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- PDB-3wb0: HcgB from Methanocaldococcus jannaschii in complex with light-dec... -

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Basic information

Entry
Database: PDB / ID: 3wb0
TitleHcgB from Methanocaldococcus jannaschii in complex with light-decomposed FeGP cofactor of [Fe]-hydrogenase
ComponentsUncharacterized protein MJ0488
KeywordsTRANSFERASE / GTP-binding domain / 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-FEG / Uncharacterized protein MJ0488
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å
AuthorsFujishiro, T. / Ermler, U. / Shima, S.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Identification of the HcgB enzyme in [Fe]-hydrogenase-cofactor biosynthesis.
Authors: Fujishiro, T. / Tamura, H. / Schick, M. / Kahnt, J. / Xie, X. / Ermler, U. / Shima, S.
History
DepositionMay 10, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 5, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
B: Uncharacterized protein MJ0488
C: Uncharacterized protein MJ0488
D: Uncharacterized protein MJ0488
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6558
Polymers75,4854
Non-polymers2,1704
Water6,774376
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13860 Å2
ΔGint-69 kcal/mol
Surface area21770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.960, 119.340, 55.650
Angle α, β, γ (deg.)90.000, 115.140, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / Refine code: _

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERAA2 - 1572 - 157
21SERSERBB2 - 1572 - 157
12LEULEUAA2 - 1592 - 159
22LEULEUCC2 - 1592 - 159
13LEULEUAA2 - 1592 - 159
23LEULEUDD2 - 1592 - 159
14SERSERBB2 - 1572 - 157
24SERSERCC2 - 1572 - 157
15SERSERBB2 - 1572 - 157
25SERSERDD2 - 1572 - 157
16LEULEUCC2 - 1592 - 159
26LEULEUDD2 - 1592 - 159

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Uncharacterized protein MJ0488


Mass: 18871.297 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 3-158
Source method: isolated from a genetically manipulated source
Details: NcoI-XhoI
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: HcgB, MJ0488 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
References: UniProt: Q57912, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#2: Chemical
ChemComp-FEG / 5'-O-[(S)-{[2-(carboxymethyl)-6-hydroxy-3,5-dimethylpyridin-4-yl]oxy}(hydroxy)phosphoryl]guanosine


Mass: 542.393 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H23N6O11P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 376 / 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: 2.11 Å3/Da / Density % sol: 41.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20 %(w/v) PEG 8000, 0.1 M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2012
RadiationMonochromator: A double crystal Si(111) monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 46660 / % possible obs: 94.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 30.577 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.17
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.9-20.6620.3232.8813981696061050.41287.7
2-2.20.260.1855.672890810473102110.22597.5
2.2-2.40.180.1437.6419862724763160.1787.2
2.4-2.90.0670.09914.084463510558104410.11298.9
2.9-3.50.0480.07817.3824960595858690.08898.5
3.5-4.30.0430.07618.9414998363735360.08797.2
4.3-5.90.0420.07319.610884263725520.08496.8
5.9-80.0450.07718.3741039999700.08897.1
8-120.030.05721.0319904854660.06596.1
120.0310.06721.298672161940.07589.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BRC

3brc


Resolution: 1.91→47.94 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / WRfactor Rfree: 0.2889 / WRfactor Rwork: 0.2347 / Occupancy max: 1 / Occupancy min: 0.55 / FOM work R set: 0.7972 / SU B: 8.608 / SU ML: 0.132 / SU R Cruickshank DPI: 0.225 / SU Rfree: 0.1928 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.225 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 2329 5.1 %RANDOM
Rwork0.2266 ---
obs0.2291 45988 94.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 78.75 Å2 / Biso mean: 29.9177 Å2 / Biso min: 11.99 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.07 Å2
2--0.1 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.91→47.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4956 0 148 376 5480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0195144
X-RAY DIFFRACTIONr_angle_refined_deg2.0312.0426905
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1665627
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39424.375192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.138151106
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0581544
X-RAY DIFFRACTIONr_chiral_restr0.1310.2830
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023536
X-RAY DIFFRACTIONr_mcbond_it1.872.0662520
X-RAY DIFFRACTIONr_mcangle_it2.6523.0823143
X-RAY DIFFRACTIONr_scbond_it3.1772.5762624
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A2050.07
12B2050.07
21A2020.08
22C2020.08
31A1970.09
32D1970.09
41B2000.06
42C2000.06
51B1990.09
52D1990.09
61C1950.09
62D1950.09
LS refinement shellResolution: 1.905→1.955 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.533 118 -
Rwork0.503 2342 -
all-2460 -
obs--68.47 %
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)
10.5204-0.11390.09690.80150.28240.14330.03910.0168-0.0144-0.1122-0.0393-0.0233-0.0241-0.00250.00030.05120.01790.01560.06810.00980.02416.3996-12.550413.8244
20.6479-0.24540.01930.8047-0.05490.0044-0.00350.0003-0.04070.09840.00530.099-0.00640.0038-0.00180.0368-0.00250.00440.05880.01590.03332.6309-13.979128.9427
30.04690.05690.02090.8041-0.07550.15890.02610.01390.0350.1791-0.0094-0.0222-0.0260.0142-0.01660.04690.00150.01170.0528-0.01480.05858.736212.029734.3669
40.62520.0527-0.06570.73240.05090.33910.10580.04070.0963-0.1563-0.03560.0891-0.0566-0.002-0.07030.0590.01860.00760.040.03260.065810.274414.173313.9859
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 17
2X-RAY DIFFRACTION1A18 - 36
3X-RAY DIFFRACTION1A37 - 72
4X-RAY DIFFRACTION1A73 - 93
5X-RAY DIFFRACTION1A94 - 138
6X-RAY DIFFRACTION1A139 - 159
7X-RAY DIFFRACTION2B2 - 16
8X-RAY DIFFRACTION2B17 - 24
9X-RAY DIFFRACTION2B25 - 36
10X-RAY DIFFRACTION2B37 - 60
11X-RAY DIFFRACTION2B61 - 72
12X-RAY DIFFRACTION2B73 - 93
13X-RAY DIFFRACTION2B94 - 138
14X-RAY DIFFRACTION2B139 - 158
15X-RAY DIFFRACTION3C2 - 16
16X-RAY DIFFRACTION3C17 - 24
17X-RAY DIFFRACTION3C25 - 36
18X-RAY DIFFRACTION3C37 - 72
19X-RAY DIFFRACTION3C73 - 93
20X-RAY DIFFRACTION3C94 - 138
21X-RAY DIFFRACTION3C139 - 159
22X-RAY DIFFRACTION4D2 - 16
23X-RAY DIFFRACTION4D17 - 36
24X-RAY DIFFRACTION4D37 - 60
25X-RAY DIFFRACTION4D61 - 72
26X-RAY DIFFRACTION4D73 - 93
27X-RAY DIFFRACTION4D94 - 138
28X-RAY DIFFRACTION4D139 - 159

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