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- PDB-2ixd: Crystal structure of the putative deacetylase BC1534 from Bacillu... -

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Basic information

Entry
Database: PDB / ID: 2ixd
TitleCrystal structure of the putative deacetylase BC1534 from Bacillus cereus
ComponentsLMBE-RELATED PROTEIN
KeywordsHYDROLASE / HEXAMER / DEACETYLASE / ROSSMANN FOLD / ZINC-DEPENDENT METALLOENZYME
Function / homology
Function and homology information


bacillithiol biosynthetic process / deacetylase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / metal ion binding
Similarity search - Function
Bacillithiol biosynthesis deacetylase, BshB1 / LmbE-like / N-acetylglucosaminyl phosphatidylinositol deacetylase-related / Putative deacetylase LmbE-like domain superfamily / GlcNAc-PI de-N-acetylase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / N-acetyl-alpha-D-glucosaminyl L-malate deacetylase 1
Similarity search - Component
Biological speciesBACILLUS CEREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsFadouloglou, V.E. / Bouriotis, V. / Kokkinidis, M.
Citation
Journal: FEBS J. / Year: 2007
Title: Crystal Structure of the Bczbp, a Zinc-Binding Protein from Bacillus Cereus
Authors: Fadouloglou, V.E. / Deli, A. / Glykos, N.M. / Psylinakis, E. / Bouriotis, V. / Kokkinidis, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: Purification, Crystallization and Preliminary Characterization of a Putative Lmbe-Like Deacetylase from Bacillus Cereus
Authors: Fadouloglou, V.E. / Kotsifaki, D. / Gazi, A.D. / Fellas, G. / Meramveliotaki, C. / Deli, A. / Psylinakis, E. / Bouriotis, V. / Kokkinidis, M.
History
DepositionJul 7, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 12, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_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

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Assembly

Deposited unit
A: LMBE-RELATED PROTEIN
B: LMBE-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7626
Polymers54,5132
Non-polymers2494
Water8,485471
1
A: LMBE-RELATED PROTEIN
B: LMBE-RELATED PROTEIN
hetero molecules

A: LMBE-RELATED PROTEIN
B: LMBE-RELATED PROTEIN
hetero molecules

A: LMBE-RELATED PROTEIN
B: LMBE-RELATED PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,28518
Polymers163,5386
Non-polymers74712
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area22010 Å2
ΔGint-356.1 kcal/mol
Surface area48180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.892, 75.892, 404.699
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11B-2020-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.94418, -0.32914, 0.01347), (-0.32929, -0.94416, 0.01119), (0.00903, -0.015, -0.99985)
Vector: 12.38713, 83.6343, 338.22656)

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Components

#1: Protein LMBE-RELATED PROTEIN / BC1534 PUTATIVE DEACETYLASE


Mass: 27256.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS CEREUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81FP2
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 471 / 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: 2.2 Å3/Da / Density % sol: 44 %
Crystal growpH: 5 / Details: 14-26% MPD, 100 MM ACETATE BUFFER, PH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X12 / Wavelength: 1.2821
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2821 Å / Relative weight: 1
ReflectionResolution: 1.8→55.8 Å / Num. obs: 40471 / % possible obs: 92.3 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 18.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.5 / % possible all: 65.4

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UAN

1uan


Resolution: 1.8→55.81 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.945 / SU B: 2.747 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1998 5.1 %RANDOM
Rwork0.177 ---
obs0.178 37533 93.2 %-
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 mean: 15.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.86 Å20.43 Å20 Å2
2--0.86 Å20 Å2
3----1.3 Å2
Refinement stepCycle: LAST / Resolution: 1.8→55.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 10 471 4107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223813
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9715126
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6665460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022844
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1920.22235
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0970.2569
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.2159
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.270
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.51.52309
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.22563721
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.82141504
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.90581405
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 107
Rwork0.237 1870
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)
11.2010.26130.30771.06890.23752.6274-0.00510.07260.1089-0.1120.0204-0.1191-0.20530.1304-0.01540.0715-0.01570.06240.130.01210.086919.267650.7025152.9337
21.0186-0.102-0.04371.1920.30592.00270.02450.022-0.1445-0.020.0186-0.07180.19280.0722-0.04310.02180.0299-0.01820.06180.01020.074915.859531.1539184.8631
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 233
2X-RAY DIFFRACTION1A234
3X-RAY DIFFRACTION1A235
4X-RAY DIFFRACTION2B2 - 231
5X-RAY DIFFRACTION2B232
6X-RAY DIFFRACTION2B233

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