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- PDB-2qup: Crystal structure of uncharacterized protein BH1478 from Bacillus... -

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Basic information

Entry
Database: PDB / ID: 2qup
TitleCrystal structure of uncharacterized protein BH1478 from Bacillus halodurans
ComponentsBH1478 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-2 / PROTEIN STRUCTURE INITIATIVE / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homologyHypothetical protein TM1646-like domain / Protein of unknown function DUF327 / TM1646-like domain superfamily / Protein of unknown function (DUF327) / Four Helix Bundle (Hemerythrin (Met), subunit A) / Up-down Bundle / Mainly Alpha / BH1478 protein
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPatskovsky, Y. / Bonanno, J.B. / Rutter, M. / Mckenzie, C. / Bain, K.T. / Smith, D. / Ozyurt, S. / Gheyi, T. / Wasserman, S. / Sauder, J.M. ...Patskovsky, Y. / Bonanno, J.B. / Rutter, M. / Mckenzie, C. / Bain, K.T. / Smith, D. / Ozyurt, S. / Gheyi, T. / 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 Uncharacterized Protein Bh1478 from Bacillus Halodurans.
Authors: Patskovsky, Y. / Bonanno, J.B. / Rutter, M. / Mckenzie, C. / Ozyurt, S. / Bain, K.T. / Gheyi, T. / Smith, D. / Wasserman, S. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionAug 6, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 30, 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

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Assembly

Deposited unit
A: BH1478 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7022
Polymers16,6101
Non-polymers921
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.836, 40.715, 39.007
Angle α, β, γ (deg.)90.00, 94.70, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein BH1478 protein


Mass: 16610.379 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Strain: C-125, DSM 18197, FERM 7344, JCM 9153 / Gene: BH1478 / Plasmid: Modified pET26 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9KCU1
#2: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.8 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6
Details: 100mM Bis-Tris pH 6.0, 24% PEG4000, 400mM LiCl, 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: Feb 14, 2007
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: 12712 / Num. obs: 12712 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.12 / Rsym value: 0.063 / Net I/σ(I): 4.4
Reflection shellResolution: 2→2.07 Å / Redundancy: 4 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.1 / Rsym value: 0.54 / % possible all: 99.5

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.3.0034refinement
MAR345CCDdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2P61

2p61


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 5.351 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2287 384 3 %RANDOM
Rwork0.20804 ---
obs0.20866 12349 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.872 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å21.09 Å2
2---2.55 Å20 Å2
3----0.76 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms962 0 6 99 1067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221030
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2882.0271379
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3115135
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58323.91346
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.52715240
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.9571511
X-RAY DIFFRACTIONr_chiral_restr0.1010.2158
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02729
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.160.3488
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2930.5716
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2320.5113
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.336
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.525
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.7332639
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.9933995
X-RAY DIFFRACTIONr_scbond_it7.6883434
X-RAY DIFFRACTIONr_scangle_it11.2665376
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.048 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 35 -
Rwork0.331 865 -
obs--96.15 %

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