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- PDB-2o4t: CRYSTAL STRUCTURE OF a protein of the DUF1048 family with a left-... -

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Entry
Database: PDB / ID: 2o4t
TitleCRYSTAL STRUCTURE OF a protein of the DUF1048 family with a left-handed superhelix fold (BH3976) FROM BACILLUS HALODURANS AT 1.95 A RESOLUTION
ComponentsBH3976 protein
KeywordsUNKNOWN FUNCTION / LEFT-HANDED SUPERHELIX FOLD / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyUncharacterised conserved protein UCP029876 / Protein of unknown function (DUF1048) / c-terminal domain of poly(a) binding protein / c-terminal domain of poly(a) binding protein / Orthogonal Bundle / Mainly Alpha / DI(HYDROXYETHYL)ETHER / BH3976 protein
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of BH3976 (10176601) from Bacillus halodurans at 1.95 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.8Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.
Remark 999SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUE 15 OF THE TARGET SEQUENCE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BH3976 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2883
Polymers11,0751
Non-polymers2122
Water1,00956
1
A: BH3976 protein
hetero molecules

A: BH3976 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5756
Polymers22,1512
Non-polymers4244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
Buried area4720 Å2
ΔGint-15 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.577, 85.577, 104.575
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-137-

HOH

DetailsSIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein BH3976 protein


Mass: 11075.263 Da / Num. of mol.: 1 / Fragment: residues 15-113
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: 10176601 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K5W1
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 3.33 Å3/Da / Density % sol: 63.02 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 4.2
Details: 0.2M (NH4)2SO4, 10.0% Glycerol, 20.0% PEG-300, 0.1M Phosphate Citrate pH 4.2, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2006 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.95→60.412 Å / Num. obs: 10900 / % possible obs: 99.8 % / Redundancy: 5.1 % / Biso Wilson estimate: 35 Å2 / Rmerge(I) obs: 0.091 / Rsym value: 0.091 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.95-23.20.5211.424637590.52198.9
2-2.063.80.4561.629707790.45699.1
2.06-2.124.90.441.736807560.44100
2.12-2.185.50.3981.841037430.398100
2.18-2.255.50.3072.339717180.307100
2.25-2.335.60.231338987000.231100
2.33-2.425.50.1933.636676630.193100
2.42-2.525.50.1614.235746440.161100
2.52-2.635.50.1354.933796110.135100
2.63-2.765.50.1294.633095990.129100
2.76-2.915.50.1154.830335520.115100
2.91-3.085.50.1025.729575410.102100
3.08-3.35.50.0866.327755080.086100
3.3-3.565.50.0747.225934740.074100
3.56-3.95.40.0776.723204320.077100
3.9-4.365.30.0797.121023960.079100
4.36-5.045.40.0717.818913520.07199.9
5.04-6.175.30.0668.615892990.06699.9
6.17-8.725.10.0727.712202370.07299.8
8.72-60.474.40.0698.66061370.06998.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT2data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb enrty 2o3l

2o3l


Resolution: 1.95→60.412 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.919 / SU ML: 0.124 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. ELECTRON DENSITIES FOR RESIDUE 15 AND RESIDUE 106-113 WERE DISORDERED, THEREFORE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. ELECTRON DENSITIES FOR RESIDUE 15 AND RESIDUE 106-113 WERE DISORDERED, THEREFORE THESE RESIDUES WERE NOT MODELED. 4. TWO MOLECULES OF POLYETHYLENE GLYCOL 300 FROM THE CRYSTALLIZATION WERE MOLDELED INTO THE STRUCTURE. ONE OF THESE PEG MOLECULES IS ON A SPECIAL POSITION BETWEEN SYMMETRY-RELATED SUBUNITS.
RfactorNum. reflection% reflectionSelection details
Rfree0.255 523 4.8 %RANDOM
Rwork0.203 ---
all0.205 ---
obs0.205 10898 99.75 %-
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: 43.239 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å21.42 Å20 Å2
2--2.84 Å20 Å2
3----4.25 Å2
Refinement stepCycle: LAST / Resolution: 1.95→60.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms686 0 14 56 756
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022727
X-RAY DIFFRACTIONr_bond_other_d0.0020.02660
X-RAY DIFFRACTIONr_angle_refined_deg1.4421.979984
X-RAY DIFFRACTIONr_angle_other_deg0.81931539
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75595
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.08426.17634
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.88415117
X-RAY DIFFRACTIONr_dihedral_angle_4_deg0.682151
X-RAY DIFFRACTIONr_chiral_restr0.0940.2111
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02819
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02138
X-RAY DIFFRACTIONr_nbd_refined0.2370.2181
X-RAY DIFFRACTIONr_nbd_other0.1610.2620
X-RAY DIFFRACTIONr_nbtor_refined0.1930.2378
X-RAY DIFFRACTIONr_nbtor_other0.0880.2404
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0350.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1730.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.23
X-RAY DIFFRACTIONr_mcbond_it2.5023495
X-RAY DIFFRACTIONr_mcbond_other0.6653192
X-RAY DIFFRACTIONr_mcangle_it3.2785724
X-RAY DIFFRACTIONr_scbond_it5.268301
X-RAY DIFFRACTIONr_scangle_it6.71211257
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 33 -
Rwork0.292 724 -
obs-757 98.83 %
Refinement TLS params.Method: refined / Origin x: 18.9019 Å / Origin y: -2.1762 Å / Origin z: 47.5245 Å
111213212223313233
T-0.1647 Å20.0732 Å2-0.0352 Å2--0.2797 Å20.0015 Å2---0.1402 Å2
L4.5907 °20.902 °2-1.4456 °2-2.5849 °20.7994 °2--5.2463 °2
S0.179 Å °0.0165 Å °-0.1646 Å °0.0956 Å °-0.1901 Å °0.1653 Å °-0.2279 Å °-0.0438 Å °0.0111 Å °
Refinement TLS groupSelection: ALL

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