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- PDB-3bhw: Crystal structure of an uncharacterized protein from Magnetospiri... -

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Basic information

Entry
Database: PDB / ID: 3bhw
TitleCrystal structure of an uncharacterized protein from Magnetospirillum magneticum
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyfold of a uncharacterized protein from magnetospirillum magneticum / uncharacterized protein from magnetospirillum magneticum domain / BrxA / BrxA superfamily / BrxA / defense response to virus / Orthogonal Bundle / Mainly Alpha / BREX protein BrxA
Function and homology information
Biological speciesMagnetospirillum magneticum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsBonanno, J.B. / Dickey, M. / Bain, K.T. / Lau, C. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of an uncharacterized protein from Magnetospirillum magneticum.
Authors: Bonanno, J.B. / Dickey, M. / Bain, K.T. / Lau, C. / Romero, R. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionNov 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary
Category: audit_author / citation_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)48,4182
Polymers48,4182
Non-polymers00
Water5,314295
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)24,2091
Polymers24,2091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)24,2091
Polymers24,2091
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)43.142, 43.627, 47.410
Angle α, β, γ (deg.)86.000, 85.890, 85.580
Int Tables number1
Space group name H-MP1
DetailsAUTHORS STATE THAT THE MONOMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE AT THE TIME OF DEPOSITION.

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Components

#1: Protein Uncharacterized protein


Mass: 24208.775 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum magneticum (bacteria) / Strain: AMB-1 / Gene: amb2038 / Plasmid: modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q2W5N3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 295 / 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: 1.83 Å3/Da / Density % sol: 32.75 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 8
Details: 100mM Tris-HCl pH 8.0, 25% PEG 3350, 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: MAR CCD 165 mm / Detector: CCD / Date: Aug 20, 2007
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97958 Å / Relative weight: 1
ReflectionResolution: 1.5→16.431 Å / Num. all: 51480 / Num. obs: 51480 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 14.3 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 11.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.444 / Mean I/σ(I) obs: 2.3 / Num. unique all: 7426 / Rsym value: 0.444 / % possible all: 91.8

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
MAR345CCDdata collection
MOSFLMdata reduction
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.5→15 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.888 / SU B: 2.595 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.116 / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.281 2559 5 %RANDOM
Rwork0.239 ---
obs0.241 51469 93.69 %-
all-51469 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.541 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20.07 Å2-0.66 Å2
2--0.06 Å21.52 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.5→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3027 0 0 295 3322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223157
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9654272
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6335391
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.56222.893159
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49715600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7661539
X-RAY DIFFRACTIONr_chiral_restr0.1030.2476
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022370
X-RAY DIFFRACTIONr_nbd_refined0.2440.21674
X-RAY DIFFRACTIONr_nbtor_refined0.310.22211
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1850.2285
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2930.2110
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1820.239
X-RAY DIFFRACTIONr_mcbond_it1.0471.51947
X-RAY DIFFRACTIONr_mcangle_it1.52223061
X-RAY DIFFRACTIONr_scbond_it2.47131376
X-RAY DIFFRACTIONr_scangle_it3.6364.51198
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 169 -
Rwork0.296 3553 -
all-3722 -
obs-3553 91.56 %

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