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- PDB-5wcx: Streptococcus pyogenes phosphoglycerol transferase GacH in comple... -

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Basic information

Entry
Database: PDB / ID: 5wcx
TitleStreptococcus pyogenes phosphoglycerol transferase GacH in complex with sn-glycerol-1-phosphate, crystal form 1
ComponentsPhosphoglycerol transferase GacH
KeywordsTRANSFERASE / Group A Streptococcus / GAS / Lancefield group A carbohydrate / metalloenzyme
Function / homologysulfuric ester hydrolase activity / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily / membrane / SN-GLYCEROL-1-PHOSPHATE / : / Sulfatase N-terminal domain-containing protein
Function and homology information
Biological speciesStreptococcus pyogenes serotype M1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsEdgar, R.J. / Korotkova, N. / Korotkov, K.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P30GM110787 United States
CitationJournal: To be published
Title: Phosphoglycerol transferase GacH from Streptococcus pyogenes
Authors: Edgar, R.J. / Korotkov, K.V. / Korotkova, N.
History
DepositionJul 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,9917
Polymers86,4972
Non-polymers4945
Water5,945330
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
MethodPISA
2
B: Phosphoglycerol transferase GacH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4753
Polymers43,2481
Non-polymers2272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.970, 77.530, 174.940
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 / Fragment: residues 444-824
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes serotype M1 (bacteria)
Gene: SPy_0793 / Plasmid: pET-NT / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q9A0F9
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 172.074 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H9O6P
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.72 Å3/Da / Density % sol: 54.71 % / Description: rectangular prism
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 0.2M CALCIUM ACETATE, 0.1M MES PH 6.0, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jan 28, 2017
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: 2→49.431 Å / Num. obs: 63957 / % possible obs: 99.6 % / Redundancy: 6.573 % / Biso Wilson estimate: 48.001 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.053 / Rrim(I) all: 0.058 / Χ2: 1.051 / Net I/σ(I): 18.94
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2-2.056.3971.1531.6646370.7441.25699.1
2.05-2.116.5660.7812.3745270.8390.84999
2.11-2.176.9480.5443.2944380.9090.58899.9
2.17-2.246.9020.4244.2443080.9420.45999.9
2.24-2.316.7810.3335.4442000.9620.36299.9
2.31-2.396.6520.2537.1540700.9770.27599.9
2.39-2.486.3730.2188.3338850.9810.23899.3
2.48-2.586.5440.15811.2737440.990.17299.1
2.58-2.76.9040.11814.9736160.9930.128100
2.7-2.836.820.09218.534780.9960.199.9
2.83-2.986.7250.07223.4533270.9970.07899.8
2.98-3.166.4780.05928.0231200.9980.06499.9
3.16-3.386.1260.04833.5329370.9980.05299.2
3.38-3.656.70.0384227670.9990.04199.8
3.65-46.4610.03445.8125510.9990.03799.7
4-4.476.2330.03149.0823180.9990.03499.7
4.47-5.165.8750.02948.6620560.9990.03199.2
5.16-6.326.5250.02950.5817600.9990.03199.8
6.32-8.946.0850.02650.9113900.9990.02899.4
8.94-49.4315.850.02254.058200.9990.02498.9

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Processing

Software
NameVersionClassification
PHENIXdev_3139refinement
XSCALEVERSION Nov 1, 2016 BUILT=20161205data scaling
PDB_EXTRACT3.22data extraction
XDSVERSION Nov 1, 2016 BUILT=20161205data reduction
REFMAC5.8.0158phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5U9Z

5u9z


Resolution: 2→49.431 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 0.89 / Phase error: 22.87
RfactorNum. reflection% reflectionSelection details
Rfree0.2118 3127 4.89 %RANDOM SELECTION
Rwork0.1813 ---
obs0.1828 63957 99.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 119.36 Å2 / Biso mean: 55.7726 Å2 / Biso min: 28.14 Å2
Refinement stepCycle: final / Resolution: 2→49.431 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6068 0 41 330 6439
Biso mean--75.15 45.79 -
Num. residues----762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036226
X-RAY DIFFRACTIONf_angle_d0.5578440
X-RAY DIFFRACTIONf_dihedral_angle_d9.6793754
X-RAY DIFFRACTIONf_chiral_restr0.042940
X-RAY DIFFRACTIONf_plane_restr0.0031084
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 (%)
2-2.02280.36962290.31813799402899
2.0228-2.04660.33061920.32243794398698
2.0466-2.07150.33642210.30173759398097
2.0715-2.09770.31791700.270538844054100
2.0977-2.12540.31821880.266638784066100
2.1254-2.15450.27991970.258939314128100
2.1545-2.18520.31052190.253338074026100
2.1852-2.21790.27081750.240838894064100
2.2179-2.25250.25952350.233238794114100
2.2525-2.28950.22342000.218638784078100
2.2895-2.32890.23541760.211538654041100
2.3289-2.37130.21432040.213938834087100
2.3713-2.41690.27631920.20939174109100
2.4169-2.46620.252020.21663831403399
2.4662-2.51980.26131830.21243712389597
2.5198-2.57850.24352030.205139154118100
2.5785-2.64290.19582180.19238714089100
2.6429-2.71440.21561860.199138374023100
2.7144-2.79430.24211740.197339244098100
2.7943-2.88440.22792090.199938744083100
2.8844-2.98750.23231630.195339324095100
2.9875-3.10710.26421880.19713845403399
3.1071-3.24850.24181900.20233801399198
3.2485-3.41970.26742140.18833829404399
3.4197-3.63390.18272030.175738584061100
3.6339-3.91440.18451980.16253845404399
3.9144-4.30810.18692210.13663850407199
4.3081-4.9310.13641950.12993806400198
4.931-6.21060.15292110.145338294040100
6.2106-49.4460.20691910.15863877406899
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)
15.3161-2.44850.45882.83440.23131.42840.26251.14460.0434-0.7995-0.3479-0.0528-0.11770.32340.09610.8405-0.01790.01030.78850.13460.455936.15521.8325106.6275
21.5435-0.04490.62150.5889-0.11882.1579-0.1030.17060.2923-0.233-0.04620.0131-0.3320.01590.14080.54510.0063-0.05460.38760.10430.469428.19717.8731130.6182
31.92370.41460.28991.8579-1.02373.3677-0.0761-0.18370.1442-0.0287-0.01730.1431-0.2528-0.48420.07540.39440.0501-0.05060.4530.00860.472719.56795.4974141.9951
42.2688-0.07880.04371.05080.0181.92970.05070.56430.2733-0.4877-0.0620.0251-0.13950.10740.00560.6125-0.0095-0.08330.48910.10350.406126.85851.6453117.3406
53.2480.48450.23935.34210.70782.8660.0613-0.5366-0.52870.70210.0143-0.24180.28570.2012-0.08180.29940.02870.03390.54760.10350.411140.0383-20.6551185.3577
61.84540.0397-0.0421.2064-0.4282.2421-0.1038-0.05630.30230.0295-0.0724-0.2364-0.33970.23490.15910.3387-0.058-0.04290.344-0.01090.421247.05633.0637166.6774
72.3026-0.36890.21913.0371-0.08032.4474-0.05570.0202-0.0805-0.09470.01990.041-0.0715-0.14180.05550.2785-0.0031-0.00960.4098-0.03340.346432.2425-10.4238171.6011
82.0397-0.1102-0.35931.6116-0.76173.1192-0.0922-0.10450.29740.08540.04160.2215-0.6388-0.45440.03430.44850.0945-0.03540.3854-0.08320.435626.94447.1937167.1555
92.1119-0.185-0.27281.6999-0.1542.8771-0.07670.09130.587-0.01940.0274-0.1414-0.44040.12760.0040.4028-0.0352-0.06540.3115-0.00450.501140.16518.5875158.7214
102.21010.0754-1.20851.76370.16756.8708-0.15410.10330.3935-0.0668-0.0974-0.163-0.59310.26850.19020.347-0.07-0.07570.3220.0530.497644.85626.8616160.1665
111.2044-0.25210.48971.8017-0.45731.8081-0.0375-0.29480.01720.1544-0.0704-0.0295-0.15150.08210.10330.2754-0.0224-0.02030.4483-0.02410.359143.7915-10.4771177.5137
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 442 through 470 )A442 - 470
2X-RAY DIFFRACTION2chain 'A' and (resid 471 through 613 )A471 - 613
3X-RAY DIFFRACTION3chain 'A' and (resid 614 through 725 )A614 - 725
4X-RAY DIFFRACTION4chain 'A' and (resid 726 through 822 )A726 - 822
5X-RAY DIFFRACTION5chain 'B' and (resid 442 through 472 )B442 - 472
6X-RAY DIFFRACTION6chain 'B' and (resid 473 through 529 )B473 - 529
7X-RAY DIFFRACTION7chain 'B' and (resid 530 through 572 )B530 - 572
8X-RAY DIFFRACTION8chain 'B' and (resid 573 through 633 )B573 - 633
9X-RAY DIFFRACTION9chain 'B' and (resid 634 through 669 )B634 - 669
10X-RAY DIFFRACTION10chain 'B' and (resid 670 through 725 )B670 - 725
11X-RAY DIFFRACTION11chain 'B' and (resid 726 through 822 )B726 - 822

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