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- PDB-3wb2: HcgB from Methanocaldococcus jannaschii in complex with the guany... -

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Basic information

Entry
Database: PDB / ID: 3wb2
TitleHcgB from Methanocaldococcus jannaschii in complex with the guanylyl-pyridinol product in a model reaction of [Fe]-hydrogenase cofactor biosynthesis
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
GUANOSINE-5'-DIPHOSPHATE / Chem-YGP / Uncharacterized protein MJ0488
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.44 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 11, 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)77,91411
Polymers75,4854
Non-polymers2,4297
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15530 Å2
ΔGint-91 kcal/mol
Surface area23340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.010, 97.370, 63.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-203-

HOH

21B-225-

HOH

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
12SERSERAA2 - 1572 - 157
22SERSERCC2 - 1572 - 157
13HISHISAA2 - 1612 - 161
23HISHISDD2 - 1612 - 161
14ILEILEBB2 - 1582 - 158
24ILEILECC2 - 1582 - 158
15SERSERBB2 - 1572 - 157
25SERSERDD2 - 1572 - 157
16SERSERCC2 - 1572 - 157
26SERSERDD2 - 1572 - 157

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
#2: Chemical
ChemComp-YGP / 5'-O-[(R)-[(3,6-dimethyl-2-oxo-1,2-dihydropyridin-4-yl)oxy](hydroxy)phosphoryl]guanosine


Mass: 484.357 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H21N6O9P
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20%(w/v) PEG 8000, 0.1M 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: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2012
RadiationMonochromator: A double crystal Si(111) monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 27204 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.414 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.53
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
2.4-2.50.7490.7792.3915451309229590.86595.7
2.5-2.70.490.5463.729007491649150.599100
2.7-30.2630.2856.5629373515151360.31499.7
3-3.50.1280.13312.4329855514251390.14799.9
3.5-4.30.0440.05325.6323468407740750.058100
4.3-5.90.030.03932.4716763298729800.04399.8
5.9-80.0340.03732.036185117111670.04199.7
8-120.0180.03141.7329335715660.03499.1
120.020.0338.0611502762670.03496.7

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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: 3WB1

3wb1


Resolution: 2.44→49.51 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2005 / WRfactor Rwork: 0.153 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8311 / SU B: 16.543 / SU ML: 0.192 / SU R Cruickshank DPI: 0.4541 / SU Rfree: 0.2545 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.454 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2263 1362 5 %RANDOM
Rwork0.1717 ---
obs0.1745 27164 99.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 110.24 Å2 / Biso mean: 43.5211 Å2 / Biso min: 6.64 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.44→49.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4986 0 162 136 5284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0195190
X-RAY DIFFRACTIONr_angle_refined_deg1.9682.0466971
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2515630
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.09424.388196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.039151110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1381544
X-RAY DIFFRACTIONr_chiral_restr0.1250.2840
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023560
X-RAY DIFFRACTIONr_mcbond_it2.5163.2132532
X-RAY DIFFRACTIONr_mcangle_it3.7564.8033158
X-RAY DIFFRACTIONr_scbond_it4.3293.8182658
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A1750.14
12B1750.14
21A1790.09
22C1790.09
31A1830.17
32D1830.17
41B1750.13
42C1750.13
51B1740.14
52D1740.14
61C1710.13
62D1710.13
LS refinement shellResolution: 2.437→2.5 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 111 -
Rwork0.248 1731 -
all-1842 -
obs--93.08 %
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)
10.29740.1735-0.29850.4651-0.08110.55110.0711-0.06210.06060.0634-0.052-0.0069-0.03980.1095-0.01910.032-0.0166-0.00190.1084-0.02810.076830.7494-27.1046.2851
20.18150.07950.02010.5404-0.16190.29190.046-0.03140.030.0275-0.00710.08250.0262-0.041-0.0390.0169-0.01240.00910.1067-0.01920.090311.5038-35.5985.0888
30.08270.19110.03380.6786-0.12011.384-0.00720.03270.041-0.14520.06330.1108-0.0619-0.2196-0.05610.10370.0127-0.05670.09180.05030.083310.2264-24.9756-20.3775
40.3110.00240.02520.22360.12120.5633-0.02440.0619-0.0264-0.15030.0646-0.0087-0.01820.0664-0.04020.1171-0.03610.01090.0948-0.02980.032730.6727-30.0375-21.9671
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 16
2X-RAY DIFFRACTION1A17 - 36
3X-RAY DIFFRACTION1A37 - 68
4X-RAY DIFFRACTION1A69 - 93
5X-RAY DIFFRACTION1A94 - 138
6X-RAY DIFFRACTION1A139 - 161
7X-RAY DIFFRACTION2B2 - 16
8X-RAY DIFFRACTION2B17 - 36
9X-RAY DIFFRACTION2B37 - 47
10X-RAY DIFFRACTION2B48 - 60
11X-RAY DIFFRACTION2B61 - 93
12X-RAY DIFFRACTION2B94 - 129
13X-RAY DIFFRACTION2B130 - 158
14X-RAY DIFFRACTION3C2 - 16
15X-RAY DIFFRACTION3C17 - 24
16X-RAY DIFFRACTION3C25 - 36
17X-RAY DIFFRACTION3C37 - 72
18X-RAY DIFFRACTION3C73 - 81
19X-RAY DIFFRACTION3C82 - 118
20X-RAY DIFFRACTION3C119 - 138
21X-RAY DIFFRACTION3C139 - 158
22X-RAY DIFFRACTION4D2 - 16
23X-RAY DIFFRACTION4D17 - 24
24X-RAY DIFFRACTION4D25 - 36
25X-RAY DIFFRACTION4D37 - 69
26X-RAY DIFFRACTION4D70 - 93
27X-RAY DIFFRACTION4D94 - 138
28X-RAY DIFFRACTION4D139 - 161

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