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- PDB-4f53: Crystal structure of a susd homolog (BACOVA_04803) from Bacteroid... -

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Basic information

Entry
Database: PDB / ID: 4f53
TitleCrystal structure of a susd homolog (BACOVA_04803) from Bacteroides ovatus ATCC 8483 at 2.25 A resolution
ComponentsSusD homolog
KeywordsSUGAR BINDING PROTEIN / TPR-like protein / mucin o-glycan binding / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologySusD-like / Susd and RagB outer membrane lipoprotein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / ACETATE ION / Uncharacterized protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.25 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a susd homolog (BACOVA_04803) from Bacteroides ovatus ATCC 8483 at 2.25 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 11, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: SusD homolog
B: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,21913
Polymers118,4512
Non-polymers76711
Water14,898827
1
A: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6417
Polymers59,2261
Non-polymers4156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,5786
Polymers59,2261
Non-polymers3525
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)217.999, 226.202, 62.927
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SusD homolog


Mass: 59225.715 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_04803 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7M3W3

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Non-polymers , 5 types, 838 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 827 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE CONSTRUCT (RESIDUES 22-540) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 22-540) 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: 3.27 Å3/Da / Density % sol: 62.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.16M calcium acetate, 20.0% Glycerol, 14.4% polyethylene glycol 8000, 0.1M sodium cacodylate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97868
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 4, 2012
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97868 Å / Relative weight: 1
ReflectionResolution: 2.25→49.097 Å / Num. obs: 73074 / % possible obs: 98.3 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 38.562 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 8.81
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.25-2.390.6072441831197798.7
2.39-2.490.4562.827373708399.6
2.49-2.60.3413.724984656399.4
2.6-2.740.2624.625464687299.1
2.74-2.910.25.924241661797.7
2.91-3.130.1468.125829665999.3
3.13-3.450.09211.926278689798.7
3.45-3.940.06515.724257662197.1
3.94-4.950.05419.125735677898
4.950.05819.325032697795.1

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 2.25→49.097 Å / Cor.coef. Fo:Fc: 0.9587 / Cor.coef. Fo:Fc free: 0.9456 / 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 MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 5. CALCIUM, CHLORIDE IONS, ACETATE, AND GLYCEROL MODELED WAS PRESENT IN THE CRYSTALLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.1744 3714 5.08 %RANDOM
Rwork0.1491 ---
obs0.1504 73070 98.34 %-
Displacement parametersBiso max: 134.33 Å2 / Biso mean: 41.9438 Å2 / Biso min: 18.24 Å2
Baniso -1Baniso -2Baniso -3
1-0.8767 Å20 Å20 Å2
2--4.0729 Å20 Å2
3----4.9496 Å2
Refine analyzeLuzzati coordinate error obs: 0.243 Å
Refinement stepCycle: LAST / Resolution: 2.25→49.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7864 0 44 827 8735
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3726SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes222HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1204HARMONIC5
X-RAY DIFFRACTIONt_it8163HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1031SEMIHARMONIC5
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_contact10091SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8163HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg11081HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion3.47
X-RAY DIFFRACTIONt_other_torsion2.84
LS refinement shellResolution: 2.25→2.31 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2305 274 5.18 %
Rwork0.2085 5014 -
all0.2097 5288 -
obs--98.34 %
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)
11.96280.836-0.27311.0521-0.12720.7922-0.18810.11220.2833-0.20810.11110.12040.05760.09090.077-0.1070.0091-0.0631-0.10340.0137-0.09287.511354.24840.855
20.87650.54840.25961.82490.39470.83530.0966-0.1276-0.07240.0885-0.1087-0.2643-0.0791-0.0480.0121-0.08090.0024-0.0057-0.11260.0554-0.084754.039891.289537.2956
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|43 - 540 }A43 - 540
2X-RAY DIFFRACTION2{ B|43 - 540 }B43 - 540

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