Non-polymers , 5 types, 288 molecules

#2: Chemical ChemComp-MTX / METHOTREXATE / Methotrexate


Mass: 454.439 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22N8O5 / Comment: chemotherapy*YM
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.01 Å3/Da / Density % sol: 38.93 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.2 M Calcium chloride, 0.1M HEPES, 30 % PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9791208 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791208 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. all: 19206 / Num. obs: 19073 / % possible obs: 99.3 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.121 / Rpim(I) all: 0.049 / Rrim(I) all: 0.131 / Χ2: 0.851 / Net I/av σ(I): 15.266 / Net I/σ(I): 9 / Num. measured all: 140157
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.05-2.094.90.5668770.7950.280.6351.03592
2.09-2.125.60.5089120.8690.230.560.81898
2.12-2.166.40.4789150.8870.2050.5210.81998.3
2.16-2.216.90.4349520.8950.1790.4710.84799.7
2.21-2.267.70.429300.9250.160.451.03699.7
2.26-2.317.70.3719360.9360.1430.3980.8399.7
2.31-2.377.70.3159340.9620.1210.3380.79799.9
2.37-2.437.70.259660.9590.0970.2680.806100
2.43-2.57.80.2289350.9720.0870.2450.775100
2.5-2.587.80.199480.9730.0740.2040.77299.9
2.58-2.687.70.1799430.9690.070.1930.85199.5
2.68-2.787.80.159620.9760.0590.1620.81699.9
2.78-2.917.80.1269460.9820.0490.1350.792100
2.91-3.067.80.1079610.9840.0430.1150.812100
3.06-3.257.90.0939630.9870.0370.10.782100
3.25-3.517.80.0899560.9850.0350.0960.86100
3.51-3.867.80.0869720.9840.0340.0920.98100
3.86-4.427.60.08110040.9880.0320.0871.01100
4.42-5.567.40.0769930.9870.030.0820.871100
5.56-5070.0710680.9890.030.0760.78799.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
MOLREPphasing
SBC-Collectdata collection
Cootmodel building
HKL-3000phasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3Q1H

3q1h


Resolution: 2.051→35.689 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 1798 5.19 %
Rwork0.1748 32878 -
obs0.1774 18557 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.81 Å2 / Biso mean: 28.2988 Å2 / Biso min: 6.7 Å2
Refinement stepCycle: final / Resolution: 2.051→35.689 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2543 0 71 281 2895
Biso mean--25.2 34.29 -
Num. residues----322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032717
X-RAY DIFFRACTIONf_angle_d0.5513696
X-RAY DIFFRACTIONf_chiral_restr0.043383
X-RAY DIFFRACTIONf_plane_restr0.003489
X-RAY DIFFRACTIONf_dihedral_angle_d13.4031592
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0513-2.10680.3371060.22592130223680
2.1068-2.16880.24121210.22012295241689
2.1688-2.23880.31331380.20512492263095
2.2388-2.31880.25181520.20342565271799
2.3188-2.41160.30721010.192726422743100
2.4116-2.52130.25921810.182425702751100
2.5213-2.65420.29611640.18525582722100
2.6542-2.82050.23771310.194326182749100
2.8205-3.03810.24891200.193426112731100
3.0381-3.34370.18841370.167426242761100
3.3437-3.8270.17691530.147125932746100
3.827-4.81980.18121540.136525832737100
4.8198-35.69460.20581400.179225972737100
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)
10.36910.013-0.01240.51710.18310.896-0.0522-0.12810.1545-0.0437-0.1727-0.0539-0.0310.045-0.33370.072-0.0253-0.0240.09180.00380.103514.72533.227729.5705
20.04690.1227-0.19440.4527-0.14050.33870.0295-0.09320.08840.10550.00860.0109-0.0644-0.142-00.18780.00710.01080.16730.00580.18817.007630.43743.4953
30.45360.058-0.30460.29210.06720.08310.0224-0.11180.01280.0984-0.0446-0.1347-0.02020.3183-0.00060.1581-0.0257-0.04830.19720.05160.203219.983833.317637.7363
40.61810.1752-0.48770.3201-0.46150.93230.02430.00920.029-0.058-0.257-0.248-0.10830.2952-0.19990.1199-0.0187-0.01480.19930.07260.207323.176736.17225.8007
50.13210.125-0.18350.0856-0.0752-0.00740.1374-0.17530.0524-0.0327-0.0702-0.085-0.12640.15760.01010.12950.00130.00730.14120.04240.111611.07813.366747.6161
60.019-0.00880.10530.1006-0.05170.0438-0.0924-0.34520.1136-0.2167-0.00910.14640.2018-0.2471-00.143-0.0296-0.00190.14060.01210.0794-4.79587.37842.2505
70.0722-0.06250.20640.1099-0.06240.01520.03280.0243-0.0518-0.0266-0.02420.13480.0476-0.0407-0.00380.10610.01830.02040.09160.01530.09553.9211-5.731341.5229
80.1536-0.1101-0.06150.2355-0.15170.3021-0.00260.0473-0.25180.1324-0.0907-0.10030.06180.0824-0.06050.12960.00250.02370.15470.04180.18545.4788-11.243550.6312
90.3691-0.00610.1405-0.00410.04870.05340.0131-0.17980.15550.07970.0226-0.0107-0.03960.01240.00370.14420.0040.00460.12460.00210.09887.59216.786349.96
100.1308-0.1168-0.40590.1069-0.12560.53860.2976-0.0311-0.2273-0.0450.1238-0.0656-0.0350.07660.27870.1394-0.0197-0.00670.1487-0.01480.08711.20811.493637.4715
110.15760.0919-0.1416-0.0164-0.01260.18870.0596-0.11990.12710.0514-0.18880.19310.05780.2953-0.01180.09620.0033-0.03240.1563-0.01640.124615.75298.562642.7679
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 39 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 86 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 87 through 116 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 117 through 160 )A0
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 13 )B0
6X-RAY DIFFRACTION6chain 'B' and (resid 14 through 25 )B0
7X-RAY DIFFRACTION7chain 'B' and (resid 26 through 63 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 64 through 97 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 98 through 130 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 131 through 151 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 152 through 160 )B0

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