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- PDB-10uh: Crystal structure of Formyl-coenzyme A transferase from Brucella ... -

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Basic information

Entry
Database: PDB / ID: 10uh
TitleCrystal structure of Formyl-coenzyme A transferase from Brucella melitensis in complex with CoA
ComponentsFormyl-coenzyme a transferase
KeywordsTRANSFERASE / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE / Formyl-coenzyme A transferase
Function / homology
Function and homology information


Transferases; Transferring sulfur-containing groups; CoA-transferases / CoA-transferase activity
Similarity search - Function
: / CoA-transferase family III / CoA-transferase family III domain 1 superfamily / CoA-transferase family III domain 3 superfamily / CoA-transferase family III
Similarity search - Domain/homology
ACETATE ION / COENZYME A / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Formyl-coenzyme a transferase
Similarity search - Component
Biological speciesBrucella melitensis 16M1W (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93022C00036 United States
National Institutes of Health/Office of the DirectorS10OD030394 United States
CitationJournal: To be published
Title: Crystal structure of Formyl-coenzyme A transferase from Brucella melitensis in complex with CoA
Authors: Liu, L. / Lovell, S. / Cooper, A. / Battaile, K.P.
History
DepositionFeb 9, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formyl-coenzyme a transferase
B: Formyl-coenzyme a transferase
C: Formyl-coenzyme a transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,91718
Polymers132,3043
Non-polymers3,61315
Water12,629701
1
A: Formyl-coenzyme a transferase
B: Formyl-coenzyme a transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,59712
Polymers88,2032
Non-polymers2,39410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18220 Å2
ΔGint-56 kcal/mol
Surface area26540 Å2
MethodPISA
2
C: Formyl-coenzyme a transferase
hetero molecules

C: Formyl-coenzyme a transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,64112
Polymers88,2032
Non-polymers2,43810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area17760 Å2
ΔGint-71 kcal/mol
Surface area27310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.054, 176.355, 213.183
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-791-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Formyl-coenzyme a transferase


Mass: 44101.301 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis 16M1W (bacteria) / Gene: BMEII0224 / Plasmid: BrmeA.18114.b.B2 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q8YDF2, Transferases; Transferring sulfur-containing groups; CoA-transferases

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Non-polymers , 6 types, 716 molecules

#2: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H36N7O16P3S / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 701 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 3.38 Å3/Da / Density % sol: 63.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Index G7: 0.20M Ammonium Acetate, 0.1M Bis-Tris pH 6.5, 20% PEG 3350. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. Cocrystallization with 2mM CoA. plate 19820 G7 drop 2, Puck: PSL-1916, Cryo: 20% ...Details: Index G7: 0.20M Ammonium Acetate, 0.1M Bis-Tris pH 6.5, 20% PEG 3350. BrmeA.18114.b.B2.PW39356 at 20.7 mg/mL. Cocrystallization with 2mM CoA. plate 19820 G7 drop 2, Puck: PSL-1916, Cryo: 20% PEG 200 + 80% crystallant

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 19-ID / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: Apr 5, 2025
RadiationMonochromator: Double Crystal Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.85→48.68 Å / Num. obs: 151962 / % possible obs: 99.9 % / Redundancy: 13.4 % / CC1/2: 0.996 / Rmerge(I) obs: 0.155 / Rpim(I) all: 0.044 / Rrim(I) all: 0.161 / Χ2: 1.43 / Net I/σ(I): 17.1 / Num. measured all: 2034117
Reflection shellResolution: 1.85→1.9 Å / % possible obs: 100 % / Redundancy: 14 % / Rmerge(I) obs: 1.726 / Num. measured all: 156594 / Num. unique obs: 11162 / CC1/2: 0.738 / Rpim(I) all: 0.476 / Rrim(I) all: 1.791 / Χ2: 0.94 / Net I/σ(I) obs: 1.7

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Processing

Software
NameVersionClassification
PHENIX(2.0_5936: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→48.68 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 20.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1912 7609 5.01 %
Rwork0.1746 --
obs0.1754 151872 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9117 0 231 701 10049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039631
X-RAY DIFFRACTIONf_angle_d0.59413081
X-RAY DIFFRACTIONf_dihedral_angle_d17.4923711
X-RAY DIFFRACTIONf_chiral_restr0.0451456
X-RAY DIFFRACTIONf_plane_restr0.0061697
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.870.37482810.32454723X-RAY DIFFRACTION100
1.87-1.890.3322800.29684763X-RAY DIFFRACTION100
1.89-1.920.29972540.26694760X-RAY DIFFRACTION100
1.92-1.940.25932600.24454765X-RAY DIFFRACTION100
1.94-1.970.25572510.234791X-RAY DIFFRACTION100
1.97-1.990.24842420.2114777X-RAY DIFFRACTION100
1.99-2.020.22442220.20744793X-RAY DIFFRACTION100
2.02-2.050.23612070.20594825X-RAY DIFFRACTION100
2.05-2.080.2432470.20714799X-RAY DIFFRACTION100
2.08-2.120.21752270.20284780X-RAY DIFFRACTION100
2.12-2.150.22362750.20654726X-RAY DIFFRACTION100
2.15-2.190.23822740.19754754X-RAY DIFFRACTION100
2.19-2.240.23032390.19064829X-RAY DIFFRACTION100
2.24-2.280.20982300.1834811X-RAY DIFFRACTION100
2.28-2.330.2112660.18194807X-RAY DIFFRACTION100
2.33-2.390.2192220.17274813X-RAY DIFFRACTION100
2.39-2.440.17862120.17044821X-RAY DIFFRACTION100
2.44-2.510.19452440.17284825X-RAY DIFFRACTION100
2.51-2.580.16742710.17334776X-RAY DIFFRACTION100
2.58-2.670.20272480.17414792X-RAY DIFFRACTION100
2.67-2.760.19832920.18824766X-RAY DIFFRACTION100
2.76-2.870.20662410.19364841X-RAY DIFFRACTION100
2.87-30.2132500.1954810X-RAY DIFFRACTION100
3-3.160.21842820.18834815X-RAY DIFFRACTION100
3.16-3.360.22372670.18614828X-RAY DIFFRACTION100
3.36-3.620.17972610.17594832X-RAY DIFFRACTION100
3.62-3.990.16232880.14694837X-RAY DIFFRACTION100
3.99-4.560.13992320.13484895X-RAY DIFFRACTION100
4.56-5.740.14862720.14534861X-RAY DIFFRACTION99
5.75-48.680.16042720.15415048X-RAY DIFFRACTION99
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)
14.4198-0.33430.27323.45220.33992.1831-0.07430.02280.24440.0826-0.0044-0.0385-0.3083-0.14370.09710.24560.0178-0.01670.1848-0.00350.1856-42.8984-10.1702-15.0129
22.16170.4694-0.99314.1088-1.39811.01020.01890.10050.1242-0.0793-0.02170.2806-0.0547-0.1963-0.01660.27240.045-0.00740.2927-0.05070.2614-53.5503-9.6474-12.9609
34.8680.4902-0.23328.5238-0.30393.44160.08910.25390.3841-0.3643-0.1385-0.092-0.4751-0.08140.06920.28420.05460.05520.25620.06170.1741-41.6546-2.0823-25.5531
40.65120.3560.04644.7397-0.53431.36670.13320.21020.0175-0.4857-0.07980.0689-0.0182-0.2175-0.04420.34420.0547-0.00440.35320.03930.2523-42.2878-11.2752-31.9727
51.9288-2.1975-0.18245.1274-0.17113.5950.07850.0222-0.265-0.153-0.14480.48650.2229-0.29660.05530.1889-0.0229-0.04960.322-0.08370.3171-55.8403-34.4924-23.2003
61.11990.1855-0.00441.4805-0.24360.4931-0.01850.0981-0.0667-0.1849-0.0870.04920.088-0.0310.09240.22550.01520.00850.2731-0.02650.2264-40.8375-31.7793-22.6308
77.1884-2.8256-4.05386.17460.46557.0197-0.1775-0.3785-0.27850.0202-0.0011-0.59120.65380.45850.16030.2541-0.0009-0.00810.29720.04490.416-43.2589-55.8645-4.3277
82.23230.4056-1.12683.66160.4016.6158-0.1115-0.1192-0.4182-0.2102-0.0499-0.10320.48960.06670.16180.2768-0.00730.05630.21290.04090.4544-46.9441-56.6657-6.7195
90.6028-0.07110.44444.1341-0.71770.3976-0.0384-0.21640.04770.7293-0.08590.1403-0.224-0.13960.13050.3747-0.02980.05360.3674-0.0260.2595-47.6409-29.30441.0821
101.6402-1.9352-1.13154.80610.50191.2677-0.1996-0.12870.23190.53370.0876-0.142-0.21040.05350.11560.3365-0.0108-0.0420.2662-0.03330.2164-43.7668-12.9412-3.7876
115.003-1.18190.27565.3364-1.12631.81610.3513-0.09030.64450.3838-0.1237-0.0634-0.9057-0.1449-0.21970.51250.04550.06110.251-0.02840.3501-47.78218.2402-13.9862
122.73490.9882-0.83035.2761-0.63891.77450.0109-0.0754-0.0955-0.0695-0.1172-0.25660.20220.21510.12590.20150.060.00490.28590.01070.2426-26.0649-35.4667-19.5559
130.7812-0.48460.25290.50470.44621.0797-0.0464-0.0874-0.10770.22150.0298-0.25260.28430.13110.01350.29770.0383-0.03030.28810.03110.3223-25.2053-38.6559-10.3751
144.2996-2.5024-0.18923.9316-0.00593.6819-0.01310.1104-0.23340.1854-0.04260.39590.0883-0.44250.03140.2198-0.05770.04530.2838-0.03550.2983-53.4117-38.2116-11.7737
151.47710.03440.14421.0056-0.0370.43490.00350.0115-0.02020.1001-0.08150.09140.0409-0.03970.07810.1940.0009-0.00260.2221-0.0220.1962-45.0124-25.2059-11.8147
166.7971-1.69682.02364.70833.15187.5989-0.04190.11110.7762-0.74790.0241-0.0902-0.7897-0.21190.01590.35250.0249-0.03720.32530.01070.3903-68.665-19.2587-30.999
172.93390.0113-0.46884.17572.10226.5310.0024-0.09720.2381-0.3577-0.13620.4163-0.3055-0.37280.13640.20670.0434-0.07140.3005-0.03830.3763-70.4956-21.9763-28.641
184.0079-1.6471-1.00552.1608-0.24780.47970.19640.6431-0.1302-0.4665-0.29560.05230.1987-0.0030.08410.44490.0623-0.02330.3957-0.08150.2476-41.7466-34.8784-35.375
192.5426-1.67941.01523.58660.16021.5960.29270.3952-0.1057-0.3731-0.1708-0.40560.31160.4086-0.0380.29410.06990.10280.43190.01350.3288-18.8321-40.1185-24.909
204.26421.0512-0.1743.28840.30141.1703-0.2911-0.05760.3523-0.09480.01470.2005-0.1107-0.24430.28820.32620.0304-0.0630.2685-0.02410.2115-15.2621-47.1922-52.0593
213.8905-1.02450.90664.2369-1.72491.7115-0.35520.0799-0.10490.06630.13220.13760.0652-0.05040.21160.3359-0.01640.06070.2922-0.06430.2343-21.832-55.8015-50.3723
228.4643-4.04920.25035.5228-1.99123.2045-0.20620.266-0.0053-0.12050.09790.09370.04450.03060.16670.2976-0.0317-0.08190.25880.06720.2133-20.966-41.5512-62.9495
232.925-2.42520.24413.3078-0.13640.7858-0.13430.4317-0.0488-0.2016-0.04320.2760.1738-0.14570.19260.4668-0.1054-0.10630.38070.03760.3007-12.9584-47.3317-68.964
248.3149-2.3141-0.44442.92610.72023.8142-0.3890.0689-0.5842-0.02370.1982-0.00240.23080.06130.16150.44-0.07970.12110.2137-0.0450.2843-1.7938-71.5499-59.1494
250.9466-0.18790.13191.583-0.32210.3917-0.21060.09940.0434-0.18580.0366-0.14770.0875-0.00720.16860.386-0.02710.01110.28630.01750.24524.2097-57.3225-58.4931
262.29032.7781-1.3856.4696-3.01096.18480.1227-0.30450.07740.2797-0.2086-0.52250.03670.63250.09580.31240.06420.04030.3070.03770.371221.2483-72.9668-38.1787
272.2820.2732-1.82623.6417-1.56866.6923-0.1138-0.0522-0.1546-0.127-0.2353-0.4170.23270.36820.37670.32220.07250.05670.28830.08420.412220.337-76.2944-40.6621
281.8452-0.470.16720.87150.0043-0.0207-0.376-0.4960.00320.34690.19870.0274-0.0114-0.10490.18630.52120.11180.0220.4243-0.01590.2627-8.9701-55.5974-37.9073
297.04320.09282.02237.7176-0.26555.2264-0.4131-0.22210.08910.31830.63671.0264-0.2876-0.9336-0.19870.33440.1269-0.02340.44910.03310.427-33.4131-41.4101-51.9812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 48 through 94 )
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 124 )
3X-RAY DIFFRACTION3chain 'A' and (resid 125 through 148 )
4X-RAY DIFFRACTION4chain 'A' and (resid 149 through 187 )
5X-RAY DIFFRACTION5chain 'A' and (resid 188 through 214 )
6X-RAY DIFFRACTION6chain 'A' and (resid 215 through 288 )
7X-RAY DIFFRACTION7chain 'A' and (resid 289 through 317 )
8X-RAY DIFFRACTION8chain 'A' and (resid 318 through 358 )
9X-RAY DIFFRACTION9chain 'A' and (resid 359 through 388 )
10X-RAY DIFFRACTION10chain 'A' and (resid 389 through 420 )
11X-RAY DIFFRACTION11chain 'A' and (resid 421 through 450 )
12X-RAY DIFFRACTION12chain 'B' and (resid 48 through 95 )
13X-RAY DIFFRACTION13chain 'B' and (resid 96 through 187 )
14X-RAY DIFFRACTION14chain 'B' and (resid 188 through 214 )
15X-RAY DIFFRACTION15chain 'B' and (resid 215 through 287 )
16X-RAY DIFFRACTION16chain 'B' and (resid 288 through 317 )
17X-RAY DIFFRACTION17chain 'B' and (resid 318 through 358 )
18X-RAY DIFFRACTION18chain 'B' and (resid 359 through 397 )
19X-RAY DIFFRACTION19chain 'B' and (resid 398 through 450 )
20X-RAY DIFFRACTION20chain 'C' and (resid 48 through 94 )
21X-RAY DIFFRACTION21chain 'C' and (resid 95 through 124 )
22X-RAY DIFFRACTION22chain 'C' and (resid 125 through 148 )
23X-RAY DIFFRACTION23chain 'C' and (resid 149 through 187 )
24X-RAY DIFFRACTION24chain 'C' and (resid 188 through 214 )
25X-RAY DIFFRACTION25chain 'C' and (resid 215 through 287 )
26X-RAY DIFFRACTION26chain 'C' and (resid 288 through 317 )
27X-RAY DIFFRACTION27chain 'C' and (resid 318 through 358 )
28X-RAY DIFFRACTION28chain 'C' and (resid 359 through 420 )
29X-RAY DIFFRACTION29chain 'C' and (resid 421 through 450 )

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