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- PDB-4b2o: Crystal structure of Bacillus subtilis YmdB, a global regulator o... -

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Basic information

Entry
Database: PDB / ID: 4b2o
TitleCrystal structure of Bacillus subtilis YmdB, a global regulator of late adaptive responses.
ComponentsYMDB PHOSPHODIESTERASE
KeywordsHYDROLASE / PHOSPHODIESTERASE / BIOFILM / SPORULATION / METALLOPROTEIN
Function / homology
Function and homology information


2',3'-cyclic-nucleotide 2'-phosphodiesterase / 2',3'-cyclic-nucleotide 2'-phosphodiesterase activity / 2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / metal ion binding / cytoplasm
Similarity search - Function
Metallophosphoesterase, YmdB-like / YmdB-like protein / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / PHOSPHATE ION / 2',3'-cyclic-nucleotide 2'-phosphodiesterase
Similarity search - Component
Biological speciesBACILLUS SUBTILIS SUBSP. SUBTILIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 Å
AuthorsNewman, J.A. / Diethmaier, C. / Kovacs, A.T. / Rodrigues, C. / Kuipers, O.P. / Stulke, J. / Lewis, R.J.
CitationJournal: J.Bacteriol. / Year: 2014
Title: The Ymdb Phosphodiesterase is a Global Regulator of Late Adaptive Responses in Bacillus Subtilis.
Authors: Diethmaier, C. / Newman, J.A. / Kovacs, A.T. / Kaever, V. / Herzberg, C. / Rodrigues, C. / Boonstra, M. / Kuipers, O.P. / Lewis, R.J. / Stulke, J.
History
DepositionJul 17, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2014Group: Database references
Revision 1.2Dec 20, 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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

Downloads & links

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Assembly

Deposited unit
A: YMDB PHOSPHODIESTERASE
B: YMDB PHOSPHODIESTERASE
C: YMDB PHOSPHODIESTERASE
D: YMDB PHOSPHODIESTERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,91216
Polymers127,0854
Non-polymers82712
Water26,4821470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11390 Å2
ΔGint-203.4 kcal/mol
Surface area37380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.855, 105.997, 77.920
Angle α, β, γ (deg.)90.00, 108.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.372, 0.001467, 0.9282), (-0.01436, -0.9999, -0.004176), (0.9281, -0.01489, 0.372)-1.10321, 107.49, 1.50409
2given(-0.8357, 0.5375, -0.1124), (0.5392, 0.7644, -0.3536), (-0.1042, -0.3561, -0.9286)59.5905, 12.178, 151.245
3given(0.2054, -0.5326, -0.8211), (-0.5253, -0.7679, 0.3666), (-0.8257, 0.3561, -0.4375)117.692, 92.9026, 112.593

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Components

#1: Protein
YMDB PHOSPHODIESTERASE


Mass: 31771.219 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS SUBTILIS SUBSP. SUBTILIS (bacteria)
Strain: 168 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: O31775
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1470 / 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: 2.28 Å3/Da / Density % sol: 46.02 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM ACETATE, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.64→19.74 Å / Num. obs: 134017 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 14.4
Reflection shellResolution: 1.64→1.73 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.9 / % possible all: 79.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T70

1t70


Resolution: 1.64→19.738 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 17.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1854 6724 5 %
Rwork0.1589 --
obs0.1603 133982 96.39 %
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.756 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1--2.1864 Å20 Å20.0044 Å2
2--1.3634 Å20 Å2
3---0.823 Å2
Refinement stepCycle: LAST / Resolution: 1.64→19.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8252 0 28 1470 9750
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0158520
X-RAY DIFFRACTIONf_angle_d1.09611584
X-RAY DIFFRACTIONf_dihedral_angle_d12.543145
X-RAY DIFFRACTIONf_chiral_restr0.0791294
X-RAY DIFFRACTIONf_plane_restr0.0061485
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.65860.29961680.27533161X-RAY DIFFRACTION72
1.6586-1.67810.27562040.26463281X-RAY DIFFRACTION76
1.6781-1.69860.30071890.26083592X-RAY DIFFRACTION82
1.6986-1.72010.28121940.24773660X-RAY DIFFRACTION84
1.7201-1.74270.28571810.25213994X-RAY DIFFRACTION90
1.7427-1.76660.29522250.22794132X-RAY DIFFRACTION94
1.7666-1.79180.24912290.21024222X-RAY DIFFRACTION97
1.7918-1.81850.23182230.19074408X-RAY DIFFRACTION99
1.8185-1.84690.21892310.18084410X-RAY DIFFRACTION100
1.8469-1.87720.21012270.17364325X-RAY DIFFRACTION100
1.8772-1.90950.20382260.16824370X-RAY DIFFRACTION100
1.9095-1.94420.21182270.15964434X-RAY DIFFRACTION100
1.9442-1.98160.1862310.15474399X-RAY DIFFRACTION100
1.9816-2.0220.17652410.15584360X-RAY DIFFRACTION100
2.022-2.06590.19772290.15894407X-RAY DIFFRACTION100
2.0659-2.11390.19032560.15094395X-RAY DIFFRACTION100
2.1139-2.16670.16552330.15354380X-RAY DIFFRACTION100
2.1667-2.22520.17542420.15064380X-RAY DIFFRACTION100
2.2252-2.29060.19682140.15084400X-RAY DIFFRACTION100
2.2906-2.36440.18592310.15444388X-RAY DIFFRACTION100
2.3644-2.44870.21292360.15834394X-RAY DIFFRACTION100
2.4487-2.54660.18362080.15334412X-RAY DIFFRACTION100
2.5466-2.66220.18832300.15864403X-RAY DIFFRACTION100
2.6622-2.80220.1882440.1554393X-RAY DIFFRACTION100
2.8022-2.97720.1872450.1524389X-RAY DIFFRACTION100
2.9772-3.20620.17812280.15784419X-RAY DIFFRACTION100
3.2062-3.52720.16652150.14254445X-RAY DIFFRACTION100
3.5272-4.03380.14872280.13544407X-RAY DIFFRACTION100
4.0338-5.06790.13032530.12274391X-RAY DIFFRACTION100
5.0679-19.73910.17132360.16244507X-RAY DIFFRACTION100

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