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- PDB-6ahi: Crystal structure of O-acetylserine dependent cystathionine beta-... -

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Basic information

Entry
Database: PDB / ID: 6ahi
TitleCrystal structure of O-acetylserine dependent cystathionine beta-synthase from Helicobacter pylori.
ComponentsCysteine synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


cystathionine beta-synthase activity / cysteine synthase / cysteine synthase activity / cysteine biosynthetic process / cysteine biosynthetic process from serine / cytoplasm
Similarity search - Function
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 / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
METHIONINE / Cysteine synthase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsTarique, F.K. / Devi, S. / Rehman, S.A.A.
CitationJournal: Mol.Microbiol. / Year: 2019
Title: Identification and characterization of Helicobacter pylori O-acetylserine-dependent cystathionine beta-synthase, a distinct member of the PLP-II family.
Authors: Devi, S. / Tarique, K.F. / Ali, M.F. / Abdul Rehman, S.A. / Gourinath, S.
History
DepositionAug 19, 2018Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 5, 2018ID: 5HBG
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Apr 27, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)68,6973
Polymers68,5482
Non-polymers1491
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3590 Å2
ΔGint-29 kcal/mol
Surface area22610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.405, 82.719, 96.141
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 1 - 306 / Label seq-ID: 1 - 306

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Cysteine synthase / CSase / O-acetylserine (thiol)-lyase / OAS-TL / O-acetylserine sulfhydrylase


Mass: 34273.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (strain ATCC 700392 / 26695) (bacteria)
Strain: ATCC 700392 / 26695 / Gene: cysM, cysK, HP_0107
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: P56067, cysteine synthase
#2: Chemical ChemComp-MET / METHIONINE


Type: L-peptide linking / Mass: 149.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.14 Å3/Da / Density % sol: 42.46 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Peg20K-Peg550MME 15%, 0.09M Amino acids mixture, 0.1M Mes-Imadazole buffer pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 45368 / % possible obs: 100 % / Redundancy: 16.3 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 47
Reflection shellResolution: 1.9→1.93 Å / Rmerge(I) obs: 0.862 / Num. unique obs: 2244

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Z7W

1z7w


Resolution: 1.9→48.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.955 / SU B: 8.444 / SU ML: 0.11 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.135 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20751 2279 5 %RANDOM
Rwork0.18322 ---
obs0.18447 43044 99.77 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 37.455 Å2
Baniso -1Baniso -2Baniso -3
1-1.47 Å20 Å20 Å2
2--2.03 Å20 Å2
3----3.51 Å2
Refinement stepCycle: 1 / Resolution: 1.9→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4666 0 9 132 4807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0144789
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174487
X-RAY DIFFRACTIONr_angle_refined_deg1.4691.6716495
X-RAY DIFFRACTIONr_angle_other_deg0.9171.64210514
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.32923.465202
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20415802
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6391518
X-RAY DIFFRACTIONr_chiral_restr0.0740.2653
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025324
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02842
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5261.2822449
X-RAY DIFFRACTIONr_mcbond_other1.5241.2822448
X-RAY DIFFRACTIONr_mcangle_it2.2711.9173056
X-RAY DIFFRACTIONr_mcangle_other2.2711.9173057
X-RAY DIFFRACTIONr_scbond_it2.6831.6372340
X-RAY DIFFRACTIONr_scbond_other2.6831.6372340
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9522.3233440
X-RAY DIFFRACTIONr_long_range_B_refined5.27715.9925130
X-RAY DIFFRACTIONr_long_range_B_other5.26415.9795124
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9403 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.11 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 169 -
Rwork0.255 3076 -
obs--97.77 %
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)
10.92350.0563-0.62580.96640.10912.88070.1571-0.17480.08360.00870.0232-0.1666-0.58730.7861-0.18030.1434-0.18210.06080.2373-0.06060.230929.751-21.286-14.002
21.1059-0.1430.82730.8787-0.74153.89030.0105-0.1025-0.00890.09150.13420.1313-0.6631-0.3923-0.14480.1470.0590.05830.04560.01050.21755.837-22.2395.456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 306
2X-RAY DIFFRACTION2B1 - 601

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