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- PDB-7k69: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobact... -

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Basic information

Entry
Database: PDB / ID: 7k69
TitleCrystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001574
ComponentsDihydrofolate reductase
KeywordsOXIDOREDUCTASE/OXIDOREDUCTASE INHIBITOR / SSGCID / SDDC / inhibitor / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / OXIDOREDUCTASE / OXIDOREDUCTASE-OXIDOREDUCTASE INHIBITOR complex
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 / Dihydrofolate reductase conserved site / Dihydrofolate reductase (DHFR) domain signature. / Dihydrofolate reductase domain / Dihydrofolate reductase / Dihydrofolate reductase (DHFR) domain profile. / Dihydrofolate reductase-like domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / SERINE / Chem-VY7 / Dihydrofolate reductase
Similarity search - Component
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal Structure of Dihydrofolate reductase (DHFR) from Mycobacterium ulcerans Agy99 in complex with NADP and inhibitor SDDC-0001574
Authors: Abendroth, J. / Dranow, D.M. / Santhakumar, V. / Walpole, C. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)20,3134
Polymers19,0521
Non-polymers1,2613
Water3,927218
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)28.710, 67.070, 44.110
Angle α, β, γ (deg.)90.000, 91.337, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Dihydrofolate reductase /


Mass: 19051.684 Da / Num. of mol.: 1 / Mutation: E96A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (strain Agy99) (bacteria)
Strain: Agy99 / Gene: dfrA, MUL_2179 / Plasmid: MyulA.01062.a.B12 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0PQG8, dihydrofolate reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


Mass: 743.405 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-VY7 / 1-{2-[2-(2,4-diamino-5,7-dihydro-6H-pyrrolo[3,4-d]pyrimidin-6-yl)-2-oxoethoxy]phenyl}piperidine-4-carboxylic acid


Mass: 412.442 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H24N6O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SER / SERINE / Serine


Type: L-peptide linking / Mass: 105.093 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 218 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.23 Å3/Da / Density % sol: 44.9 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Morpheus screen, condition D2: 112.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM MES/imidazole pH ...Details: Morpheus screen, condition D2: 112.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each sodium L-glutamate, DL-alanine, glycine, DL-lysine HCl, DL-serine: 100mM MES/imidazole pH 6.5: MyulA.01062.a.B12.PS38539 and 15.75mg/ml + 2.5mM NADP and 4mM SDDC compound SDDC-0001574: tray: 317895h4: cryo: direct: puck: xhf8-3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 20986 / % possible obs: 95 % / Redundancy: 6.326 % / Biso Wilson estimate: 21.237 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.03 / Rrim(I) all: 0.033 / Χ2: 0.96 / Net I/σ(I): 35.22
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.6-1.644.2050.2256.4412740.950.25480
1.64-1.694.5030.1897.4613800.9720.21286.2
1.69-1.744.6260.1588.7613910.9820.17790.4
1.74-1.794.7830.13210.5413450.9890.14888.8
1.79-1.854.8650.10313.513370.9920.11592.5
1.85-1.914.970.08416.4313410.9960.09493.4
1.91-1.985.0030.06720.5713190.9970.07499.7
1.98-2.075.1420.05723.912780.9980.06397.3
2.07-2.165.3770.04829.1612450.9980.053100
2.16-2.265.6610.04134.5611980.9990.04599.8
2.26-2.396.5190.0438.7111570.9990.044100
2.39-2.536.9550.03543.6210690.9990.038100
2.53-2.77.3220.03151.2810140.9990.033100
2.7-2.927.8320.02955.539640.9990.032100
2.92-3.28.9060.02568.7487510.027100
3.2-3.5810.9540.02385.4578310.025100
3.58-4.1311.1650.02196.4770310.022100
4.13-5.0611.1370.02199.8858510.02299.8
5.06-7.1610.9030.02490.147210.025100
7.16-5010.4340.023101.6525610.02499.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.25data extraction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: NAD and P218-bound structure, PDB entry 6uww
Resolution: 1.6→44.1 Å / SU ML: 0.1607 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.5376
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1915 2117 10.09 %0
Rwork0.1605 18866 --
obs0.1637 20983 95.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.22 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1232 0 85 218 1535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00861440
X-RAY DIFFRACTIONf_angle_d1.13061996
X-RAY DIFFRACTIONf_chiral_restr0.0585218
X-RAY DIFFRACTIONf_plane_restr0.0088271
X-RAY DIFFRACTIONf_dihedral_angle_d21.2928554
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.640.26111030.21711050X-RAY DIFFRACTION79.63
1.64-1.680.22091280.18421164X-RAY DIFFRACTION86.48
1.68-1.720.20371200.16691156X-RAY DIFFRACTION89.36
1.72-1.770.24541210.17131204X-RAY DIFFRACTION89.47
1.77-1.830.2151340.1681207X-RAY DIFFRACTION91.29
1.83-1.90.20241570.17081186X-RAY DIFFRACTION93.07
1.9-1.970.21211370.16761315X-RAY DIFFRACTION98.17
1.97-2.060.20481390.16591301X-RAY DIFFRACTION97.56
2.06-2.170.17851600.16441315X-RAY DIFFRACTION100
2.17-2.310.20581640.16481293X-RAY DIFFRACTION99.86
2.31-2.490.21481590.17471315X-RAY DIFFRACTION100
2.49-2.740.17231480.16411329X-RAY DIFFRACTION100
2.74-3.130.22511410.16331341X-RAY DIFFRACTION100
3.13-3.940.17681490.14721330X-RAY DIFFRACTION100
3.95-44.10.14891570.13831360X-RAY DIFFRACTION99.93
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.745638477890.172559235433-0.2048735966433.163104054230.1875492465022.25275193237-0.00498658194842-0.2013815684460.07090057382130.158118462944-0.0142686963199-0.14051504819-0.2112954382210.1072432636090.05444544973640.0712998660614-0.020452025985-0.0093246690530.0401848492294-0.01281089222130.09369002167274.902600811770.92303021785516.0966573518
22.20343473671-0.826965741897-0.1410185626112.038940004781.083647080771.72328762086-0.0805835337727-0.2750135029210.291775350134-0.0544134115598-0.1822908903810.269772716176-0.571580799874-0.3346310435550.01476468063160.127228302480.022009030297-0.02016039490640.111047927622-0.04188832965220.127946893406-8.121044766321.8969110936713.6713766646
32.87338187738-1.152309520310.5500945128612.471085813940.06963807636082.68543169447-0.0479568713467-0.185388583783-0.1182815146080.1391189909990.02080721542750.08311822524820.0380796870666-0.1192986421590.0442480871070.0600390535827-0.01679101001180.01263262410190.03559064025230.00226743426060.0805232448298-3.22730117364-10.956482547613.0312895611
44.85107355993-0.876487787295-0.642219476873.074790976030.7917763300382.02038603974-0.1009653884340.266421810907-0.37509548061-0.180444617086-0.042575823926-0.1858052292710.2508073128910.09573848421240.1016480313850.1415552897810.01355452749670.03120923628660.0797591865833-0.02467894286650.1444888552261.9922945797-17.89808245556.08026993628
52.00612593487-0.133101830995-1.196027637885.566792201512.651374297192.55172544038-0.02575541231880.477071958659-0.269369628573-0.954971805775-0.2209689495560.491176821228-0.0143694640095-0.528448648750.2079230011860.217307477396-0.0363454147089-0.06604521320940.176084211142-0.02923968367530.178239424757-2.74129338663-8.23243606550.283096348662
62.29798626341-1.19225861875-0.2814746442242.540721650780.1901697475381.772506429480.04882391166540.1008608059540.0334472094339-0.0787116224034-0.142928044305-0.112979658117-0.1750587245160.08033029403240.07106906358760.0790939601215-0.0232019984359-0.0003187187072230.04930446017830.01598243110250.08900384430735.25718187680.9767601546126.39612628442
76.06760606035-4.99747195597-1.977343549684.392277503481.922058345430.956118792089-0.207922152328-0.9340698814910.8558662780510.2307349495940.672994301669-1.23632381857-0.1443366538130.391688770745-0.4784417253550.174326594416-0.00420036283611-0.05148755791140.277666050031-0.1033603498980.28894640627413.43829498921.5041178011522.7451227248
80.0686728989173-0.1578434751150.5225296312611.12966737804-0.7610915614754.160853103550.05121077905180.1221846352380.245685839629-0.053771750189-0.172071916085-0.290936093341-0.5498463950130.4096150259480.06874112018390.164973356368-0.03665862672380.03051386791520.1273218767620.04019578876180.1562953164128.524984713798.019298520313.5357786786
91.72585022663-0.474459930442-2.506606456610.917775508691.254494978565.505796248540.119073515750.02107525047660.1333586128220.195180450651-0.0861422729717-0.139192391818-0.254718857824-0.196007223643-0.01976266309730.261423875140.00948279000568-0.001871028559390.0847277136244-0.01721704277440.135482788477-0.47750836398911.655233872812.2603621039
102.00000063148-5.75376752928-5.000306736882.000000908381.999998777962.000000394681.18488105133-0.4017810569880.604799917095.04881704848-1.34579706422-0.6720435163930.5902186159650.6747589064890.1340981732670.643679487151-0.0359428152688-0.05888993965030.7451585194870.04385971596850.6231424102117.9218034485910.647980029510.3239660058
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A

IDRefine TLS-IDSelection detailsLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 26 )A3 - 261 - 24
22chain 'A' and (resid 27 through 37 )A27 - 3725 - 35
33chain 'A' and (resid 38 through 62 )A38 - 6236 - 60
44chain 'A' and (resid 63 through 87 )A63 - 8761 - 85
55chain 'A' and (resid 88 through 102 )A88 - 10286 - 100
66chain 'A' and (resid 103 through 122 )A103 - 122101 - 120
77chain 'A' and (resid 123 through 132 )A123 - 132121 - 130
88chain 'A' and (resid 133 through 145 )A133 - 145131 - 143
99chain 'A' and (resid 146 through 165 )A146 - 165144 - 163
1010chain 'A' and (resid 301 through 301 )C3012

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