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- PDB-7p97: Structure of 3-phospho-D-glycerate guanylyltransferase with produ... -

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Basic information

Entry
Database: PDB / ID: 7p97
TitleStructure of 3-phospho-D-glycerate guanylyltransferase with product 3-GPPG bound
Components3-phospho-D-glycerate guanylyltransferase
KeywordsTRANSFERASE / F420 synthesis / FbiD / CofC / guanylyltransferase / 3-phospho-glycerate
Function / homology3-phospho-D-glycerate guanylyltransferase / phospholactate guanylyltransferase activity / Phosphoenolpyruvate guanylyltransferase CofC / Guanylyl transferase CofC like / Nucleotide-diphospho-sugar transferases / GTP binding / 3-(guanosine-5'-diphospho)-D-glycerate / 3-phospho-D-glycerate guanylyltransferase
Function and homology information
Biological speciesMycetohabitans rhizoxinica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsPalm, G.J. / Berndt, L. / Lammers, M.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation (DFG)LA2984-5/1 Germany
German Research Foundation (DFG)LA2984-6/1 Germany
CitationJournal: Mbio / Year: 2022
Title: Diversification by CofC and Control by CofD Govern Biosynthesis and Evolution of Coenzyme F 420 and Its Derivative 3PG-F 420.
Authors: Hasan, M. / Schulze, S. / Berndt, L. / Palm, G.J. / Braga, D. / Richter, I. / Last, D. / Lammers, M. / Lackner, G.
History
DepositionJul 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: 3-phospho-D-glycerate guanylyltransferase
BBB: 3-phospho-D-glycerate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,07911
Polymers51,8132
Non-polymers1,2669
Water3,477193
1
AAA: 3-phospho-D-glycerate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5225
Polymers25,9071
Non-polymers6154
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: 3-phospho-D-glycerate guanylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5576
Polymers25,9071
Non-polymers6515
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.090, 57.090, 228.970
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11BBB-305-

CL

21BBB-491-

HOH

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Components

#1: Protein 3-phospho-D-glycerate guanylyltransferase / 3PG guanylyltransferase


Mass: 25906.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycetohabitans rhizoxinica (strain DSM 19002 / CIP 109453 / HKI 454) (bacteria)
Strain: DSM 19002 / CIP 109453 / HKI 454 / Gene: cofC, RBRH_02550 / Plasmid: pACYCduet / Details (production host): N-terminal His-tag / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: E5ASS2, 3-phospho-D-glycerate guanylyltransferase
#2: Chemical ChemComp-6WI / 3-(guanosine-5'-diphospho)-D-glycerate / 3GPPG / (2~{R})-3-[[[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-2-oxidanyl-propanoic acid


Mass: 531.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H19N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.56 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10% PEG 3000, 200 mm MgCl2, 100 mm sodium cacodylate pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 28, 2021 / Details: Si111
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 18963 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Biso Wilson estimate: 29.9 Å2 / CC1/2: 0.975 / Rrim(I) all: 0.489 / Rsym value: 0.465 / Net I/σ(I): 5.4
Reflection shellResolution: 2.35→2.49 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 31546 / CC1/2: 0.511 / Rrim(I) all: 1.898 / Rsym value: 1.805 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSFeb 5, 2021data reduction
XDSFeb 5, 2021data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6bwg

6bwg


Resolution: 2.35→49.49 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.904 / SU B: 22.024 / SU ML: 0.221 / Cross valid method: FREE R-VALUE / ESU R: 0.35 / ESU R Free: 0.24
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2381 878 4.63 %
Rwork0.1865 18084 -
all0.189 --
obs-18962 99.832 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 26.473 Å2
Baniso -1Baniso -2Baniso -3
1-0.004 Å20.002 Å20 Å2
2--0.004 Å2-0 Å2
3----0.013 Å2
Refinement stepCycle: LAST / Resolution: 2.35→49.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2945 0 75 194 3214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133091
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172916
X-RAY DIFFRACTIONr_angle_refined_deg1.8221.6664220
X-RAY DIFFRACTIONr_angle_other_deg1.2991.596699
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3215400
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.42919.404151
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.58515459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.791532
X-RAY DIFFRACTIONr_chiral_restr0.0760.2412
X-RAY DIFFRACTIONr_chiral_restr_other0.0360.24
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02700
X-RAY DIFFRACTIONr_nbd_refined0.2040.2628
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1810.22673
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21467
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21570
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2140
X-RAY DIFFRACTIONr_metal_ion_refined0.0530.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.212
X-RAY DIFFRACTIONr_nbd_other0.20.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1040.29
X-RAY DIFFRACTIONr_mcbond_it0.691.561594
X-RAY DIFFRACTIONr_mcbond_other0.6781.5591593
X-RAY DIFFRACTIONr_mcangle_it1.1582.3361990
X-RAY DIFFRACTIONr_mcangle_other1.1592.3381991
X-RAY DIFFRACTIONr_scbond_it1.0321.7321497
X-RAY DIFFRACTIONr_scbond_other1.0321.7321498
X-RAY DIFFRACTIONr_scangle_it1.7312.5232228
X-RAY DIFFRACTIONr_scangle_other1.732.5232229
X-RAY DIFFRACTIONr_lrange_it3.10918.5183380
X-RAY DIFFRACTIONr_lrange_other3.09918.5013370
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.35-2.410.375540.3061302X-RAY DIFFRACTION98.4749
2.41-2.4760.285470.291311X-RAY DIFFRACTION99.9264
2.476-2.5480.285670.2621190X-RAY DIFFRACTION100
2.548-2.6260.361580.2391220X-RAY DIFFRACTION100
2.626-2.7120.258480.2111197X-RAY DIFFRACTION99.9197
2.712-2.8080.269450.2171123X-RAY DIFFRACTION99.9145
2.808-2.9140.302540.2051118X-RAY DIFFRACTION99.9147
2.914-3.0330.278510.2051042X-RAY DIFFRACTION100
3.033-3.1670.28720.2041012X-RAY DIFFRACTION100
3.167-3.3220.262430.193987X-RAY DIFFRACTION99.903
3.322-3.5020.239490.167915X-RAY DIFFRACTION99.8964
3.502-3.7140.195470.144876X-RAY DIFFRACTION99.7838
3.714-3.970.188350.148846X-RAY DIFFRACTION99.8866
3.97-4.2880.191450.142794X-RAY DIFFRACTION100
4.288-4.6970.142490.125708X-RAY DIFFRACTION100
4.697-5.2520.202260.133666X-RAY DIFFRACTION100
5.252-6.0630.229290.177596X-RAY DIFFRACTION100
6.063-7.4250.146170.163521X-RAY DIFFRACTION100
7.425-10.4950.256290.124402X-RAY DIFFRACTION100
10.495-49.490.177130.245260X-RAY DIFFRACTION99.2727
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)
12.9297-0.58060.7121.9892-0.39122.15910.01-0.0140.02330.0847-0.08320.0729-0.0184-0.09290.07320.0118-0.00540.00730.0315-0.00540.0091-18.374819.908342.882
22.12470.6149-0.12542.4971-0.56282.6654-0.00730.0091-0.07610.04090.00790.0520.0777-0.0976-0.00060.04570.005-0.00160.0526-0.00790.0064-17.7896-2.839166.2015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA12 - 214
2X-RAY DIFFRACTION2ALLBBB12 - 206

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