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- PDB-6g60: Choline sulfatase from Ensifer (Sinorhizobium) meliloti cocrystal... -

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Basic information

Entry
Database: PDB / ID: 6g60
TitleCholine sulfatase from Ensifer (Sinorhizobium) meliloti cocrystalized with choline
ComponentsCholine-sulfatase
KeywordsHYDROLASE / Choline-sulfatase
Function / homology
Function and homology information


choline biosynthetic process / choline-sulfatase / choline-sulfatase activity / metal ion binding / cytoplasm
Similarity search - Function
Choline-sulfatase / Choline sulfatase enzyme C-terminal domain / Choline sulfatase enzyme C terminal / Sulfatases signature 2. / Sulfatases signature 1. / Sulfatase, conserved site / Sulfatase, N-terminal / Sulfatase / Alkaline-phosphatase-like, core domain superfamily
Similarity search - Domain/homology
CHOLINE ION / Choline-sulfatase
Similarity search - Component
Biological speciesRhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.84 Å
AuthorsMartinez-Rodriguez, S. / Camara-Artigas, A.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: Structural insights into choline-O-sulfatase reveal the molecular determinants for ligand binding.
Authors: Gavira, J.A. / Camara-Artigas, A. / Neira, J.L. / Torres de Pinedo, J.M. / Sanchez, P. / Ortega, E. / Martinez-Rodriguez, S.
History
DepositionMar 30, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2019Provider: repository / Type: Initial release
Revision 2.0Apr 24, 2019Group: Data collection / Polymer sequence / Category: entity_poly / pdbx_seq_map_depositor_info
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_seq_map_depositor_info.one_letter_code
Revision 2.1Mar 8, 2023Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / struct_conn / struct_conn_type
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 2.2Nov 13, 2024Group: Data collection / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Choline-sulfatase
B: Choline-sulfatase
C: Choline-sulfatase
D: Choline-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,77919
Polymers232,5924
Non-polymers1,18615
Water21,9421218
1
A: Choline-sulfatase
C: Choline-sulfatase
hetero molecules

A: Choline-sulfatase
C: Choline-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,68318
Polymers232,5924
Non-polymers1,09014
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area20110 Å2
ΔGint-95 kcal/mol
Surface area64070 Å2
MethodPISA
2
A: Choline-sulfatase
C: Choline-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8419
Polymers116,2962
Non-polymers5457
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-52 kcal/mol
Surface area38150 Å2
MethodPISA
3
B: Choline-sulfatase
D: Choline-sulfatase
hetero molecules

B: Choline-sulfatase
D: Choline-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,87520
Polymers232,5924
Non-polymers1,28216
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area19130 Å2
ΔGint-106 kcal/mol
Surface area64100 Å2
MethodPISA
4
B: Choline-sulfatase
D: Choline-sulfatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,93710
Polymers116,2962
Non-polymers6418
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-54 kcal/mol
Surface area37720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.538, 206.898, 116.602
Angle α, β, γ (deg.)90.000, 110.170, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-605-

SO4

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Components

#1: Protein
Choline-sulfatase


Mass: 58148.066 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium meliloti (strain 1021) (bacteria)
Strain: 1021 / Gene: betC, R00949, SMc00127 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O69787, choline-sulfatase
#2: Chemical
ChemComp-CHT / CHOLINE ION


Mass: 104.171 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H14NO
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1218 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.13 Å3/Da / Density % sol: 60.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.0 M Lithium sulfate, 0.1M Hepes pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 25, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965 Å / Relative weight: 1
ReflectionResolution: 1.84→103.45 Å / Num. obs: 411516 / % possible obs: 95.1 % / Redundancy: 2.4 % / Biso Wilson estimate: 27.65 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.031 / Rrim(I) all: 0.051 / Net I/σ(I): 13.1 / Num. measured all: 563519 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.84-1.872.40.50127428114490.6970.40.645294.1
10.08-103.452.50.023367914530.9980.0170.02835.195.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.5.27data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→75.183 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.92 / Phase error: 20.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1987 20514 4.98 %
Rwork0.1688 391002 -
obs0.1703 411516 84.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.68 Å2 / Biso mean: 34.0352 Å2 / Biso min: 13.54 Å2
Refinement stepCycle: final / Resolution: 1.84→75.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16000 0 67 1218 17285
Biso mean--51.37 37.55 -
Num. residues----2024
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116528
X-RAY DIFFRACTIONf_angle_d1.01822553
X-RAY DIFFRACTIONf_chiral_restr0.0592385
X-RAY DIFFRACTIONf_plane_restr0.0072970
X-RAY DIFFRACTIONf_dihedral_angle_d5.04411681
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 (%)
1.84-1.86090.34347410.2922128361357784
1.8609-1.88280.31296940.2733123551304979
1.8828-1.90580.29176150.2575121871280278
1.9058-1.92990.28847040.243124921319681
1.9299-1.95530.28316480.2343120951274379
1.9553-1.98210.2686590.2195128601351983
1.9821-2.01040.24357980.2113139381473690
2.0104-2.04040.21726970.1982139071460490
2.0404-2.07230.24947610.1945138351459690
2.0723-2.10630.22447080.1983139521466090
2.1063-2.14260.23567580.1993137631452189
2.1426-2.18160.23027010.1902137871448889
2.1816-2.22350.23366320.1882137701440289
2.2235-2.26890.216320.178137191435188
2.2689-2.31830.22656860.1753135121419887
2.3183-2.37220.21326980.1754134851418386
2.3722-2.43150.20956770.1672133141399185
2.4315-2.49730.19216960.1671130121370884
2.4973-2.57070.18516060.1625126721327882
2.5707-2.65370.19776410.1741118601250177
2.6537-2.74860.22656040.1806118821248677
2.7486-2.85860.21776270.1764118401246776
2.8586-2.98870.21596940.1807135381423287
2.9887-3.14630.21237480.1765133041405286
3.1463-3.34340.18977170.1698131801389785
3.3434-3.60160.16696580.1534129901364884
3.6016-3.9640.15877330.1344128061353983
3.964-4.53750.15845970.1271125141311180
4.5375-5.71650.1626370.141114981213574
5.7165-75.24560.17647470.1596140991484691
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)
10.3627-0.1073-0.05040.0629-0.04340.3682-0.1398-0.07430.04610.10240.10620.07860.0785-0.1143-0.00060.28130.0355-0.02610.21960.00070.178322.68742.690960.3153
20.0195-0.0437-0.04910.09930.06730.0439-0.0580.09060.0956-0.15190.0485-0.0778-0.0239-0.082-0.00180.3103-0.0254-0.07990.28340.0060.189320.7297.799739.6863
30.3829-0.26870.13960.2764-0.08360.1083-0.1483-0.030.01380.01760.110.0102-0.0264-0.0054-0.01020.26370.0308-0.0240.1885-0.01050.136135.7455-2.035657.1804
40.12030.07960.02030.0760.07010.1133-0.10180.2141-0.1523-0.1570.00810.16380.1227-0.124-0.00020.3758-0.0752-0.05810.3446-0.05640.271611.7142-6.729936.3313
50.2641-0.2737-0.04720.2798-0.06240.1347-0.1333-0.0013-0.07880.08680.06710.08820.1618-0.0641-0.00660.2826-0.0029-0.01090.1976-0.00760.150525.5367-7.92552.4666
60.218-0.1717-0.09820.22620.21690.2308-0.1859-0.0764-0.05010.15520.10230.20770.183-0.1694-0.010.3054-0.02380.03890.29550.0320.23827.8792-2.55660.5776
70.27330.088-0.00950.47180.39790.4175-0.1233-0.00590.1280.0326-0.00440.081-0.0354-0.1321-0.03440.16680.0458-0.01110.28620.0050.210210.826514.048251.598
80.0302-0.0224-0.00620.0043-0.0086-0.002-0.0731-0.25380.0940.36060.1125-0.0539-0.01190.0579-00.45350.0383-0.05630.3495-0.03540.267654.79556.193170.8315
90.4627-0.1473-0.24490.25160.09380.783-0.0116-0.0780.0341-0.02050.105-0.02190.04560.12610.07150.16710.02580.01450.2093-0.03060.159537.9842-36.673492.1749
10-0.0433-0.1102-0.11660.08290.13240.0303-0.0357-0.1331-0.21480.18760.16530.22920.3159-0.32010.01240.2766-0.0657-0.05380.26510.0340.289420.1405-42.072581.7998
110.20440.0031-0.09270.33890.09470.41930.0643-0.14320.0431-0.02520.06270.01250.0345-0.03030.04440.15490.0320.0150.2573-0.02320.144228.744-31.5837102.1277
120.0843-0.03210.08380.0834-0.06590.1460.13380.06090.035-0.12360.0919-0.0183-0.2077-0.3090.00870.21650.02780.02060.32060.07380.229620.7644-27.912371.892
130.23890.0006-0.39750.07240.18550.60930.0821-0.04120.1230.00120.0632-0.0314-0.1051-0.05720.20340.14950.01770.03810.2018-0.01630.156629.5672-26.13491.635
140.1378-0.0344-0.24540.4226-0.28470.6016-0.0288-0.06730.0429-0.01040.1193-0.038-0.07160.26180.1030.1235-0.00210.02050.2619-0.06920.197546.8996-33.118485.926
150.3914-0.37750.05630.3718-0.27671.12920.09850.01860.028-0.14950.0278-0.00040.05250.10450.21810.1571-0.01060.01910.1546-0.03110.166639.4379-36.889268.7281
160.0626-0.0577-0.06760.1393-0.05950.1256-0.0778-0.10090.03850.21320.19010.0622-0.16630.266500.50590.05570.03830.4672-0.00750.453729.772-46.5881113.8196
170.6609-0.1072-0.08220.49930.09090.2427-0.0378-0.02950.22380.0750.06630.05060.00290.04240.00320.15290.0562-0.04970.1803-0.01360.275625.266641.55959.5409
180.20860.12040.03280.1739-0.06250.0610.0240.0550.3169-0.01260.02880.04-0.04950.05970.00010.18410.0231-0.04450.251-0.03880.373632.955249.527857.7407
190.28150.13160.20240.7646-0.12820.27950.1453-0.46190.36870.41310.16910.1764-0.07570.05610.14990.3920.13060.01340.3744-0.26180.4418.545251.887381.701
200.1519-0.00940.02250.1078-0.10640.08950.0032-0.07610.4314-0.03460.02540.0143-0.00810.1426-0.00110.20930.0373-0.05470.2713-0.07760.455432.538156.078763.1876
210.343-0.0098-0.04870.32960.02180.1008-0.01420.01130.3355-0.00620.00720.1584-0.0824-0.0606-0.00610.18840.0727-0.04860.24410.00170.427617.302948.45655.0115
22-0.0155-0.0454-0.04250.22630.14620.0934-0.0527-0.08340.30290.2061-0.03660.09280.0208-0.127-0.08450.17470.1248-0.06090.25740.02890.43818.538844.172458.2577
230.0365-0.0518-0.07910.0650.07770.10720.0329-0.03890.36510.22470.08550.15980.0279-0.01980.02250.19270.13770.06170.2125-0.050.54231.445850.651971.5573
240.0199-0.0022-0.06430.16820.16030.2168-0.1242-0.11560.00670.33720.1310.18690.10840.0090.00450.25450.09680.02460.2443-0.00030.33815.216333.605569.4194
250.18280.05380.03720.16520.0181-0.011-0.08330.18660.3226-0.12840.2251-0.014-0.0340.0010.00010.3257-0.04-0.06280.39370.04160.363144.31532.494646.893
260.22040.17740.10870.2052-0.06660.3045-0.0543-0.0776-0.0209-0.15970.04480.03180.16820.0731-00.37560.04050.06830.22640.01490.305334.0995-76.358289.5565
27-0.0280.0309-0.07020.0607-0.03860.02780.0476-0.11890.0530.33130.091-0.0152-0.11260.1130.00010.39780.1625-0.05390.4958-0.01940.501250.5646-71.5555101.7924
280.15070.2442-0.05380.3535-0.07120.1054-0.0885-0.21060.0245-0.01930.01740.09010.2918-0.0694-00.34230.02620.07770.2840.06770.361328.28-81.3125101.6687
290.10480.039-0.15620.5872-0.00440.8545-0.1371-0.1713-0.2273-0.187-0.0701-0.18780.8190.0352-0.13130.39310.29610.11770.19110.14070.439745.4297-86.572596.8269
300.23130.2422-0.16770.5352-0.20240.0385-0.20230.0035-0.1732-0.30090.1325-0.16460.24660.04040.00560.52530.05270.10120.2499-0.04440.357443.4163-81.576578.3238
310.38260.1520.08590.2513-0.12340.1288-0.2693-0.0079-0.03870.06030.1532-0.36230.2455-0.0471-0.07360.40150.06950.06840.2765-0.05480.338153.2305-67.073380.1598
320.0832-0.1019-0.07780.2548-0.06830.0865-0.2450.0508-0.1394-0.01060.11480.29740.3094-0.1416-0.00010.5221-0.00980.05620.5689-0.02990.54618.2271-66.1501106.2826
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 121 )A5 - 121
2X-RAY DIFFRACTION2chain 'A' and (resid 122 through 159 )A122 - 159
3X-RAY DIFFRACTION3chain 'A' and (resid 160 through 214 )A160 - 214
4X-RAY DIFFRACTION4chain 'A' and (resid 215 through 251 )A215 - 251
5X-RAY DIFFRACTION5chain 'A' and (resid 252 through 313 )A252 - 313
6X-RAY DIFFRACTION6chain 'A' and (resid 314 through 431 )A314 - 431
7X-RAY DIFFRACTION7chain 'A' and (resid 432 through 487 )A432 - 487
8X-RAY DIFFRACTION8chain 'A' and (resid 488 through 512 )A488 - 512
9X-RAY DIFFRACTION9chain 'B' and (resid 5 through 121 )B5 - 121
10X-RAY DIFFRACTION10chain 'B' and (resid 122 through 159 )B122 - 159
11X-RAY DIFFRACTION11chain 'B' and (resid 160 through 214 )B160 - 214
12X-RAY DIFFRACTION12chain 'B' and (resid 215 through 251 )B215 - 251
13X-RAY DIFFRACTION13chain 'B' and (resid 252 through 313 )B252 - 313
14X-RAY DIFFRACTION14chain 'B' and (resid 314 through 391 )B314 - 391
15X-RAY DIFFRACTION15chain 'B' and (resid 392 through 472 )B392 - 472
16X-RAY DIFFRACTION16chain 'B' and (resid 473 through 510 )B473 - 510
17X-RAY DIFFRACTION17chain 'C' and (resid 5 through 182 )C5 - 182
18X-RAY DIFFRACTION18chain 'C' and (resid 183 through 214 )C183 - 214
19X-RAY DIFFRACTION19chain 'C' and (resid 215 through 251 )C215 - 251
20X-RAY DIFFRACTION20chain 'C' and (resid 252 through 282 )C252 - 282
21X-RAY DIFFRACTION21chain 'C' and (resid 283 through 360 )C283 - 360
22X-RAY DIFFRACTION22chain 'C' and (resid 361 through 391 )C361 - 391
23X-RAY DIFFRACTION23chain 'C' and (resid 392 through 431 )C392 - 431
24X-RAY DIFFRACTION24chain 'C' and (resid 432 through 472 )C432 - 472
25X-RAY DIFFRACTION25chain 'C' and (resid 473 through 509 )C473 - 509
26X-RAY DIFFRACTION26chain 'D' and (resid 5 through 121 )D5 - 121
27X-RAY DIFFRACTION27chain 'D' and (resid 122 through 159 )D122 - 159
28X-RAY DIFFRACTION28chain 'D' and (resid 160 through 214 )D160 - 214
29X-RAY DIFFRACTION29chain 'D' and (resid 215 through 313 )D215 - 313
30X-RAY DIFFRACTION30chain 'D' and (resid 314 through 431 )D314 - 431
31X-RAY DIFFRACTION31chain 'D' and (resid 432 through 472 )D432 - 472
32X-RAY DIFFRACTION32chain 'D' and (resid 473 through 509 )D473 - 509

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