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- PDB-5d5q: HcgB from Methanocaldococcus jannaschii with the pyridinol derive... -

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Basic information

Entry
Database: PDB / ID: 5d5q
TitleHcgB from Methanocaldococcus jannaschii with the pyridinol derived from FeGP cofactor of [Fe]-hydrogenase
ComponentsUncharacterized protein MJ0488, Guanylyltransferase
KeywordsTRANSFERASE / Guanylyltransferase
Function / homology
Function and homology information


FeGP cofactor biosynthesis protein HcgB, guanylyltransferase / FeGP cofactor biosynthesis protein HcgB, guanylyltransferase / Helix hairpin bin / B12-dependent dehydatase associated subunit / B12-dependent dehydratases, beta subunit / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-57O / Uncharacterized protein MJ0488
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsFujishiro, T. / Ermler, U. / Shima, S.
Funding support Japan, Germany, 2items
OrganizationGrant numberCountry
JST-PRESTO Japan
Max Planck Society Germany
CitationJournal: Faraday Discuss. / Year: 2017
Title: Towards artificial methanogenesis: biosynthesis of the [Fe]-hydrogenase cofactor and characterization of the semi-synthetic hydrogenase.
Authors: Bai, L. / Fujishiro, T. / Huang, G. / Koch, J. / Takabayashi, A. / Yokono, M. / Tanaka, A. / Xu, T. / Hu, X. / Ermler, U. / Shima, S.
History
DepositionAug 11, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Jun 14, 2017Group: Database references / Structure summary / Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description
Revision 1.3Jan 10, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uncharacterized protein MJ0488, Guanylyltransferase
B: Uncharacterized protein MJ0488, Guanylyltransferase
C: Uncharacterized protein MJ0488, Guanylyltransferase
D: Uncharacterized protein MJ0488, Guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,2748
Polymers75,4854
Non-polymers7894
Water1,00956
1
A: Uncharacterized protein MJ0488, Guanylyltransferase
B: Uncharacterized protein MJ0488, Guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1374
Polymers37,7432
Non-polymers3942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-24 kcal/mol
Surface area14080 Å2
MethodPISA
2
C: Uncharacterized protein MJ0488, Guanylyltransferase
D: Uncharacterized protein MJ0488, Guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,1374
Polymers37,7432
Non-polymers3942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4340 Å2
ΔGint-16 kcal/mol
Surface area14590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.910, 76.500, 65.100
Angle α, β, γ (deg.)90.000, 106.770, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL

Dom-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LEULEUchain AAA3 - 1593 - 159
2SERSERchain BBB3 - 1573 - 157
3LEULEUchain CCC3 - 1593 - 159
4LEULEUchain DDD3 - 1593 - 159

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Components

#1: Protein
Uncharacterized protein MJ0488, Guanylyltransferase / HcgB


Mass: 18871.297 Da / Num. of mol.: 4 / Fragment: Rossmann-like domain, residues 1-158 / Mutation: I2V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Gene: MJ0488 / Plasmid: pET24b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q57912
#2: Chemical
ChemComp-57O / (4,6-dihydroxy-3,5-dimethylpyridin-2-yl)acetic acid


Mass: 197.188 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H11NO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1 M sodium cacodylate (pH 6.5), 20 % (w/v) PEG8000, 0.2 M magnesium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2015
RadiationMonochromator: A double-crystal Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: l,-k,h / Fraction: 0.48
ReflectionResolution: 2.5→50 Å / Num. obs: 20900 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.048 / Rrim(I) all: 0.057 / Χ2: 1.024 / Net I/σ(I): 16.65 / Num. measured all: 69158
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.5-2.60.9390.3383.987981233823310.40199.7
2.6-2.70.9660.2445.346767200019920.2999.6
2.7-2.90.9760.1936.5310488322332130.23299.7
2.9-3.10.990.12110.218499249224740.14499.3
3.1-3.20.9940.08413.8433689769730.09999.7
3.2-3.30.9950.08113.2229798958900.09799.4
3.3-3.50.9950.06714.914726149914840.08199
3.5-3.80.9960.05417.644633169315080.06589.1
3.8-40.9980.0422.828298658370.04796.8
4-4.30.9980.03228.753335102510120.03998.7
4.3-5.90.9980.02833.828367259025550.03498.6
5.9-80.9980.02538.7930459779600.0398.3
8-120.9990.0254.115034694630.02398.7
120.9990.02252.336382152080.02696.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WB0
Resolution: 2.5→48.237 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.81 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.232 1049 5.02 %
Rwork0.2064 19836 -
obs0.2075 20900 98.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.23 Å2 / Biso mean: 61.5988 Å2 / Biso min: 5.4 Å2
Refinement stepCycle: final / Resolution: 2.5→48.237 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4920 0 56 56 5032
Biso mean--45.78 36.24 -
Num. residues----626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065004
X-RAY DIFFRACTIONf_angle_d1.1286690
X-RAY DIFFRACTIONf_chiral_restr0.048804
X-RAY DIFFRACTIONf_plane_restr0.005834
X-RAY DIFFRACTIONf_dihedral_angle_d14.4362014
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2967X-RAY DIFFRACTION10.15TORSIONAL
12B2967X-RAY DIFFRACTION10.15TORSIONAL
13C2967X-RAY DIFFRACTION10.15TORSIONAL
14D2967X-RAY DIFFRACTION10.15TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5009-2.63270.30731490.29812821297095
2.6327-2.79770.32041510.28972869302095
2.7977-3.01360.26371500.25142855300595
3.0136-3.31680.26811510.24382858300995
3.3168-3.79650.25431410.22022676281789
3.7965-4.78220.19871500.15672850300093
4.7822-43.11240.1931530.17272907306094
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)
15.90110.18282.44166.26462.23952.0096-0.35380.74880.4662-0.63890.2296-0.0795-0.45950.98450.16560.418-0.07550.15310.38590.11420.516827.32880.662412.6862
22.55610.65813.97125.19973.76972.2504-0.38260.47550.5449-0.56890.21510.145-0.40040.34810.40540.733-0.16190.05760.47030.11070.481420.1837-1.10471.7746
33.08210.2225-1.30063.1894-2.26999.18520.12330.664-0.3446-0.70730.19990.69350.78550.47970.02421.0038-0.0764-0.09460.3153-0.0510.673510.475-14.5856-6.7302
40.74850.22150.19713.2167-0.62181.4947-0.48830.18360.4673-0.6977-0.0834-0.1645-0.26671.10310.17770.98040.0431-0.1879-1.04680.12040.557110.9915-13.6771.9179
52.28870.14861.43472.2788-0.57351.1415-0.43270.8870.2459-0.709-0.19570.1282-0.1454-0.90760.20291.02460.0859-0.1719-0.32970.13650.61644.3087-6.54660.176
61.9650.87220.09915.04860.15351.3741-0.04080.75950.7373-0.78130.01380.4452-0.3032-0.44050.27581.2867-0.0686-0.4468-0.01050.06440.79827.0702-1.3797-6.6742
73.3616-1.7575-1.09324.75133.49674.10270.1802-0.1929-0.1180.24130.24160.77130.0886-0.7643-0.02470.4977-0.0030.31360.7223-0.06020.5278-6.9075-22.302711.1975
80.293-0.6346-0.63975.09990.99731.68940.3330.12360.23070.0664-0.61520.7475-0.034-1.2650.26810.34970.0185-0.00830.717-0.1890.7252-7.1282-9.21912.7606
96.43795.0327-1.60787.12661.90618.0605-0.8625-0.29842.264-0.4593-0.14561.0971-1.5452-0.48631.09430.64960.0869-0.08610.3725-0.16010.9924-2.78529.059619.8725
107.3663-2.40050.8331.46021.14942.93310.3622-0.3989-0.03360.4321-0.27380.30870.10910.1377-0.1460.7215-0.04980.40170.3287-0.11030.81141.81222.979926.3158
119.90460.4092-8.41365.3482-3.06148.7431-0.0271-0.0615-0.23020.419-0.252-0.13430.33330.18850.270.30290.0530.04880.3709-0.1070.396311.9172-5.067519.8264
129.98383.0146-4.48796.5037-2.66527.9911-0.5506-0.87450.51560.5165-0.48920.9362-1.0872-0.7480.15530.19720.49110.4094-0.6957-0.72350.40042.5396-2.485820.8936
131.9766-0.97771.02226.188-0.43475.5164-0.383-0.28590.1656-0.2549-0.20850.5757-0.2569-0.67170.27980.2055-0.03170.00050.3445-0.08940.44725.6299-4.817613.6292
146.96373.2238-5.50691.5897-2.71244.65240.5102-0.44131.68890.1883-0.31470.9465-0.7790.1549-0.09660.6695-0.0242-0.22230.3461-0.05760.72787.54737.08038.0747
153.5455-1.9611-1.8097.3870.26874.44030.32920.17210.4491-0.0301-0.23830.5873-0.5011-0.1044-0.00930.7870.072-0.21260.3447-0.14520.9637-3.16333.76848.5688
169.18342.8942-2.51454.8161-3.03189.087-0.1241-0.47930.41461.5567-0.0374-0.0533-0.512-0.36560.13270.91820.1144-0.15820.2963-0.02520.573610.3965-6.732634.7744
176.98587.2549-2.1188.8028-3.08522.42830.6077-0.516-0.03571.4059-0.45960.2080.43240.0429-0.15490.9523-0.129-0.12080.30870.00440.69913.1676-14.707338.4078
183.697-0.178-2.37095.4552-0.77765.99010.692-0.2953-0.21280.9842-0.11680.48560.0637-0.3446-0.39990.683-0.18120.15860.42990.03270.7298-0.3295-29.656225.9917
192.40150.2942-0.70374.4947-2.10833.69160.6961-0.2194-0.2570.9311-0.06310.03170.5275-0.2248-0.22460.8675-0.1415-0.04540.2764-0.08280.6933.1491-32.722922.0595
204.05420.3104-0.51011.5492-0.85722.21210.6561-0.1650.01750.5899-0.23750.27720.1775-0.1793-0.36270.6446-0.02590.01650.2397-0.02120.51677.825-25.518319.9179
218.7737-2.7863-0.99326.111-0.77166.33130.5867-0.13510.00620.4222-0.36430.8875-0.1661-0.2896-0.45550.5067-0.13510.1310.3268-0.06820.467210.0735-21.943526.8694
228.5790.8923-2.15427.6465-1.33672.01090.0548-0.2625-1.10660.5213-0.10630.08681.26130.06950.12410.9740.1656-0.34430.1094-0.09490.864921.2872-40.30618.185
234.5727-0.1972-2.30442.3121-0.04384.82220.4676-0.6966-0.96181.1477-0.09880.48971.090.1345-0.05920.8955-0.2243-0.10140.33610.12760.594913.4037-34.44430.9752
242.4581-1.38782.11770.9997-0.76392.28390.84360.8134-0.52320.0396-0.0389-0.24921.14910.3976-0.61330.91190.1374-0.08690.2362-0.13340.671621.6189-31.68335.1756
258.3417-2.0908-0.19077.9425-0.7212.0692-0.10110.00430.69790.91140.7279-1.4984-0.06020.5323-0.63060.45170.0909-0.0750.4747-0.16840.921737.3558-17.729522.2303
267.9214-3.4645-2.30153.82241.3990.68720.4561-0.43080.45260.4735-0.0461-1.3597-0.25440.7892-0.77080.6086-0.14760.05920.91270.10880.566327.9442-10.191521.8096
273.71110.1282-0.55626.75610.37914.7868-0.19680.704-0.37990.0559-0.1353-1.00750.2210.35850.2260.2582-0.01360.20770.3818-0.05290.519524.334-16.707419.0811
284.1347-1.5751-1.41556.70172.2175.584-0.0304-0.8068-0.34811.83340.2359-0.58991.17620.8525-0.03630.9220.0592-0.16370.35050.0230.587129.4517-25.865230.2758
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 16 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 47 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 48 through 81 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 118 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 138 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 139 through 159 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 3 through 16 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 17 through 47 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 48 through 61 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 62 through 74 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 75 through 93 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 94 through 104 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 105 through 122 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 123 through 141 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 142 through 157 )B0
16X-RAY DIFFRACTION16chain 'C' and (resid 3 through 16 )C0
17X-RAY DIFFRACTION17chain 'C' and (resid 17 through 36 )C0
18X-RAY DIFFRACTION18chain 'C' and (resid 37 through 47 )C0
19X-RAY DIFFRACTION19chain 'C' and (resid 48 through 81 )C0
20X-RAY DIFFRACTION20chain 'C' and (resid 82 through 118 )C0
21X-RAY DIFFRACTION21chain 'C' and (resid 119 through 129 )C0
22X-RAY DIFFRACTION22chain 'C' and (resid 130 through 138 )C0
23X-RAY DIFFRACTION23chain 'C' and (resid 139 through 159 )C0
24X-RAY DIFFRACTION24chain 'D' and (resid 3 through 36 )D0
25X-RAY DIFFRACTION25chain 'D' and (resid 37 through 61 )D0
26X-RAY DIFFRACTION26chain 'D' and (resid 62 through 81 )D0
27X-RAY DIFFRACTION27chain 'D' and (resid 82 through 129 )D0
28X-RAY DIFFRACTION28chain 'D' and (resid 130 through 159 )D0

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