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- PDB-4hbs: Crystal structure of a putative hydrolase (BACOVA_04882) from Bac... -

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Basic information

Entry
Database: PDB / ID: 4hbs
TitleCrystal structure of a putative hydrolase (BACOVA_04882) from Bacteroides ovatus ATCC 8483 at 2.80 A resolution
ComponentsPutative hydrolase
KeywordsHYDROLASE / 5-bladed beta-propeller / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyProtein of unknown function DUF5005 / Domain of unknown function (DUF5005) / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Uncharacterized protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative hydrolase (BACOVA_04882) from Bacteroides ovatus ATCC 8483 at 2.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3195
Polymers48,9511
Non-polymers3684
Water63135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.400, 104.400, 116.131
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Putative hydrolase


Mass: 48950.797 Da / Num. of mol.: 1 / Fragment: UNP residues 19-434
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Gene: ZP_02067871.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7M441
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 20-434) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 20-434) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE.

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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: 3.73 Å3/Da / Density % sol: 67.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.00M di-ammonium hydrogen phosphate, 0.1M TRIS pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97929
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 2, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979291
ReflectionResolution: 2.8→48.857 Å / Num. obs: 18376 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 74.273 Å2 / Rmerge(I) obs: 0.126 / Net I/σ(I): 10.64
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.8-2.90.9061.987101812199.6
2.9-3.020.6722.892951858199.8
3.02-3.150.4863.783751718199.6
3.15-3.320.3165.487501874199.8
3.32-3.520.2147.989701758199.8
3.52-3.790.1510.892931819199
3.79-4.170.09514.689291847199.7
4.17-4.770.0718.291721868199.6
4.77-5.980.06918.690751835198.3
5.98-48.8570.0621.190461987198

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEMarch 15, 2012data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→48.857 Å / Cor.coef. Fo:Fc: 0.9353 / Cor.coef. Fo:Fc free: 0.9135 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1). 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 ...Details: 1). 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. 2). ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3). THE STRUCTURE REFINEMENT WAS RESTRAINED AGAINST THE EXPERIMENTAL (MAD) PHASES. 4) RAMACHANDRAN OUTLIER AT SER49 IS IN REGION OF DENSITY THAT IS NOT WELL-DEFINED. 5) HYDROGEN ATOMS WITH ZERO OCCUPANCY WERE USED IN REFINEMENT TO REDUCE CLASHES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2093 935 5.1 %RANDOM
Rwork0.1862 ---
obs0.1874 18336 99.4 %-
Displacement parametersBiso max: 150.7 Å2 / Biso mean: 57.1597 Å2 / Biso min: 25.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.178 Å20 Å20 Å2
2---1.178 Å20 Å2
3---2.3559 Å2
Refine analyzeLuzzati coordinate error obs: 0.383 Å
Refinement stepCycle: LAST / Resolution: 2.8→48.857 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 24 35 3370
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1731SINUSOIDAL1.5
X-RAY DIFFRACTIONt_trig_c_planes97HARMONIC2
X-RAY DIFFRACTIONt_gen_planes984HARMONIC5
X-RAY DIFFRACTIONt_it6528HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion424SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7070SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6528HARMONIC1.50.01
X-RAY DIFFRACTIONt_angle_deg11643HARMONIC21.01
X-RAY DIFFRACTIONt_omega_torsion3.68
X-RAY DIFFRACTIONt_other_torsion3.24
LS refinement shellResolution: 2.8→2.97 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2559 145 4.96 %
Rwork0.2224 2776 -
all0.2241 2921 -
obs--99.4 %
Refinement TLS params.Method: refined / Origin x: 57.1291 Å / Origin y: 9.8185 Å / Origin z: 16.7583 Å
111213212223313233
T-0.0843 Å20.0893 Å20.0276 Å2--0.0684 Å2-0.035 Å2---0.1824 Å2
L1.4705 °2-0.5205 °20.1245 °2-1.5617 °2-0.2776 °2--1.5185 °2
S0.1631 Å °0.2092 Å °0.049 Å °-0.2787 Å °-0.1875 Å °-0.048 Å °-0.035 Å °0.1792 Å °0.0244 Å °
Refinement TLS groupSelection details: { A|28 - A|433 }

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