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- PDB-3wvc: Guanylylpyridinol (GP)-bound HcgF from Methanocaldococcus jannaschii -

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Basic information

Entry
Database: PDB / ID: 3wvc
TitleGuanylylpyridinol (GP)-bound HcgF from Methanocaldococcus jannaschii
ComponentsUPF0254 protein MJ1251
KeywordsHYDROLASE / Thioesterase
Function / homologyFeGP cofactor biosynthesis protein HcgF / FeGP cofactor biosynthesis protein HcgF / Chem-FEG / Chem-ZGP / UPF0254 protein MJ1251
Function and homology information
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFujishiro, T. / Ermler, U. / Shima, S.
CitationJournal: Nat Commun / Year: 2015
Title: Protein-pyridinol thioester precursor for biosynthesis of the organometallic acyl-iron ligand in [Fe]-hydrogenase cofactor
Authors: Fujishiro, T. / Kahnt, J. / Ermler, U. / Shima, S.
History
DepositionMay 16, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2015Provider: 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: UPF0254 protein MJ1251
B: UPF0254 protein MJ1251
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,18610
Polymers38,5092
Non-polymers1,6778
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3830 Å2
ΔGint-96 kcal/mol
Surface area14770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.570, 97.530, 47.120
Angle α, β, γ (deg.)90.00, 111.17, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: _ / Auth seq-ID: -1 - 167 / Label seq-ID: 2 - 170

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein UPF0254 protein MJ1251


Mass: 19254.324 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: MJ1251 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Star
References: UniProt: Q58649, Hydrolases; Acting on ester bonds; Thioester hydrolases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ZGP / 5'-O-[(R)-hydroxy{[2-hydroxy-3,5-dimethyl-6-(2-oxo-2-sulfanylethyl)pyridin-4-yl]oxy}phosphoryl]guanosine


Mass: 558.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H23N6O10PS
#4: 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.: 1 / Source method: obtained synthetically / Formula: C19H23N6O11P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 40%(v/v)MPD, 200mM lithium sulfate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.98 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Oct 30, 2013
RadiationMonochromator: A Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 22368 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 20.35
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2-2.10.12411.13198.9
2.1-2.30.09114.3198.5
2.3-2.80.07418.17199.2
2.8-3.30.05124.53199.3
3.3-4.30.03831.42199.6
4.3-5.90.03731.97198.7
5.9-80.04430.53198.9
8-120.03932.071100
120.03734.34197.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMAC5.8.0071refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet-labelled HcgF from Methanocaldococcus jannaschii PDB ENTRY 3WVA

3wva


Resolution: 2→48.76 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.913 / SU B: 8.13 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.22973 1118 5 %RANDOM
Rwork0.16289 ---
obs0.16621 21248 99.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.807 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20.05 Å2
2---0.09 Å20 Å2
3----0.14 Å2
Refinement stepCycle: LAST / Resolution: 2→48.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2700 0 104 219 3023
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022879
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9762.0113891
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075346
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.68424.876121
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.05515542
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8081510
X-RAY DIFFRACTIONr_chiral_restr0.1510.2437
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022080
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5821.5381360
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.3322.2931699
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8312.0981519
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 207 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.21 83 -
Rwork0.164 1583 -
obs--98.93 %
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)
10.2720.0942-0.32860.53460.31520.7721-0.00740.0279-0.00260.0002-0.01670.02010.0199-0.04360.02410.00860.01060.0050.0244-0.00080.01155.41170.389719.5024
20.0626-0.2092-0.13641.12340.02880.73190.01130.0018-0.0118-0.043-0.02150.0644-0.01170.00630.01030.0083-0.00440.0090.0096-0.01130.02447.671122.719118.1504
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 13
2X-RAY DIFFRACTION1A14 - 36
3X-RAY DIFFRACTION1A37 - 53
4X-RAY DIFFRACTION1A54 - 72
5X-RAY DIFFRACTION1A73 - 82
6X-RAY DIFFRACTION1A83 - 101
7X-RAY DIFFRACTION1A102 - 129
8X-RAY DIFFRACTION1A130 - 142
9X-RAY DIFFRACTION1A143 - 167
10X-RAY DIFFRACTION2B-1 - 13
11X-RAY DIFFRACTION2B14 - 36
12X-RAY DIFFRACTION2B37 - 53
13X-RAY DIFFRACTION2B54 - 64
14X-RAY DIFFRACTION2B65 - 82
15X-RAY DIFFRACTION2B83 - 101
16X-RAY DIFFRACTION2B102 - 129
17X-RAY DIFFRACTION2B130 - 142
18X-RAY DIFFRACTION2B143 - 167

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