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- PDB-6dgm: Streptococcus pyogenes phosphoglycerol transferase GacH in comple... -

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Basic information

Entry
Database: PDB / ID: 6dgm
TitleStreptococcus pyogenes phosphoglycerol transferase GacH in complex with sn-glycerol-1-phosphate
ComponentsPhosphoglycerol transferase GacH
KeywordsTRANSFERASE / Group A Streptococcus (GAS) / Lancefield group A carbohydrate / glycero-1-phosphate / L-glycerol 1-phosphate / D-glycerol-3-phosphate
Function / homology
Function and homology information


sulfuric ester hydrolase activity / transferase activity / membrane => GO:0016020 / membrane
Similarity search - Function
Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
SN-GLYCEROL-1-PHOSPHATE / : / Phosphoglycerol transferase / Sulfatase N-terminal domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pyogenes MGAS5005 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.49 Å
AuthorsEdgar, R.J. / Korotkova, N. / Korotkov, K.V.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1R21AI113253 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: Nat.Chem.Biol. / Year: 2019
Title: Discovery of glycerol phosphate modification on streptococcal rhamnose polysaccharides.
Authors: Edgar, R.J. / van Hensbergen, V.P. / Ruda, A. / Turner, A.G. / Deng, P. / Le Breton, Y. / El-Sayed, N.M. / Belew, A.T. / McIver, K.S. / McEwan, A.G. / Morris, A.J. / Lambeau, G. / Walker, M. ...Authors: Edgar, R.J. / van Hensbergen, V.P. / Ruda, A. / Turner, A.G. / Deng, P. / Le Breton, Y. / El-Sayed, N.M. / Belew, A.T. / McIver, K.S. / McEwan, A.G. / Morris, A.J. / Lambeau, G. / Walker, M.J. / Rush, J.S. / Korotkov, K.V. / Widmalm, G. / van Sorge, N.M. / Korotkova, N.
History
DepositionMay 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3May 1, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4May 8, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation_author.identifier_ORCID
Revision 1.5Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Oct 11, 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
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_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglycerol transferase GacH
B: Phosphoglycerol transferase GacH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,0318
Polymers86,4972
Non-polymers5346
Water15,241846
1
A: Phosphoglycerol transferase GacH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5154
Polymers43,2481
Non-polymers2673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoglycerol transferase GacH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5154
Polymers43,2481
Non-polymers2673
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-11 kcal/mol
Surface area29710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.650, 82.970, 130.360
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Phosphoglycerol transferase GacH


Mass: 43248.344 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes MGAS5005 (bacteria)
Gene: SPy_0793 / Plasmid: pET-NT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: Q9A0F9, UniProt: Q48UA4*PLUS
#2: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-1GP / SN-GLYCEROL-1-PHOSPHATE


Mass: 172.074 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H9O6P / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 846 / 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: 2.33 Å3/Da / Density % sol: 47.29 % / Description: rectangular prism
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2M calcium acetate, 0.1M MES pH 6.0, 20% PEG8000, 0.01M sn-glycerol-1-phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 13, 2018
Details: Rh coated flat bent M0, toroidal focusing post-monochromator M1
RadiationMonochromator: Si(111) and Si(220) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.49→39.532 Å / Num. obs: 127541 / % possible obs: 96.3 % / Redundancy: 6.488 % / Biso Wilson estimate: 24.326 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.086 / Χ2: 1.008 / Net I/σ(I): 14.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.49-1.534.9631.1431.271440.4961.28173.4
1.53-1.575.3950.9441.5981500.631.04886.4
1.57-1.626.4770.8322.1489360.7810.90497.4
1.62-1.676.8850.6842.7888660.8640.73998.7
1.67-1.726.780.5613.4185850.90.60799.2
1.72-1.786.6260.4464.282820.9310.48498.9
1.78-1.856.4210.345.2980270.9510.3798.8
1.85-1.926.9290.2577.3677670.9780.27799.2
1.92-2.016.8490.1859.9274490.9870.299.6
2.01-2.116.6830.14312.6171550.9910.15599.5
2.11-2.226.320.11514.5667320.9930.12698.6
2.22-2.366.9480.117.9264650.9960.10899.7
2.36-2.526.8440.08720.1160800.9960.09499.6
2.52-2.726.6310.06924.0957090.9980.07599.9
2.72-2.986.480.05429.2651870.9980.05998.9
2.98-3.336.8680.04338.0747570.9990.04799.8
3.33-3.856.5510.03347.1342350.9990.03699.6
3.85-4.716.3090.02751.5835630.9990.0398.6
4.71-6.666.550.02949.6828420.9990.03199.9
6.66-39.5326.0670.0255.96161010.02297.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.88 Å39.53 Å
Translation6.88 Å39.53 Å

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Processing

Software
NameVersionClassification
PHENIXdev_3139refinement
XDSVERSION Jan 26, 2018 BUILT=20180126data reduction
XSCALEVERSION Jan 26, 2018 BUILT=20180126data scaling
PHASER2.8.2phasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5U9Z

5u9z


Resolution: 1.49→39.532 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.14 / Phase error: 18.55
Details: REMARK 3 REFINEMENT TARGET : ML REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
RfactorNum. reflection% reflectionSelection details
Rfree0.1754 6361 4.99 %RANDOM SELECTION
Rwork0.1529 ---
obs0.154 127526 95.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.47 Å2 / Biso mean: 24.5507 Å2 / Biso min: 11.98 Å2
Refinement stepCycle: final / Resolution: 1.49→39.532 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6074 0 42 846 6962
Biso mean--28.74 32.21 -
Num. residues----763
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.49-1.50690.35362800.34285629590970
1.5069-1.52460.31413580.33315972633074
1.5246-1.54320.31553440.31376483682780
1.5432-1.56280.29243820.30397076745887
1.5628-1.58330.29424020.28667591799394
1.5833-1.6050.26934150.26197864827997
1.605-1.6280.29384350.24757933836898
1.628-1.65230.23014500.22877931838198
1.6523-1.67810.22094240.22577959838399
1.6781-1.70560.23893690.21618027839699
1.7056-1.7350.22764170.2128032844999
1.735-1.76650.24343910.20868035842699
1.7665-1.80050.22284280.19277945837398
1.8005-1.83730.20253910.18537986837798
1.8373-1.87720.17344050.16497985839099
1.8772-1.92090.16413830.15758028841199
1.9209-1.96890.17294590.14837977843699
1.9689-2.02220.17944560.14528026848299
2.0222-2.08170.17794030.1418011841499
2.0817-2.14880.16013950.14088073846899
2.1488-2.22560.17224200.13427915833598
2.2256-2.31470.13694190.12138048846799
2.3147-2.42010.14434350.1238045848099
2.4201-2.54760.15954210.12568019844099
2.5476-2.70720.1534250.12578056848199
2.7072-2.91620.1524540.12947906836098
2.9162-3.20950.15754470.1318035848299
3.2095-3.67370.15284050.12838032843799
3.6737-4.62730.1323840.11888014839898
4.6273-39.54540.18854150.15377976839199
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)
12.5312-0.59070.8041.5218-0.28981.8248-0.043-0.6309-0.15790.335-0.07340.25650.0722-0.3680.09080.2371-0.08780.07770.3699-0.01780.2203-41.1201-22.557753.2963
21.54150.277-0.15250.8780.5862.2023-0.0482-0.188-0.16180.16620.0304-0.09720.41380.06580.03270.20740.00310.00740.14170.03950.1767-16.7737-26.319541.5903
30.84580.0358-0.20310.4958-0.08391.3743-0.0779-0.0582-0.21250.0228-0.0152-0.05460.31630.05960.08840.23-00.02510.15560.01440.2216-14.5127-32.806533.3201
41.88680.44960.84920.9278-0.12372.00170.0029-0.15350.07270.0258-0.06980.0571-0.0345-0.1930.06980.1578-0.00360.01560.1747-0.01620.1602-30.0839-15.186339.9017
50.5692-0.3384-0.30140.8480.24881.63220.0466-0.06060.11020.00020.0017-0.1169-0.17630.1177-0.05210.1771-0.02470.00380.1585-0.01060.1834-12.3608-9.462136.8487
61.0436-0.3192-0.51810.45670.03021.5864-0.03590.0293-0.08-0.0359-0.0042-0.06530.12520.06770.03670.1411-0.01040.01290.12260.00850.1685-9.7286-23.098329.3302
70.9132-0.2895-0.40221.0290.66033.1107-0.050.0352-0.12080.02790.0003-0.05130.32960.1055-0.03260.1609-0.00180.02080.09480.01180.1664-11.3566-27.733131.0502
81.31090.0502-0.41640.64020.18110.955-0.0121-0.2529-0.18870.13-0.04380.01830.2544-0.08770.04860.2377-0.02830.02070.20580.04680.1984-23.2979-29.285845.9787
92.4453-0.42970.35531.9372-0.22311.4463-0.0488-0.3427-0.1020.0968-0.05380.27870.0034-0.2010.10140.1461-0.05520.05570.2472-0.01480.1882-39.457-22.274747.3358
101.62841.37720.00154.09270.14311.5208-0.12760.2522-0.1168-0.44460.13250.03770.0926-0.0917-0.00650.12620.024-0.0070.169-0.02450.149-12.6467-21.6905-22.8915
110.86830.3761-0.36170.2679-0.1761.59760.0390.06460.111-0.0301-0.00680.0087-0.1841-0.0435-0.0550.16070.00990.00120.13670.0120.1519-11.6794-4.6717-1.5079
120.58570.1303-0.45070.16370.01831.1795-0.00370.01880.04420.02580.02620.0532-0.1909-0.0948-0.02770.19460.0198-0.00430.16930.00620.1686-19.908-1.41474.6182
130.77440.02050.42480.67170.01261.5027-0.01880.0304-0.1031-0.0167-0.0128-0.02670.15080.08370.03210.14460.01610.01860.14840.00050.1544-6.8778-20.7683-1.113
140.96760.0768-0.23420.5676-0.02321.9087-0.0091-0.04770.02170.03120.0009-0.1024-0.04150.315-0.00670.1357-0.0103-0.00320.20580.00530.16620.5581-9.765211.8771
151.4301-0.4472-0.8410.55250.27941.843-0.0391-0.05110.0540.05920.04010.0312-0.06090.1041-0.01770.148-0.0184-0.01550.11090.00390.1586-12.7546-5.039212.9107
164.93520.7603-3.45220.6334-0.69684.09650.1099-0.03490.08170.0742-0.03330.0341-0.28330.0165-0.10080.16640.0013-0.00750.1194-0.0090.1438-14.09420.095113.467
173.03410.9023-1.58631.2596-0.19472.2142-0.04620.19260.0640.0013-0.0080.0913-0.0747-0.21190.04050.13880.0177-0.02160.13480.00440.1273-18.4336-6.43934.5425
180.27470.0142-0.06880.72810.16961.03210.00580.0504-0.0184-0.051-0.02170.0177-0.0364-0.03660.01640.13550.0017-0.00540.15850.00580.1509-14.6224-13.1592-12.7029
194.5495.76871.75377.31792.16821.90813.9897-6.4158-10.91.6512-1.8985-1.60683.73110.6978-2.10310.76040.0356-0.09040.68480.24060.7201-1.8013-11.8866-23.5943
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 442 through 472 )A442 - 472
2X-RAY DIFFRACTION2chain 'A' and (resid 473 through 498 )A473 - 498
3X-RAY DIFFRACTION3chain 'A' and (resid 499 through 529 )A499 - 529
4X-RAY DIFFRACTION4chain 'A' and (resid 530 through 572 )A530 - 572
5X-RAY DIFFRACTION5chain 'A' and (resid 573 through 633 )A573 - 633
6X-RAY DIFFRACTION6chain 'A' and (resid 634 through 669 )A634 - 669
7X-RAY DIFFRACTION7chain 'A' and (resid 670 through 725 )A670 - 725
8X-RAY DIFFRACTION8chain 'A' and (resid 726 through 780 )A726 - 780
9X-RAY DIFFRACTION9chain 'A' and (resid 781 through 822 )A781 - 822
10X-RAY DIFFRACTION10chain 'B' and (resid 442 through 472 )B442 - 472
11X-RAY DIFFRACTION11chain 'B' and (resid 473 through 498 )B473 - 498
12X-RAY DIFFRACTION12chain 'B' and (resid 499 through 529 )B499 - 529
13X-RAY DIFFRACTION13chain 'B' and (resid 530 through 595 )B530 - 595
14X-RAY DIFFRACTION14chain 'B' and (resid 596 through 633 )B596 - 633
15X-RAY DIFFRACTION15chain 'B' and (resid 634 through 669 )B634 - 669
16X-RAY DIFFRACTION16chain 'B' and (resid 670 through 699 )B670 - 699
17X-RAY DIFFRACTION17chain 'B' and (resid 700 through 725 )B700 - 725
18X-RAY DIFFRACTION18chain 'B' and (resid 726 through 822 )B726 - 822
19X-RAY DIFFRACTION19chain 'B' and (resid 823 through 823 )B823

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