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- PDB-3rr2: Structure of a Cysteine synthase (O-Acetylserine Sulfhydrylase (O... -

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Basic information

Entry
Database: PDB / ID: 3rr2
TitleStructure of a Cysteine synthase (O-Acetylserine Sulfhydrylase (OASS)) from Mycobacterium marinum ATCC BAA-535 / M
ComponentsCysteine synthase
KeywordsTRANSFERASE / O-Acetylserine Sulfhydrylase (OASS) / Cysteine synthase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
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 marinum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 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
DepositionApr 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)32,8041
Polymers32,8041
Non-polymers00
Water3,225179
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Cysteine synthase

A: Cysteine synthase


Theoretical massNumber of molelcules
Total (without water)65,6072
Polymers65,6072
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area3550 Å2
ΔGint-21 kcal/mol
Surface area24140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.190, 51.190, 229.900
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-445-

HOH

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Components

#1: Protein Cysteine synthase


Mass: 32803.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium marinum (bacteria) / Strain: ATCC BAA-535 / M / Gene: cysK1, MMAR_3645 / Production host: Escherichia coli (E. coli) / References: UniProt: B2HL85, cysteine synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.3 Å3/Da / Density % sol: 46.42 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→46.76 Å / Num. obs: 23516 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 27.822 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 19.29
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.95-20.5084.05143961682100
2-2.060.4134.9144341660100
2.06-2.120.3756.0913764159799.9
2.12-2.180.2797.6139011545100
2.18-2.250.2668.4713636152999.7
2.25-2.330.21410.4413356147999.5
2.33-2.420.16812.62133751416100
2.42-2.520.15713.62129271351100
2.52-2.630.13915.73127301317100
2.63-2.760.12617.85124441271100
2.76-2.910.10221.07121171210100
2.91-3.080.08325.46117891161100
3.08-3.30.06830.84112801091100
3.3-3.560.05935.24107051020100
3.56-3.90.05239.829967957100
3.9-4.360.04743.75914885999.9
4.36-5.030.04147.38311789100
5.03-6.170.04243.187228676100
6.17-8.720.03645.895694552100
8.720.03248306735498.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.19 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å19.65 Å
Translation3 Å19.65 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→46.76 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.918 / WRfactor Rfree: 0.2128 / WRfactor Rwork: 0.1741 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8661 / SU B: 7.469 / SU ML: 0.096 / SU R Cruickshank DPI: 0.1564 / SU Rfree: 0.148 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 1197 5.1 %RANDOM
Rwork0.188 ---
obs0.1902 23281 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 44.2 Å2 / Biso mean: 24.792 Å2 / Biso min: 2.37 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20 Å20 Å2
2--0.56 Å20 Å2
3----1.12 Å2
Refinement stepCycle: LAST / Resolution: 1.95→46.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2089 0 0 179 2268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222128
X-RAY DIFFRACTIONr_bond_other_d0.0010.021374
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9772906
X-RAY DIFFRACTIONr_angle_other_deg0.90733377
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9115290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.06424.21176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.99715319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9121514
X-RAY DIFFRACTIONr_chiral_restr0.0750.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212414
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02394
X-RAY DIFFRACTIONr_mcbond_it0.7411.51446
X-RAY DIFFRACTIONr_mcbond_other0.1791.5591
X-RAY DIFFRACTIONr_mcangle_it1.3322307
X-RAY DIFFRACTIONr_scbond_it1.9163682
X-RAY DIFFRACTIONr_scangle_it3.194.5598
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 89 -
Rwork0.205 1576 -
all-1665 -
obs--99.23 %
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)
10.647-0.1552-0.3120.56880.16240.7324-0.0360.0465-0.00210.08780.0289-0.0407-0.0326-0.01960.00720.0467-0.0114-0.01360.08990.01280.070415.221911.2861107.8274
23.56280.5045-0.73960.9598-1.04971.2964-0.0780.5813-0.1641-0.17450.14310.08050.1941-0.2797-0.06510.032-0.0281-0.01370.179-0.04530.0396-0.11289.87496.5553
32.0288-0.27920.60631.72560.46713.11010.02930.2620.0344-0.0684-0.0753-0.02890.0718-0.03310.0460.0074-0.00750.01030.15030.00370.053825.27944.351398.2094
40.2762-0.20120.69180.88330.54493.9406-0.02410.0239-0.08160.0808-0.02420.06860.0784-0.22180.04830.0316-0.04190.01570.1348-0.0680.125216.8283-5.0053100.7658
53.02530.553-0.4422.12210.28111.6634-0.0031-0.1439-0.31340.08740.03170.06750.1155-0.0834-0.02860.047-0.0129-0.01560.08960.01720.071623.7851-2.2046106.693
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 59
2X-RAY DIFFRACTION2A60 - 161
3X-RAY DIFFRACTION3A162 - 218
4X-RAY DIFFRACTION4A219 - 275
5X-RAY DIFFRACTION5A276 - 299

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