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- PDB-3i76: The crystal structure of the orthorhombic form of the putative HA... -

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Basic information

Entry
Database: PDB / ID: 3i76
TitleThe crystal structure of the orthorhombic form of the putative HAD-hydrolase YfnB from Bacillus subtilis bound to magnesium reveals interdomain movement
ComponentsPutative HAD-hydrolase yfnB
KeywordsHYDROLASE / STRUCTURAL GENOMICS / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


Hydrolases / 5'-nucleotidase activity
Similarity search - Function
HAD-superfamily hydrolase, subfamily IA, YjjG/PynA / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...HAD-superfamily hydrolase, subfamily IA, YjjG/PynA / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Putative HAD-hydrolase YfnB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Tang, B.K. / Romero, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: The crystal structure of the orthorhombic form of the putative HAD-hydrolase YfnB from Bacillus subtilis bound to magnesium reveals interdomain movement
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Tang, B.K. / Romero, R. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionJul 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 21, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 21, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Revision 1.5Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative HAD-hydrolase yfnB
B: Putative HAD-hydrolase yfnB
C: Putative HAD-hydrolase yfnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,89812
Polymers85,5673
Non-polymers3319
Water7,296405
1
A: Putative HAD-hydrolase yfnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7105
Polymers28,5221
Non-polymers1874
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative HAD-hydrolase yfnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6064
Polymers28,5221
Non-polymers843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative HAD-hydrolase yfnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5823
Polymers28,5221
Non-polymers602
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.685, 67.964, 271.404
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative HAD-hydrolase yfnB


Mass: 28522.201 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: BSU07330, yfnB / Plasmid: modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O06480
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.35 Å3/Da / Density % sol: 47.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8.5
Details: 100mM Tris HCl pH 8.5, 30% PEG 4K, 200mM magnesium chloride, vapor diffusion, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97958 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 15, 2009
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 55918 / Num. obs: 51221 / % possible obs: 91.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Biso Wilson estimate: 20.3 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Χ2: 1.137 / Net I/σ(I): 33.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 8.9 / Num. unique all: 2392 / Rsym value: 0.397 / Χ2: 1.12 / % possible all: 87.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3ED5

3ed5


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.21 / WRfactor Rwork: 0.17 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.863 / SU B: 3.523 / SU ML: 0.1 / SU R Cruickshank DPI: 0.182 / SU Rfree: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.182 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.219 2573 5 %RANDOM
Rwork0.175 ---
obs0.177 51018 91.34 %-
all-55855 --
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 max: 56.57 Å2 / Biso mean: 23.739 Å2 / Biso min: 5.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---1.39 Å20 Å2
3---1.44 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5569 0 14 405 5988
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0225720
X-RAY DIFFRACTIONr_bond_other_d0.0010.023884
X-RAY DIFFRACTIONr_angle_refined_deg1.4841.9617738
X-RAY DIFFRACTIONr_angle_other_deg0.92939447
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8115684
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.35224.773308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.072151001
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4911531
X-RAY DIFFRACTIONr_chiral_restr0.0930.2836
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026381
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021208
X-RAY DIFFRACTIONr_mcbond_it0.941.53391
X-RAY DIFFRACTIONr_mcbond_other0.2541.51378
X-RAY DIFFRACTIONr_mcangle_it1.70725464
X-RAY DIFFRACTIONr_scbond_it2.7332329
X-RAY DIFFRACTIONr_scangle_it4.2824.52270
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 160 -
Rwork0.188 3252 -
all-3412 -
obs-3252 84.77 %

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