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- PDB-2oa2: Crystal structure of BH2720 (10175341) from Bacillus halodurans a... -

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Basic information

Entry
Database: PDB / ID: 2oa2
TitleCrystal structure of BH2720 (10175341) from Bacillus halodurans at 1.41 A resolution
ComponentsBH2720 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / 10175341 / BH2720 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homology
Function and homology information


: / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / Ferritin-like superfamily / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.41 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of BH2720 (10175341) from Bacillus halodurans at 1.41 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: 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_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.6Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
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, FOLLOWED BY THE TARGET SEQUENCE. THE CONSTRUCT IS A TRUNCATION OF THE FULL LENGTH PROTEIN, WITH ONLY RESIDUES 149-225 EXPRESSED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BH2720 protein


Theoretical massNumber of molelcules
Total (without water)17,1881
Polymers17,1881
Non-polymers00
Water2,576143
1
A: BH2720 protein

A: BH2720 protein


Theoretical massNumber of molelcules
Total (without water)34,3752
Polymers34,3752
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area2970 Å2
ΔGint-25 kcal/mol
Surface area11120 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)68.610, 68.610, 60.106
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
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 BH2720 protein


Mass: 17187.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: 10175341 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K9C9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 6
Details: 10.0% MPD, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837, 0.97971, 0.97925
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 19, 2006 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979711
30.979251
ReflectionResolution: 1.41→48.507 Å / Num. obs: 26400 / % possible obs: 91.5 % / Biso Wilson estimate: 23.109 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 21.48
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique all% possible all
1.41-1.460.4572.65654163859.5
1.46-1.520.3883.38649209173.4
1.52-1.590.301512084240986.2
1.59-1.670.2477.217096260097.7
1.67-1.780.1831020665289499
1.78-1.910.1211522357263699
1.91-2.110.08424.232410292799.7
2.11-2.410.0653438854278399.8
2.410.05142.840047286599.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
SHELXphasing
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.41→48.507 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.766 / SU ML: 0.049 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.061 / ESU R Free: 0.062
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RESIDUES 149-157 AND 290-295 ARE DISORDERED AND WERE NOT MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1314 5 %RANDOM
Rwork0.165 ---
obs0.166 26355 93.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.041 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2---0.85 Å20 Å2
3---1.69 Å2
Refinement stepCycle: LAST / Resolution: 1.41→48.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1052 0 0 143 1195
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211157
X-RAY DIFFRACTIONr_bond_other_d0.0010.021046
X-RAY DIFFRACTIONr_angle_refined_deg1.7091.9281593
X-RAY DIFFRACTIONr_angle_other_deg0.82332440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1655154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41723.93461
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.41515193
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.268158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2175
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021322
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02236
X-RAY DIFFRACTIONr_nbd_refined0.1980.2195
X-RAY DIFFRACTIONr_nbd_other0.1860.21028
X-RAY DIFFRACTIONr_nbtor_refined0.1750.2523
X-RAY DIFFRACTIONr_nbtor_other0.0880.2699
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.297
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0580.23
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.230
X-RAY DIFFRACTIONr_mcbond_it2.0063739
X-RAY DIFFRACTIONr_mcbond_other0.53280
X-RAY DIFFRACTIONr_mcangle_it2.66651139
X-RAY DIFFRACTIONr_scbond_it4.1688497
X-RAY DIFFRACTIONr_scangle_it5.48511442
LS refinement shellResolution: 1.411→1.448 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 71 -
Rwork0.328 1263 -
obs-1334 64.79 %
Refinement TLS params.Method: refined / Origin x: 21.4539 Å / Origin y: 24.7055 Å / Origin z: 19.7693 Å
111213212223313233
T-0.0658 Å2-0.0089 Å2-0.0057 Å2--0.049 Å2-0.0103 Å2---0.008 Å2
L0.7261 °20.076 °20.2592 °2-0.6543 °20.4532 °2--2.0416 °2
S-0.0307 Å °0.151 Å °0.0273 Å °-0.1218 Å °-0.0273 Å °0.0869 Å °-0.1762 Å °0.0261 Å °0.0579 Å °
Refinement TLS groupSelection: ALL

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