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- PDB-2hh6: Crystal structure of BH3980 (10176605) from BACILLUS HALODURANS a... -

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Basic information

Entry
Database: PDB / ID: 2hh6
TitleCrystal structure of BH3980 (10176605) from BACILLUS HALODURANS at 2.04 A resolution
ComponentsBH3980 protein
KeywordsSTRUCTURAL GENOMICS / unknown function / 10176605 / BH3980 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
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 / BH3980 protein
Function and homology information
Biological speciesBacillus halodurans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of BH3980 (10176605) from BACILLUS HALODURANS at 2.04 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 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 1.4Jan 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 1.5Nov 20, 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 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 GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BH3980 protein


Theoretical massNumber of molelcules
Total (without water)13,2611
Polymers13,2611
Non-polymers00
Water1,40578
1
A: BH3980 protein

A: BH3980 protein


Theoretical massNumber of molelcules
Total (without water)26,5222
Polymers26,5222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area2540 Å2
ΔGint-14 kcal/mol
Surface area13040 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.540, 93.540, 115.320
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-137-

HOH

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Components

#1: Protein BH3980 protein


Mass: 13261.146 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus halodurans (bacteria) / Gene: 10176605 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9K5V7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 78 / 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: 5.26 Å3/Da / Density % sol: 76.43 %
Description: THE STRUCTURE WAS INITIALLY PHASED USING PEAK DATA COLLECTED ON SSRL BEAMLINE 11-1. A LOW RESOLUTION PASS TO FILL IN OVERLOADED REFLECTIONS WAS COLLECTED LATER ON SSRL BEAMLINE 1-5. THE ...Description: THE STRUCTURE WAS INITIALLY PHASED USING PEAK DATA COLLECTED ON SSRL BEAMLINE 11-1. A LOW RESOLUTION PASS TO FILL IN OVERLOADED REFLECTIONS WAS COLLECTED LATER ON SSRL BEAMLINE 1-5. THE TWO SWEEPS WERE MERGED FOR REFINEMENT. ALL DATA WAS COLLECTED AT THE PEAK WAVELENGTH FROM A SELENIUM SAD EXPERIMENT. THE PEAK WAVELENGTH ON EACH BEAMLINE WAS SELECTED USING CHOOCH FROM AN X-RAY FLUORESCENCE SCAN COLLECTED ON THAT BEAMLINE. THE STATISTICS DESCRIBED ABOVE ARE FOR THE MERGED DATA.
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.5
Details: 2.0M (NH4)2SO4, 0.1M TRIS pH 8.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL1-510.979075
SYNCHROTRONSSRL BL11-120.979075
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 3151CCDMay 26, 20061m long Rh coated bent cylindrical mirror forhorizontal and vertical focussing
ADSC Q3152CCDApr 9, 2006Flat mirror (vertical focusing)
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double-crystal monochromatorSINGLE WAVELENGTHMx-ray1
2Single crystal Si(111) bent monochromator (horizontal focusing)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.979075 Å / Relative weight: 1
ReflectionResolution: 2.04→46.984 Å / Num. obs: 19622 / % possible obs: 98.1 % / Biso Wilson estimate: 40.266 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 12.24
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allDiffraction-ID% possible all
2.04-2.110.8932.22409132961,295.3
2.11-2.20.67332838137281,297.5
2.2-2.30.5893.42655534941,297.9
2.3-2.420.4634.32671034991,298.1
2.42-2.570.3645.42651434651,297.7
2.57-2.770.2397.72719335661,298.4
2.77-3.040.156112651134651,298.6
3.04-3.480.07819.82747036071,299.7
3.48-46.980.05292715336071,299.8

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT2data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.04→46.984 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.938 / SU B: 7.403 / SU ML: 0.102 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.114
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 1) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 2) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3) A MET-INHIBITION PROTOCOL WAS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 1) ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 2) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4) ELECTRON DENSITY MAPS INDICATE THAT SEVERAL SIDECHAINS INCLUDING TRP 17 AND TRP 43 ARE DISORDERED. 5) UNEXPLAINED DIFFERENCE ELECTRON DENSITIES WERE OBSERVED AT SEVERAL LOCATIONS AND COULD NOT BE RELIABLY MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.238 999 5.1 %RANDOM
Rwork0.224 ---
all0.225 ---
obs0.22491 19577 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.351 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.04→46.984 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms888 0 0 78 966
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022936
X-RAY DIFFRACTIONr_bond_other_d0.0010.02826
X-RAY DIFFRACTIONr_angle_refined_deg1.0531.9321267
X-RAY DIFFRACTIONr_angle_other_deg0.7231924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.795119
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29724.77344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.01715170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7154
X-RAY DIFFRACTIONr_chiral_restr0.0630.2130
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021053
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02194
X-RAY DIFFRACTIONr_nbd_refined0.210.2229
X-RAY DIFFRACTIONr_nbd_other0.170.2794
X-RAY DIFFRACTIONr_nbtor_refined0.1890.2477
X-RAY DIFFRACTIONr_nbtor_other0.0870.2523
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.350.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.20.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.070.27
X-RAY DIFFRACTIONr_mcbond_it2.1263605
X-RAY DIFFRACTIONr_mcbond_other0.4163237
X-RAY DIFFRACTIONr_mcangle_it2.7635904
X-RAY DIFFRACTIONr_scbond_it5.0718425
X-RAY DIFFRACTIONr_scangle_it6.44611359
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 78 -
Rwork0.34 1343 -
obs-1421 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5962-0.85011.02364.0293-1.12020.7488-0.01750.0448-0.09120.37190.01470.04280.01330.26660.00280.21170.07380.00870.1629-0.0128-0.182624.98419.510.788
21.23721.08192.02541.65562.52066.38760.06-0.0360.14660.1563-0.13450.1649-0.40180.02990.07450.1898-0.0059-0.00750.138-0.0289-0.161918.77331.9355.011
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
111 - 422 - 43
2243 - 11244 - 113

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