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- PDB-5tgd: Crystal structure of FolM Alternative dihydrofolate reductase 1 f... -

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Basic information

Entry
Database: PDB / ID: 5tgd
TitleCrystal structure of FolM Alternative dihydrofolate reductase 1 from Brucella suis in complex with NADP
ComponentsFolM Alternative dihydrofolate reductase
KeywordsOXIDOREDUCTASE / SSGCID / short chain dehydrogenase/reductase family / dihydrofolate reductase / NADP / Brucella suis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homologyNAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / :
Function and homology information
Biological speciesBrucella suis 92/29 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: Crystal structures of FolM alternative dihydrofolate reductase 1 from Brucella suis and Brucella canis.
Authors: Porter, I. / Neal, T. / Walker, Z. / Hayes, D. / Fowler, K. / Billups, N. / Rhoades, A. / Smith, C. / Smith, K. / Staker, B.L. / Dranow, D.M. / Mayclin, S.J. / Subramanian, S. / Edwards, T.E. ...Authors: Porter, I. / Neal, T. / Walker, Z. / Hayes, D. / Fowler, K. / Billups, N. / Rhoades, A. / Smith, C. / Smith, K. / Staker, B.L. / Dranow, D.M. / Mayclin, S.J. / Subramanian, S. / Edwards, T.E. / Myler, P.J. / Asojo, O.A.
History
DepositionSep 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2 / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Oct 4, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FolM Alternative dihydrofolate reductase
B: FolM Alternative dihydrofolate reductase
C: FolM Alternative dihydrofolate reductase
D: FolM Alternative dihydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,08913
Polymers118,7754
Non-polymers3,3149
Water13,385743
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19650 Å2
ΔGint-81 kcal/mol
Surface area32060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.350, 76.520, 98.260
Angle α, β, γ (deg.)90.000, 109.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
FolM Alternative dihydrofolate reductase


Mass: 29693.789 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella suis 92/29 (bacteria) / Gene: C062_00524 / Plasmid: BrsuA.00010.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0F6ITS6
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.31 Å3/Da / Density % sol: 48 % / Mosaicity: 0.21 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: MCSG1 A1(272563a1): 20% w/v PEG8000, 100mM HEPES:NaOH pH7.5; 20eg; protein 19mg/mL; icw9-7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 22, 2016
RadiationMonochromator: [111] Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 116233 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.22 % / Biso Wilson estimate: 18.85 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.044 / Net I/σ(I): 19.84
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2% possible all
1.7-1.744.250.4392.870.91598.4
1.74-1.790.3633.490.93998.6
1.79-1.840.2794.460.96598.7
1.84-1.90.2165.820.97798.6
1.9-1.960.1697.380.98598.6
1.96-2.030.1359.170.9999.1
2.03-2.110.10211.820.99499.2
2.11-2.190.08414.440.99599
2.19-2.290.06817.360.99799.4
2.29-2.40.05919.890.99899.2
2.4-2.530.0523.50.99899.4
2.53-2.690.04327.360.99899.5
2.69-2.870.03731.460.99999.3
2.87-3.10.03237.210.99999.4
3.1-3.40.02742.360.99999.7
3.4-3.80.02548.460.99999.6
3.8-4.390.02252.720.99999.5
4.39-5.380.02154.420.99999.7
5.38-7.60.02152.580.99999.8
7.60.01956.410.99996

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.2data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5bt9

5bt9


Resolution: 1.7→50 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.37
RfactorNum. reflection% reflection
Rfree0.1979 1785 1.54 %
Rwork0.1628 --
obs0.1634 116170 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.18 Å2 / Biso mean: 32.1221 Å2 / Biso min: 10.68 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7503 0 214 748 8465
Biso mean--33.51 39.84 -
Num. residues----983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068041
X-RAY DIFFRACTIONf_angle_d0.82811013
X-RAY DIFFRACTIONf_chiral_restr0.051245
X-RAY DIFFRACTIONf_plane_restr0.0061523
X-RAY DIFFRACTIONf_dihedral_angle_d16.5634953
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 (%)
1.7-1.7460.28251530.28168678883199
1.746-1.79730.27681350.26638683881899
1.7973-1.85540.251380.24218733887199
1.8554-1.92170.2281400.22818694883499
1.9217-1.99860.25291390.21748769890899
1.9986-2.08960.24141480.20338746889499
2.0896-2.19970.2431120.18618800891299
2.1997-2.33750.22811250.18238808893399
2.3375-2.5180.1951180.17148853897199
2.518-2.77130.19511420.16198852899499
2.7713-3.17220.20391170.146688939010100
3.1722-3.9960.18211580.12488839041100
3.996-39.63650.15031600.11798993915399
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)
15.1354-0.62080.04623.47750.89273.6190.03070.42170.1949-0.0376-0.0291-0.2031-0.09310.22140.01710.0806-0.03260.02650.28180.05010.168922.98534.052916.2533
20.2662-0.01530.81282.4635-0.99722.8877-0.1870.78380.3465-0.12040.1234-0.1883-0.22720.26740.08740.1735-0.04550.01020.5260.12820.268927.74129.02938.8268
34.4334-0.54172.9791.5648-1.17152.5054-0.17110.9755-0.0063-0.44490.0729-0.18780.30430.18440.15560.2886-0.09490.0360.70480.02660.21721.88712.65153.4084
42.1079-0.80081.31331.8721-0.4840.88940.01920.81230.2823-0.30990.062-0.18360.0355-0.0035-0.05160.2026-0.03650.03260.55910.11130.227212.79033.86596.0063
51.22520.14130.69210.6216-0.50621.9837-0.05540.78550.0921-0.17360.07-0.12590.0467-0.0207-0.01480.1561-0.06050.01260.45910.03730.17787.14820.84639.1759
60.70090.1640.07961.6391-0.16761.6625-0.05220.5110.1551-0.14130.1037-0.1145-0.1113-0.1146-0.05680.1176-0.01260.01970.32050.06260.19535.43534.196314.1157
73.284.0602-2.68386.4657-1.8776.19380.12350.42330.4721-0.16670.0275-0.0724-0.65230.1091-0.03350.26960.00560.06550.21890.12350.33345.894222.867522.8343
82.1651-0.15790.77381.3368-0.45741.6644-0.050.19440.26320.0220.0522-0.0135-0.15090.03030.01090.1188-0.00880.01770.12950.04630.14276.96357.030224.6603
91.4419-0.41560.38381.43920.13940.937-0.15670.5904-0.1305-0.4830.26280.220.0308-0.13430.09890.1708-0.2856-0.25471.2089-0.16590.0796-28.4495-7.2896-3.1316
100.7386-0.23110.61140.97850.11660.62280.0170.8061-0.0017-0.53030.098-0.0506-0.04740.0015-0.04910.3355-0.1297-0.05531.06060.04020.186-16.5903-3.2513-3.949
110.66290.5076-0.26730.411-0.11491.2196-0.12320.73810.0084-0.19570.19680.0584-0.056-0.0605-0.05270.2041-0.07110.00330.6960.01130.1761-12.0622-0.84564.2761
121.9740.5957-0.38780.82360.02271.1739-0.11080.8603-0.1327-0.1880.08980.04760.02060.0213-0.00430.1572-0.0496-0.01290.5417-0.03640.1673-12.9988-3.84418.6445
130.02590.2508-0.07733.69772.20097.8014-0.16690.6662-0.6478-0.06420.0136-0.02770.5269-0.01920.15260.1976-0.03390.05480.3635-0.21940.4409-18.267-22.337215.9644
143.0940.40010.78461.07260.55331.89890.00490.6523-0.1786-0.1342-0.00440.15890.1068-0.083-0.02110.1217-0.02890.0320.3225-0.02510.1297-19.9623-6.839217.0204
157.2428-2.21911.01264.46661.74416.9070.0876-0.19680.48350.0262-0.0392-0.3123-0.41070.38960.01120.09830.0189-0.02070.1779-0.02990.092514.25817.271345.1445
162.79430.99680.83013.03050.04162.30320.0928-0.6025-0.24280.3202-0.0649-0.15710.13740.3675-0.02560.19280.0185-0.05270.3170.04750.169712.9841-0.27151.5739
175.14792.99970.74594.0140.67651.68990.2136-0.4385-0.01240.2128-0.14730.01430.0809-0.1185-0.07390.13680.00920.00530.18740.01880.0811-1.75221.445247.5793
183.45131.9020.71972.46030.96121.69840.0316-0.0337-0.0435-0.00640.0268-0.063-0.0247-0.0096-0.05310.08920.0220.01250.09930.01610.1011-1.95391.382436.6532
192.0045-0.1128-0.05311.36650.47871.9717-0.0142-0.1186-0.5430.40230.0311-0.06590.51690.0949-0.03040.22130.0087-0.00740.16110.05060.27697.3881-10.782434.3056
202.55770.40550.57621.80530.64522.34740.04890.0491-0.16380.0377-0.031-0.07450.11760.0817-0.03590.09650.01960.02840.1333-0.00370.11577.3412-2.674229.4829
216.8434-0.2974-1.75872.58873.14017.0033-0.18780.2968-0.1552-0.3585-0.05440.47520.055-0.35170.28460.1175-0.0106-0.02330.18390.01020.1663-36.5177-5.486632.5932
225.02360.10380.65652.3271-0.08813.1873-0.0076-0.05760.44280.1177-0.00910.1741-0.1736-0.26210.02960.10390.02820.01770.1708-0.00320.2265-41.2871.415434.148
234.0232.66515.16574.0352.40277.14090.4318-0.676-0.42740.4645-0.13-0.0870.3179-0.3584-0.28280.1978-0.01170.00380.2559-0.00990.214-35.1522-3.524343.1096
246.89974.83061.80497.66140.4623.21370.1822-0.2175-0.04480.3431-0.07370.26080.119-0.3053-0.10320.11080.02140.01750.09870.01930.1679-35.3514-10.215738.2539
254.32465.60492.59657.50752.81362.88190.091-0.43370.84650.2048-0.15450.3608-0.27040.0669-0.02720.2148-0.02240.05960.269-0.09140.3563-17.588212.343642.0105
263.72071.8505-0.06341.9139-0.20782.15340.0288-0.1050.04210.0047-0.02670.00510.0342-0.0685-0.00310.07850.04360.00650.11310.00180.121-21.2219-1.840136.4911
272.56360.9712-0.21021.57520.40493.3294-0.02320.08580.0949-0.0368-0.0040.1331-0.097-0.1328-0.01250.06030.0174-0.00160.13950.0120.1335-19.6927-1.043631.1217
284.71021.8887-2.36475.2633-4.63715.3539-0.33920.35641.24460.43450.15110.2524-0.8571-0.0830.06930.32250.0072-0.13250.29020.17810.5935-24.463717.498119.2153
292.27410.57340.21441.91840.45441.3491-0.06060.42850.2434-0.05530.04150.0724-0.139-0.09470.00050.11350.0181-0.00450.2240.06470.1546-22.53143.307220.9947
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 43 )A14 - 43
2X-RAY DIFFRACTION2chain 'A' and (resid 44 through 67 )A44 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 85 )A68 - 85
4X-RAY DIFFRACTION4chain 'A' and (resid 86 through 116 )A86 - 116
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 165 )A117 - 165
6X-RAY DIFFRACTION6chain 'A' and (resid 166 through 207 )A166 - 207
7X-RAY DIFFRACTION7chain 'A' and (resid 208 through 225 )A208 - 225
8X-RAY DIFFRACTION8chain 'A' and (resid 226 through 262 )A226 - 262
9X-RAY DIFFRACTION9chain 'B' and (resid 17 through 68 )B17 - 68
10X-RAY DIFFRACTION10chain 'B' and (resid 69 through 116 )B69 - 116
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 165 )B117 - 165
12X-RAY DIFFRACTION12chain 'B' and (resid 166 through 207 )B166 - 207
13X-RAY DIFFRACTION13chain 'B' and (resid 208 through 225 )B208 - 225
14X-RAY DIFFRACTION14chain 'B' and (resid 226 through 263 )B226 - 263
15X-RAY DIFFRACTION15chain 'C' and (resid 15 through 30 )C15 - 30
16X-RAY DIFFRACTION16chain 'C' and (resid 31 through 85 )C31 - 85
17X-RAY DIFFRACTION17chain 'C' and (resid 86 through 141 )C86 - 141
18X-RAY DIFFRACTION18chain 'C' and (resid 142 through 186 )C142 - 186
19X-RAY DIFFRACTION19chain 'C' and (resid 187 through 225 )C187 - 225
20X-RAY DIFFRACTION20chain 'C' and (resid 226 through 263 )C226 - 263
21X-RAY DIFFRACTION21chain 'D' and (resid 18 through 30 )D18 - 30
22X-RAY DIFFRACTION22chain 'D' and (resid 31 through 67 )D31 - 67
23X-RAY DIFFRACTION23chain 'D' and (resid 68 through 85 )D68 - 85
24X-RAY DIFFRACTION24chain 'D' and (resid 86 through 102 )D86 - 102
25X-RAY DIFFRACTION25chain 'D' and (resid 103 through 116 )D103 - 116
26X-RAY DIFFRACTION26chain 'D' and (resid 117 through 165 )D117 - 165
27X-RAY DIFFRACTION27chain 'D' and (resid 166 through 211 )D166 - 211
28X-RAY DIFFRACTION28chain 'D' and (resid 212 through 225 )D212 - 225
29X-RAY DIFFRACTION29chain 'D' and (resid 226 through 263 )D226 - 263

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