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- PDB-7swh: Crystal Structure of Putative cystathionine gamma-synthase from B... -

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Basic information

Entry
Database: PDB / ID: 7swh
TitleCrystal Structure of Putative cystathionine gamma-synthase from Burkholderia pseudomallei in Complex with PLP
ComponentsPutative cystathionine gamma-synthase
KeywordsLIGASE / SSGCID / PLP / LLP / cystathionine gamma-synthase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


transsulfuration / catalytic activity / pyridoxal phosphate binding
Similarity search - Function
Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Putative cystathionine gamma-synthase
Similarity search - Component
Biological speciesBurkholderia pseudomallei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: to be published
Title: Crystal Structure of Putative cystathionine gamma-synthase from Burkholderia pseudomallei in Complex with PLP
Authors: DeBouver, N.D. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionNov 19, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 1, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cystathionine gamma-synthase
B: Putative cystathionine gamma-synthase
C: Putative cystathionine gamma-synthase
D: Putative cystathionine gamma-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,0685
Polymers197,0064
Non-polymers621
Water14,178787
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19170 Å2
ΔGint-133 kcal/mol
Surface area52940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.730, 156.890, 81.710
Angle α, β, γ (deg.)90.000, 113.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 67 or resid 79...
21(chain B and (resid 5 or (resid 6 and (name...
31(chain C and (resid 5 through 8 or (resid 9...
41(chain D and (resid 5 or (resid 6 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 5 through 67 or resid 79...A5 - 67
121(chain A and (resid 5 through 67 or resid 79...A79 - 119
131(chain A and (resid 5 through 67 or resid 79...A120
141(chain A and (resid 5 through 67 or resid 79...A5 - 502
151(chain A and (resid 5 through 67 or resid 79...A5 - 502
161(chain A and (resid 5 through 67 or resid 79...A5 - 502
211(chain B and (resid 5 or (resid 6 and (name...B5
221(chain B and (resid 5 or (resid 6 and (name...B6
231(chain B and (resid 5 or (resid 6 and (name...B5 - 427
241(chain B and (resid 5 or (resid 6 and (name...B5 - 427
251(chain B and (resid 5 or (resid 6 and (name...B5 - 427
261(chain B and (resid 5 or (resid 6 and (name...B5 - 427
311(chain C and (resid 5 through 8 or (resid 9...C5 - 8
321(chain C and (resid 5 through 8 or (resid 9...C9 - 12
331(chain C and (resid 5 through 8 or (resid 9...C5 - 428
341(chain C and (resid 5 through 8 or (resid 9...C5 - 428
351(chain C and (resid 5 through 8 or (resid 9...C5 - 428
361(chain C and (resid 5 through 8 or (resid 9...C5 - 428
411(chain D and (resid 5 or (resid 6 and (name...D5
421(chain D and (resid 5 or (resid 6 and (name...D6
431(chain D and (resid 5 or (resid 6 and (name...D5 - 427
441(chain D and (resid 5 or (resid 6 and (name...D5 - 427
451(chain D and (resid 5 or (resid 6 and (name...D5 - 427
461(chain D and (resid 5 or (resid 6 and (name...D5 - 427

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Components

#1: Protein
Putative cystathionine gamma-synthase /


Mass: 49251.406 Da / Num. of mol.: 4 / Fragment: RityA.18390.a.B2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei (strain K96243) (bacteria)
Strain: K96243 / Gene: BPSS0913 / Plasmid: RityA.18390.a.B2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q63LU9
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 787 / 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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: RityA.18390.a.B2 + SycoA.20508.e.PG1 [Barcode: 320527g9, PuckID: oce7-3, Cryo: 15% EG, Concentration: 9.9 mg/mL] (100mM Sodium acetate/Hydrochloric acid pH 4.6, 25% (w/v) PEG 4000, 200mM ...Details: RityA.18390.a.B2 + SycoA.20508.e.PG1 [Barcode: 320527g9, PuckID: oce7-3, Cryo: 15% EG, Concentration: 9.9 mg/mL] (100mM Sodium acetate/Hydrochloric acid pH 4.6, 25% (w/v) PEG 4000, 200mM Ammonium sulfate) Cryo: 15 EG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 15, 2021 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.25→48.53 Å / Num. obs: 75200 / % possible obs: 99.7 % / Redundancy: 3.825 % / Biso Wilson estimate: 31.32 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.092 / Rrim(I) all: 0.108 / Χ2: 0.899 / Net I/σ(I): 11.28 / Num. measured all: 287664 / Scaling rejects: 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.25-2.313.8350.6052.2921358557855690.7610.70399.8
2.31-2.373.8350.5442.5120780542854190.8080.63299.8
2.37-2.443.8450.4513.0320150524652400.8590.52499.9
2.44-2.523.8470.3843.5619702513751220.8930.44799.7
2.52-2.63.8490.3194.2619039495649460.920.37199.8
2.6-2.693.8420.2625.1818399479347890.9460.30599.9
2.69-2.793.8480.2076.5217880465846460.9630.24199.7
2.79-2.93.8440.1777.5317180448144690.9740.20699.7
2.9-3.033.840.1459.1416308425242470.9810.16999.9
3.03-3.183.8420.11711.1115736411340960.9860.13699.6
3.18-3.353.8190.08814.2114762388138650.9920.10299.6
3.35-3.563.8080.06917.3614095371737010.9940.0899.6
3.56-3.83.7830.05920.0713065347334540.9950.06999.5
3.8-4.113.7880.05122.2212144322532060.9960.0699.4
4.11-4.53.7890.04425.4211197296829550.9970.05199.6
4.5-5.033.8040.04126.6610205269726830.9970.04899.5
5.03-5.813.830.04324.549104238823770.9980.0599.5
5.81-7.123.8250.0425.497676201220070.9980.04699.8
7.12-10.063.760.03231.85855157115570.9980.03899.1
10.06-48.533.5550.02933.5830298818520.9980.03596.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.20rc3_4406refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O3V

4o3v


Resolution: 2.25→48.53 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2064 2066 2.75 %
Rwork0.1624 73117 -
obs0.1636 75183 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.26 Å2 / Biso mean: 37.3054 Å2 / Biso min: 17.68 Å2
Refinement stepCycle: final / Resolution: 2.25→48.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12434 0 4 789 13227
Biso mean--49.01 36.61 -
Num. residues----1653
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A7460X-RAY DIFFRACTION7.954TORSIONAL
12B7460X-RAY DIFFRACTION7.954TORSIONAL
13C7460X-RAY DIFFRACTION7.954TORSIONAL
14D7460X-RAY DIFFRACTION7.954TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.25-2.30.29891370.222148364973100
2.3-2.360.28391610.216848695030100
2.36-2.420.28631460.207348534999100
2.42-2.490.25091170.199648784995100
2.49-2.580.2851080.189849145022100
2.58-2.670.22321230.190248564979100
2.67-2.770.24091500.189748675017100
2.77-2.90.26061280.194949135041100
2.9-3.050.21581290.189448524981100
3.05-3.240.22961280.181148945022100
3.24-3.50.24231330.167348654998100
3.5-3.850.19211570.146548585015100
3.85-4.40.16731660.126948525018100
4.4-5.550.14761400.122548875027100
5.55-48.530.15771430.13614923506699
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)
13.32410.98921.69592.88280.51691.8664-0.1005-0.20140.05340.13080.0872-0.28870.05470.33320.03540.1620.05870.00790.3497-0.00230.289151.6534-1.19992.3578
21.4094-1.68290.78332.3095-1.26261.3034-0.18990.01510.3620.2689-0.0165-0.5778-0.26280.19240.22270.2648-0.0498-0.07350.3196-0.02830.399644.661226.473483.3461
30.834-0.39851.00121.8659-0.60552.3011-0.03860.11490.12520.24610.0475-0.24430.0740.2015-0.01040.25970.009-0.01910.2737-0.05640.313437.665926.510395.142
42.4047-0.9798-0.31542.5251-0.09272.7111-0.3995-0.54050.01160.52390.24670.12440.2062-0.11510.17980.43210.09150.0340.3098-0.06390.271421.300834.478110.9422
51.3211-0.74670.24171.6629-0.17891.1354-0.1298-0.11060.29130.23930.0499-0.1386-0.1916-0.02970.06520.21770.0146-0.00790.1865-0.05150.258623.246738.209994.6766
61.69020.2086-0.46332.3977-0.84412.76090.0092-0.12220.08060.05570.01740.41170.0455-0.2348-0.02250.24510.05590.04580.2899-0.06260.34244.085934.644490.1326
70.70070.5031-0.16953.329-0.19320.67510.01830.0116-0.0493-0.1826-0.01930.4496-0.0355-0.18940.04560.20220.016-0.02880.3153-0.01920.33929.008117.698867.663
80.87210.46130.33311.4255-0.69142.3676-0.08970.17150.0526-0.18820.01620.13010.05640.0230.07480.16940.0064-0.01040.2303-0.00610.248722.619928.153747.5807
91.4054-0.48640.63231.3406-0.64391.7995-0.10780.26330.4479-0.0888-0.2756-0.3879-0.26130.44310.25770.2554-0.0376-0.01540.29620.11580.393835.636741.615161.3803
100.4151.08660.41734.3257-0.77012.9496-0.01480.1972-0.0889-0.10760.0449-1.01540.02290.5322-0.09520.2162-0.02060.05620.4121-0.01820.479947.50634.152175.1434
110.71680.25860.11553.8305-0.86540.19880.04750.34540.3064-0.1912-0.213-0.32260.04640.22660.23260.30940.00670.03490.42040.07760.351245.298518.422862.1626
120.45790.111-0.1780.7105-0.10381.2206-0.05250.0983-0.0773-0.1325-0.01650.02010.1207-0.05360.06910.2238-0.00480.03490.225-0.03030.23830.791-5.205454.9789
134.1996-0.55992.84943.9135-0.23122.5343-0.106-0.0015-0.0088-0.3480.01280.35180.1252-0.24610.0980.2478-0.06880.06490.2683-0.07110.254812.103-11.017965.9253
141.8115-0.8530.68711.190.62972.0669-0.1757-0.1226-0.33030.11050.14920.57720.2313-0.456-0.04560.2393-0.05090.110.33560.00230.352813.6552-2.071581.9198
150.6236-1.25410.02432.422-0.0285-0.0112-0.06140.0272-0.15630.2639-0.05560.42840.0948-0.14440.15270.3293-0.04010.09660.3452-0.02630.31499.799213.821292.5979
160.6627-0.0962-0.13540.80610.07311.2007-0.0622-0.0926-0.03640.14370.0397-0.02980.09280.05620.01880.19640.01340.01930.2106-0.0120.224231.9777-0.9645102.8008
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 352 through 428 )C352 - 428
2X-RAY DIFFRACTION2chain 'D' and (resid 5 through 61 )D5 - 61
3X-RAY DIFFRACTION3chain 'D' and (resid 62 through 118 )D62 - 118
4X-RAY DIFFRACTION4chain 'D' and (resid 119 through 192 )D119 - 192
5X-RAY DIFFRACTION5chain 'D' and (resid 193 through 350 )D193 - 350
6X-RAY DIFFRACTION6chain 'D' and (resid 351 through 427 )D351 - 427
7X-RAY DIFFRACTION7chain 'A' and (resid 5 through 96 )A5 - 96
8X-RAY DIFFRACTION8chain 'A' and (resid 97 through 276 )A97 - 276
9X-RAY DIFFRACTION9chain 'A' and (resid 277 through 427 )A277 - 427
10X-RAY DIFFRACTION10chain 'B' and (resid 5 through 41 )B5 - 41
11X-RAY DIFFRACTION11chain 'B' and (resid 42 through 96 )B42 - 96
12X-RAY DIFFRACTION12chain 'B' and (resid 97 through 351 )B97 - 351
13X-RAY DIFFRACTION13chain 'B' and (resid 352 through 427 )B352 - 427
14X-RAY DIFFRACTION14chain 'C' and (resid 5 through 41 )C5 - 41
15X-RAY DIFFRACTION15chain 'C' and (resid 42 through 96 )C42 - 96
16X-RAY DIFFRACTION16chain 'C' and (resid 97 through 351 )C97 - 351

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