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- PDB-1o58: Crystal structure of O-acetylserine sulfhydrylase (TM0665) from T... -

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Basic information

Entry
Database: PDB / ID: 1o58
TitleCrystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.80 A resolution
ComponentsO-acetylserine sulfhydrylase
KeywordsTRANSFERASE / TM0665 / O-ACETYLSERINE SULFHYDRYLASE / STRUCTURAL GENOMICS / JCSG / PSI / PROTEIN STRUCTURE INITIATIVE / JOINT CENTER FOR STRUCTURAL GENOMICS
Function / homology
Function and homology information


cysteine synthase / cysteine synthase activity / L-cysteine desulfhydrase activity / cysteine biosynthetic process from serine / pyridoxal phosphate binding / cytoplasm
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
PHOSPHATE ION / Cysteine synthase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of O-acetylserine sulfhydrylase (TM0665) from Thermotoga maritima at 1.8 A resolution
Authors: Heine, A. / Canaves, J.M. / von Delft, F. / Brinen, L.S. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshaghi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Guda, C. / ...Authors: Heine, A. / Canaves, J.M. / von Delft, F. / Brinen, L.S. / Dai, X. / Deacon, A.M. / Elsliger, M.A. / Eshaghi, S. / Floyd, R. / Godzik, A. / Grittini, C. / Grzechnik, S.K. / Guda, C. / Jaroszewski, L. / Karlak, C. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / Lesley, S.A. / McMullan, D. / McPhillips, T.M. / Miller, M.A. / Miller, M.D. / Morse, A. / Moy, K. / Ouyang, J. / Page, R. / Robb, A. / Rodrigues, K. / Schwarzenbacher, R. / Selby, T.L. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Velasquez, J. / Vincent, J. / Wang, X. / West, B. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Wilson, I.A.
History
DepositionAug 20, 2003Deposition site: RCSB / Processing site: RCSB
SupersessionSep 2, 2003ID: 1J6N
Revision 1.0Sep 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Database references / Category: pdbx_database_related
Revision 1.4Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-acetylserine sulfhydrylase
B: O-acetylserine sulfhydrylase
C: O-acetylserine sulfhydrylase
D: O-acetylserine sulfhydrylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,28812
Polymers130,5284
Non-polymers7608
Water16,880937
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12320 Å2
ΔGint-117 kcal/mol
Surface area35810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.570, 84.590, 107.220
Angle α, β, γ (deg.)90.00, 95.39, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / Refine code: 6

Dom-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1LEULEUAA-1 - 29111 - 303
2LEULEUBB0 - 29112 - 303
3ILEILECC0 - 29012 - 302
4LEULEUDD-1 - 29111 - 303

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Components

#1: Protein
O-acetylserine sulfhydrylase


Mass: 32631.938 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0665 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZD3, cysteine synthase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 937 / 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: 2.32 Å3/Da / Density % sol: 46.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9.2
Details: 50% PEG-400, 0.1M CHES pH 9.5, 0.2M NaCl, pH 9.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal grow
*PLUS
pH: 7.9 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mMTris1reservoirpH7.9
2150 mM1reservoirNaCl
30.25 TCEP1reservoir
413 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97999, 0.97980, 0.91837
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 10, 2001
RadiationMonochromator: double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979991
20.97981
30.918371
ReflectionResolution: 1.8→48.66 Å / Num. all: 97122 / Num. obs: 97122 / % possible obs: 87.6 % / Redundancy: 4.1 % / Biso Wilson estimate: 29.14 Å2 / Rsym value: 0.038 / Net I/σ(I): 20.2
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 4897 / Rsym value: 0.273 / % possible all: 59.7
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 48.8 Å / Num. measured all: 400214 / Rmerge(I) obs: 0.038
Reflection shell
*PLUS
% possible obs: 69.7 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
SOLVEphasing
RESOLVEmodel building
REFMAC5.1.9999refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→48.66 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.252 / SU ML: 0.069 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.125 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. THE STRAND-TURN-HELIX OF RESIDUES 102-126 IS FULLY ORDERED ONLY IN CHAIN A; WHAT IS INTERPRETABLE (VARIABLY) IN THE OTHER CHAINS DOES NOT OBEY NCS. IN PARTICULAR, STRONG DENSITY IS ...Details: 1. THE STRAND-TURN-HELIX OF RESIDUES 102-126 IS FULLY ORDERED ONLY IN CHAIN A; WHAT IS INTERPRETABLE (VARIABLY) IN THE OTHER CHAINS DOES NOT OBEY NCS. IN PARTICULAR, STRONG DENSITY IS VISIBLE AROUND THE ESTIMATED (BY NCS) RESIDUES C112-126 AND D109-118, BUT IS TOO AMBIGUOUS FOR INTERPRETATION. 2. DIFFERENCE DENSITY AROUND 83-85 IN CHAINS BCD INDICATE DISORDER, PRESUMABLY RELATED TO THE DISORDER OF ADJACENT RESIDUES 102-126 (POINT 1). 3. RESIDUES C60-61 DISOBEY NCS, BUT DIFFERENCE DENSITY INDICATES SUPERIMPOSED PRESENCE OF CONFORMATION FROM CHAINS ABD. LIKEWISE, DIFFERENCE DENSITY AT D60-61 INDICATES PRESENCE OF C CONFORMATION. NEITHER DENSITY WAS CLEAR ENOUGH TO BE MODELED AS ALTERNATIVE CONFORMATIONS. 4. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19807 4874 5 %RANDOM
Rwork0.15738 ---
obs0.15938 92219 87.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.156 Å2
Baniso -1Baniso -2Baniso -3
1--1.43 Å20 Å20.86 Å2
2--1.2 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8391 0 40 937 9368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0228588
X-RAY DIFFRACTIONr_bond_other_d0.0010.028268
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.97311594
X-RAY DIFFRACTIONr_angle_other_deg0.862319175
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.55251116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.4323.808323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.097151535
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2481559
X-RAY DIFFRACTIONr_chiral_restr0.0860.21343
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029472
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021607
X-RAY DIFFRACTIONr_nbd_refined0.2110.21835
X-RAY DIFFRACTIONr_nbd_other0.1850.28719
X-RAY DIFFRACTIONr_nbtor_other0.0810.25120
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0210.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1090.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2750.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.219
X-RAY DIFFRACTIONr_mcbond_it0.9771.56002
X-RAY DIFFRACTIONr_mcangle_it1.30728900
X-RAY DIFFRACTIONr_scbond_it2.33833220
X-RAY DIFFRACTIONr_scangle_it3.2064.52694
Refine LS restraints NCS

Ens-ID: 1 / Number: 3827 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.365
2Bloose positional0.395
3Cloose positional0.45
4Dloose positional0.345
1Aloose thermal3.8510
2Bloose thermal1.7110
3Cloose thermal2.4910
4Dloose thermal2.6710
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.208 259 5.3 %
Rwork0.177 4631 -
Refinement TLS params.Method: refined / Origin x: 41.501 Å / Origin y: 5.778 Å / Origin z: 80.26 Å
111213212223313233
T-0.0715 Å20.0031 Å2-0.0077 Å2--0.1393 Å20.0029 Å2---0.1051 Å2
L0.7806 °20.0219 °2-0.1866 °2-0.2815 °2-0.1603 °2--0.4172 °2
S0.0147 Å °0.0478 Å °-0.0452 Å °-0.0053 Å °-0.0526 Å °-0.0395 Å °0.0022 Å °0.0576 Å °0.0379 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 291
2X-RAY DIFFRACTION1B0 - 291
3X-RAY DIFFRACTION1C0 - 290
4X-RAY DIFFRACTION1D-1 - 291
Refinement
*PLUS
Num. reflection obs: 97093 / % reflection Rfree: 4.9 % / Rfactor Rfree: 0.198 / Rfactor Rwork: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.017
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.41

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