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- PDB-4ex6: Crystal structure of the alnumycin P phosphatase AlnB -

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Basic information

Entry
Database: PDB / ID: 4ex6
TitleCrystal structure of the alnumycin P phosphatase AlnB
ComponentsAlnB
KeywordsHYDROLASE / modified Rossman fold / phosphatase / Magnesium binding
Function / homology
Function and homology information


Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD hydrolase, subfamily IA / 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
Biological speciesStreptomyces sp. CM020 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsOja, T. / Niiranen, L. / Sandalova, T. / Klika, K.D. / Niemi, J. / Mantsala, P. / Schneider, G. / Metsa-Ketela, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Structural basis for C-ribosylation in the alnumycin A biosynthetic pathway.
Authors: Oja, T. / Niiranen, L. / Sandalova, T. / Klika, K.D. / Niemi, J. / Mantsala, P. / Schneider, G. / Metsa-Ketela, M.
History
DepositionApr 30, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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

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Assembly

Deposited unit
A: AlnB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3403
Polymers24,2541
Non-polymers862
Water6,720373
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.929, 62.378, 62.873
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AlnB


Mass: 24253.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces sp. CM020 (bacteria) / Strain: sp. CM020 / Gene: alnB / Plasmid: pBADdelHisB / Production host: Escherichia coli (E. coli) / Strain (production host): TOP10 / References: UniProt: B6SEG4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-BO3 / BORIC ACID / Boric acid


Mass: 61.833 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BH3O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 1.94 Å3/Da / Density % sol: 36.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30% PEG1500, 0.1M MIB buffer, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.072 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072 Å / Relative weight: 1
ReflectionResolution: 1.25→44.28 Å / Num. obs: 46971 / % possible obs: 89.1 % / Redundancy: 7.8 % / Biso Wilson estimate: 9.7 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 25.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.25-1.325.80.1817.54015153.4
3.95-38.127.30.035541759196.5

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Processing

Software
NameVersionClassification
DNAdata collection
MOLREPphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HSZ

2hsz


Resolution: 1.25→44.28 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.973 / SU ML: 0.02 / Cross valid method: THROUGHOUT / ESU R: 0.044 / ESU R Free: 0.043 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15315 2377 5.1 %RANDOM
Rwork0.119 ---
obs0.12073 44554 88.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.897 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0 Å20 Å2
2--0.23 Å2-0 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.25→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1555 0 5 373 1933
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191660
X-RAY DIFFRACTIONr_bond_other_d0.0020.021113
X-RAY DIFFRACTIONr_angle_refined_deg1.84222282
X-RAY DIFFRACTIONr_angle_other_deg1.09132725
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4295243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.00121.55258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.27315259
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8591520
X-RAY DIFFRACTIONr_chiral_restr0.1310.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211917
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02331
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr6.26732773
X-RAY DIFFRACTIONr_sphericity_free23.511570
X-RAY DIFFRACTIONr_sphericity_bonded8.07653067
LS refinement shellResolution: 1.25→1.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.181 97 -
Rwork0.126 1683 -
obs--46.87 %
Refinement TLS params.Method: refined / Origin x: 11.0228 Å / Origin y: 22.0703 Å / Origin z: 14.3426 Å
111213212223313233
T0.0018 Å2-0 Å20.0001 Å2-0.0003 Å2-0.0012 Å2--0.0079 Å2
L0.2163 °20.0466 °2-0.067 °2-0.0563 °2-0.0279 °2--0.0622 °2
S-0.005 Å °0.005 Å °-0.0042 Å °-0.002 Å °0.0009 Å °-0.0007 Å °-0.0028 Å °-0.003 Å °0.004 Å °

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