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- PDB-3tmd: Bd1817, a HDG"Y"P protein from Bdellovibrio bacteriovorus -

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Basic information

Entry
Database: PDB / ID: 3tmd
TitleBd1817, a HDG"Y"P protein from Bdellovibrio bacteriovorus
ComponentsUncharacterized protein
KeywordsHYDROLASE / SIGNALING PROTEIN / HD-GYP / phosphodiesterase / UNKNOWN FUNCTION
Function / homology
Function and homology information


HD domain / HD-GYP domain / HD-GYP domain profile. / HDIG domain / Hypothetical protein af1432 / Hypothetical protein af1432 / HD domain / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / PHOSPHATE ION / HD-GYP domain-containing protein
Similarity search - Component
Biological speciesBdellovibrio bacteriovorus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.641 Å
AuthorsLovering, A.L.
CitationJournal: MBio / Year: 2011
Title: The structure of an unconventional HD-GYP protein from Bdellovibrio reveals the roles of conserved residues in this class of cyclic-di-GMP phosphodiesterases.
Authors: Lovering, A.L. / Capeness, M.J. / Lambert, C. / Hobley, L. / Sockett, R.E.
History
DepositionAug 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _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_ref_seq_dif.details / _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: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2214
Polymers37,0141
Non-polymers2073
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.010, 101.010, 94.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Uncharacterized protein / Bd1817


Mass: 37013.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bdellovibrio bacteriovorus (bacteria) / Strain: HD100 / Gene: Bd1817 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q6MM30
#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 3.76 Å3/Da / Density % sol: 67.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2.1M DL-Malic Acid pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2011
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→64.2 Å / Num. all: 4700 / Num. obs: 16481 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 5.9
Reflection shellResolution: 2.6→2.78 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
MOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.641→43.739 Å / SU ML: 0.4 / σ(F): 1.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2512 803 4.87 %random
Rwork0.2119 ---
all0.2139 4700 --
obs0.2139 16481 98.29 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.91 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-14.8901 Å2-0 Å2-0 Å2
2--14.8901 Å2-0 Å2
3----29.7803 Å2
Refinement stepCycle: LAST / Resolution: 2.641→43.739 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2424 0 7 11 2442
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082469
X-RAY DIFFRACTIONf_angle_d1.0923332
X-RAY DIFFRACTIONf_dihedral_angle_d15.992942
X-RAY DIFFRACTIONf_chiral_restr0.073374
X-RAY DIFFRACTIONf_plane_restr0.004433
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6415-2.8070.43961310.38052619X-RAY DIFFRACTION99
2.807-3.02360.42211250.33592596X-RAY DIFFRACTION100
3.0236-3.32780.29321480.26282610X-RAY DIFFRACTION100
3.3278-3.80910.2691450.21382618X-RAY DIFFRACTION100
3.8091-4.79810.19941170.17522684X-RAY DIFFRACTION100
4.7981-43.74450.21711370.18262551X-RAY DIFFRACTION92

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