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- PDB-6ydm: beta-phosphoglucomutase from Lactococcus lactis with citrate, tri... -

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Basic information

Entry
Database: PDB / ID: 6ydm
Titlebeta-phosphoglucomutase from Lactococcus lactis with citrate, tris and acetate bound
ComponentsBeta-phosphoglucomutase
KeywordsISOMERASE / cis-trans proline isomerization / allomorphy / phosphoryl transfer / citrate
Function / homology
Function and homology information


beta-phosphoglucomutase / beta-phosphoglucomutase activity / carbohydrate metabolic process / magnesium ion binding / cytoplasm
Similarity search - Function
Beta-phosphoglucomutase / Beta-phosphoglucomutase hydrolase / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily
Similarity search - Domain/homology
ACETATE ION / CITRIC ACID / 1,3-PROPANDIOL / Beta-phosphoglucomutase
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsWood, H.P. / Cruz-Navarrete, F.A. / Baxter, N.J. / Trevitt, C.R. / Robertson, A.J. / Dix, S.R. / Hounslow, A.M. / Cliff, M.J. / Waltho, J.P.
Funding support United Kingdom, Mexico, 6items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)X/009906-20-26 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/M021637/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S007965/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P007066/1 United Kingdom
Consejo Nacional de Ciencia y Tecnologia (CONACYT)472448 Mexico
Royal SocietyR/152968 United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: Allomorphy as a mechanism of post-translational control of enzyme activity.
Authors: Wood, H.P. / Cruz-Navarrete, F.A. / Baxter, N.J. / Trevitt, C.R. / Robertson, A.J. / Dix, S.R. / Hounslow, A.M. / Cliff, M.J. / Waltho, J.P.
History
DepositionMar 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 28, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-phosphoglucomutase
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,09810
Polymers48,4792
Non-polymers6198
Water3,351186
1
A: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5915
Polymers24,2401
Non-polymers3524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-phosphoglucomutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5075
Polymers24,2401
Non-polymers2684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.130, 76.640, 117.260
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain: (Details: Chains A B)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Beta-phosphoglucomutase / Beta-PGM


Mass: 24239.594 Da / Num. of mol.: 2 / Mutation: K125R, Y206H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (strain IL1403) (lactic acid bacteria)
Gene: pgmB, LL0429, L0001 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P71447, beta-phosphoglucomutase

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Non-polymers , 7 types, 194 molecules

#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PDO / 1,3-PROPANDIOL


Mass: 76.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O2
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 186 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 9.86 Å3/Da / Density % sol: 87.52 % / Description: Rod shaped.
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 4000, sodium acetate (200 mM), TRIS (100 mM), HEPES (50 mM), magnesium chloride (5 mM), EDTA (1 mM), sodium azide (2 mM), trisodium citrate (50 mM), beta-phosphoglucomutase (0.6 mM)
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97179 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97179 Å / Relative weight: 1
ReflectionResolution: 2.1→117.3 Å / Num. obs: 27995 / % possible obs: 97.5 % / Redundancy: 8.6 % / Biso Wilson estimate: 24.2 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.033 / Rrim(I) all: 0.098 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.1-2.167.60.5363.720950.8990.1980.57490.1
8.91-46.577.50.02930.533490.9990.0110.04598.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0257refinement
XDSdata reduction
xia2data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2WHE

2whe


Resolution: 2.1→46.61 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.9 / SU B: 11.717 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.23
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2897 1349 4.827 %RANDOM
Rwork0.2299 ---
all0.233 ---
obs-27947 97.332 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.766 Å2
Baniso -1Baniso -2Baniso -3
1--0.242 Å20 Å20 Å2
2--2.269 Å20 Å2
3----2.027 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3374 0 40 186 3600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133472
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173319
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.6314695
X-RAY DIFFRACTIONr_angle_other_deg1.3021.5857717
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6285438
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.01924.371167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.72215607
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.7031514
X-RAY DIFFRACTIONr_chiral_restr0.0680.2455
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023869
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02653
X-RAY DIFFRACTIONr_nbd_refined0.2130.2669
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.22985
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21681
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2157
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1590.214
X-RAY DIFFRACTIONr_nbd_other0.1450.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1880.214
X-RAY DIFFRACTIONr_mcbond_it2.1482.0541755
X-RAY DIFFRACTIONr_mcbond_other2.0642.0491751
X-RAY DIFFRACTIONr_mcangle_it2.7953.0682187
X-RAY DIFFRACTIONr_mcangle_other2.7953.0692188
X-RAY DIFFRACTIONr_scbond_it2.832.3851717
X-RAY DIFFRACTIONr_scbond_other2.832.3861718
X-RAY DIFFRACTIONr_scangle_it4.093.452507
X-RAY DIFFRACTIONr_scangle_other4.0893.4512508
X-RAY DIFFRACTIONr_lrange_it5.48824.9663771
X-RAY DIFFRACTIONr_lrange_other5.4924.9763772
X-RAY DIFFRACTIONr_ncsr_local_group_10.0790.056755
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.1540.369880.2831767X-RAY DIFFRACTION89.1827
2.154-2.2130.281860.2611821X-RAY DIFFRACTION92.2593
2.213-2.2780.341780.2441773X-RAY DIFFRACTION94.3906
2.278-2.3480.284820.2341752X-RAY DIFFRACTION95.3222
2.348-2.4250.307850.2161726X-RAY DIFFRACTION97.0525
2.425-2.510.25710.2121737X-RAY DIFFRACTION99.6692
2.51-2.6040.266940.1971636X-RAY DIFFRACTION99.2542
2.604-2.7110.274920.2251578X-RAY DIFFRACTION99.1686
2.711-2.8310.315910.2351542X-RAY DIFFRACTION99.3914
2.831-2.9690.257760.2321445X-RAY DIFFRACTION98.8947
2.969-3.130.285710.2281404X-RAY DIFFRACTION99.1263
3.13-3.3190.29580.2271346X-RAY DIFFRACTION99.9288
3.319-3.5480.323600.2341252X-RAY DIFFRACTION99.3939
3.548-3.8320.284740.2321159X-RAY DIFFRACTION99.5157
3.832-4.1980.253520.2151080X-RAY DIFFRACTION99.8236
4.198-4.6930.229480.206996X-RAY DIFFRACTION99.2395
4.693-5.4170.331500.221871X-RAY DIFFRACTION99.3528
5.417-6.6310.248440.268762X-RAY DIFFRACTION99.8761
6.631-9.3630.365310.23594X-RAY DIFFRACTION98.5804
9.363-46.610.359180.265357X-RAY DIFFRACTION98.6842
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)
12.1314-0.439-0.44711.20050.0241.98570.10860.3099-0.1607-0.1429-0.0671-0.06210.148-0.0495-0.04140.03690.0141-0.01430.0479-0.01610.04545.0895-22.1546-12.8184
22.50060.6871-0.64251.2323-0.24881.31090.1264-0.3404-0.07160.1612-0.09070.02360.0220.0148-0.03580.0373-0.0153-0.01810.05350.00530.02961.0178-22.3217-45.6037
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA*1 - 219
2X-RAY DIFFRACTION2ALLB*1 - 219

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