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- PDB-4i1y: The structure of Cysteine synthase from Mycobacterium ulcerans Agy99 -

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Basic information

Entry
Database: PDB / ID: 4i1y
TitleThe structure of Cysteine synthase from Mycobacterium ulcerans Agy99
ComponentsCysteine synthase
KeywordsTRANSFERASE / SSGCID / Seattle Structural Genomics Center for Infectious Disease / Cysteine synthase / NIAID / National Institute of Allergy and Infectious Diseases / SYNTHASE
Function / homology
Function and homology information


cysteine synthase / cysteine synthase activity / cysteine biosynthetic process from serine
Similarity search - Function
Cysteine synthase CysK / Cysteine synthase / Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium ulcerans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Tuberculosis (Edinb) / Year: 2015
Title: Increasing the structural coverage of tuberculosis drug targets.
Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / ...Authors: Baugh, L. / Phan, I. / Begley, D.W. / Clifton, M.C. / Armour, B. / Dranow, D.M. / Taylor, B.M. / Muruthi, M.M. / Abendroth, J. / Fairman, J.W. / Fox, D. / Dieterich, S.H. / Staker, B.L. / Gardberg, A.S. / Choi, R. / Hewitt, S.N. / Napuli, A.J. / Myers, J. / Barrett, L.K. / Zhang, Y. / Ferrell, M. / Mundt, E. / Thompkins, K. / Tran, N. / Lyons-Abbott, S. / Abramov, A. / Sekar, A. / Serbzhinskiy, D. / Lorimer, D. / Buchko, G.W. / Stacy, R. / Stewart, L.J. / Edwards, T.E. / Van Voorhis, W.C. / Myler, P.J.
History
DepositionNov 21, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cysteine synthase
B: Cysteine synthase
C: Cysteine synthase
D: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,5859
Polymers131,2864
Non-polymers2985
Water79344
1
A: Cysteine synthase
D: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7754
Polymers65,6432
Non-polymers1322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-41 kcal/mol
Surface area21850 Å2
MethodPISA
2
B: Cysteine synthase
C: Cysteine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8105
Polymers65,6432
Non-polymers1673
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-42 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.965, 77.900, 87.101
Angle α, β, γ (deg.)114.210, 104.860, 94.370
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Cysteine synthase /


Mass: 32821.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium ulcerans (bacteria) / Strain: Agy99 / Gene: cysK1, MUL_1465 / Production host: Escherichia coli (E. coli) / References: UniProt: A0PNS1, cysteine synthase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / 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: 2.66 Å3/Da / Density % sol: 53.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 27.42 mg/ml MyulA.01147.b, 20% PEG3350, 200mM sodium sulfate, bis-tris propane pH 6.5, 20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 21, 2010
RadiationMonochromator: Asymmetric curved crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 40349 / % possible obs: 97.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.052 / Χ2: 0.98 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.643.30.43218030.928189.3
2.64-2.693.30.41119120.946192
2.69-2.743.40.37519360.97195.2
2.74-2.83.50.33720610.928197.8
2.8-2.863.50.29519900.963198.1
2.86-2.933.60.2520420.989198.4
2.93-33.60.22420501.018198.6
3-3.083.60.18320341.074198.6
3.08-3.173.60.15420081.046198.7
3.17-3.283.60.11920741.081198.8
3.28-3.393.60.09420161.089198.9
3.39-3.533.60.07620350.941198.8
3.53-3.693.60.0620640.942199
3.69-3.883.60.04520301.045199.1
3.88-4.133.60.03920450.814199.2
4.13-4.453.60.03420271.092199.2
4.45-4.893.60.03120650.905199.4
4.89-5.63.50.03120511.052199.5
5.6-7.053.50.02720470.928199.7
7.05-503.70.0220590.842199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.59 Å48.67 Å
Translation2.59 Å48.67 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RR2

3rr2


Resolution: 2.6→48.71 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.883 / WRfactor Rfree: 0.2889 / WRfactor Rwork: 0.2564 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7749 / SU B: 27.388 / SU ML: 0.264 / SU R Cruickshank DPI: 0.6635 / SU Rfree: 0.3461 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.664 / ESU R Free: 0.346 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2935 2029 5 %RANDOM
Rwork0.2611 ---
obs0.2626 40348 97.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 304.34 Å2 / Biso mean: 82.3106 Å2 / Biso min: 57.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å21.2 Å21.04 Å2
2---3.55 Å21.66 Å2
3---2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.6→48.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7445 0 13 44 7502
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197567
X-RAY DIFFRACTIONr_bond_other_d0.0010.027154
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.97710322
X-RAY DIFFRACTIONr_angle_other_deg1.2316359
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.73951057
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.10324.138261
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78151085
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4491552
X-RAY DIFFRACTIONr_chiral_restr0.0630.21262
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218769
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021515
LS refinement shellResolution: 2.6→2.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 118 -
Rwork0.344 2507 -
all-2625 -
obs--85.56 %
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)
11.03620.01010.41671.8282-0.54992.18-0.0151-0.0324-0.25470.2336-0.0160.0412-0.1026-0.08650.03120.76980.00040.09070.83620.03970.732313.238245.4458-4.4634
23.90951.1972-1.50012.4301-0.38253.1994-0.0238-0.2808-0.02450.2612-0.0894-0.2935-0.1409-0.1010.11310.83-0.05020.01980.89590.14710.63417.416940.290116.1627
32.5109-0.1230.26473.265-0.57891.17590.0218-0.09590.19710.5042-0.00410.0866-0.3368-0.0293-0.01770.86360.00710.1130.8290.06770.66318.94957.6299-5.8165
43.98731.0125-0.55116.059-0.17980.63940.1853-0.36950.12270.9738-0.15790.589-0.1682-0.4228-0.02740.80430.04020.23750.97140.0240.7418-5.989650.1464-3.8686
53.6350.59751.89123.110.53733.0061-0.3367-0.33720.86950.2052-0.12530.1524-0.5059-0.22140.4620.81220.07080.0040.8365-0.05390.82281.531920.226746.2889
64.3868-0.44216.34065.49220.06299.9097-2.0931-3.82520.19050.41641.16144.4566-2.6498-5.11640.93171.38561.50410.13234.21790.51424.2383-15.013826.565832.8706
74.0329-1.76490.3064.08370.64845.44670.29980.92660.2739-0.9369-0.43621.9763-2.0831-2.54420.13641.47180.9992-0.23192.4420.25672.0419-10.366734.930624.5459
82.063-1.32650.47914.5566-0.15741.6224-0.6543-0.30231.04721.11190.1169-1.346-0.6160.13570.53741.1197-0.031-0.55930.8546-0.08431.26954.625732.750552.89
91.68220.0798-0.11211.4875-0.46131.5108-0.04230.0716-0.2086-0.18350.0418-0.22820.29630.26250.00050.78450.05070.08890.91090.02650.72727.91078.941139.8446
107.4067-0.4101-2.59962.6525-0.05651.6332-0.6622-1.5508-1.30850.12460.1615-1.37720.17870.96280.50080.81820.12410.1181.56780.4071.582925.210515.220830.665
1120.1707-9.4157-8.44216.68285.39224.4972-1.96274.0463-3.64341.7665-0.33892.77141.142-0.68892.30161.7415-0.32070.61622.9676-0.91622.16723.3415-2.123542.4274
123.7399-1.527-1.65511.95531.04572.99770.13341.7566-1.655-0.0807-0.71720.66960.424-0.82680.58370.66090.0195-0.09011.5596-0.71981.3566-0.8293-0.378227.2541
131.6198-0.7836-0.20712.3827-0.1021.32250.00050.1925-0.2298-0.08910.00080.2187-0.0022-0.1999-0.00130.7363-0.04190.11660.8640.04310.753613.070631.77-14.0002
142.5209-0.14953.43728.32543.1576.7618-0.17030.1889-0.51610.68150.00860.15250.31090.13820.16170.7369-0.11390.27260.9360.07631.1053-4.03821.7214-8.3201
1510.1458-1.5538-0.91272.75136.746718.82260.2215-0.4959-0.56820.22740.2638-0.20941.6611-0.4738-0.48531.1009-0.3208-0.04640.9572-0.14971.5848-8.031313.2965-16.0736
161.0316-0.5441-0.25111.59880.18162.459-0.0036-0.0336-0.24740.0781-0.03480.0040.36450.04660.03840.7175-0.01190.07460.80020.07880.805824.494521.2165-12.1644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 63
2X-RAY DIFFRACTION2A64 - 141
3X-RAY DIFFRACTION3A142 - 197
4X-RAY DIFFRACTION4A198 - 295
5X-RAY DIFFRACTION5B0 - 50
6X-RAY DIFFRACTION6B51 - 92
7X-RAY DIFFRACTION7B93 - 141
8X-RAY DIFFRACTION8B142 - 296
9X-RAY DIFFRACTION9C1 - 67
10X-RAY DIFFRACTION10C68 - 142
11X-RAY DIFFRACTION11C150 - 169
12X-RAY DIFFRACTION12C170 - 297
13X-RAY DIFFRACTION13D-1 - 63
14X-RAY DIFFRACTION14D64 - 121
15X-RAY DIFFRACTION15D122 - 142
16X-RAY DIFFRACTION16D150 - 298

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