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- PDB-3oqq: Crystal structure of a Putative lipoprotein (BACOVA_00967) from B... -

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Basic information

Entry
Database: PDB / ID: 3oqq
TitleCrystal structure of a Putative lipoprotein (BACOVA_00967) from Bacteroides ovatus at 2.08 A resolution
ComponentsPutative lipoprotein
KeywordsStructural Genomics / Unknown Function / EXTRACELLULAR PROTEIN / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homologyLruC domain / Domain of unknown function DUF4841 / Domain of unknown function DUF4842 / Domain of unknown function (DUF4841) / Domain of unknown function (DUF4842) / metal ion binding / ACETATE ION / TRIETHYLENE GLYCOL / Uncharacterized protein
Function and homology information
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.08 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Putative lipoprotein (BACOVA_00967) from Bacteroides ovatus at 2.08 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.2Feb 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4128
Polymers48,8921
Non-polymers5207
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.640, 118.580, 49.330
Angle α, β, γ (deg.)90.00, 110.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-461-

ACT

21A-461-

ACT

31A-737-

HOH

41A-738-

HOH

DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein Putative lipoprotein


Mass: 48892.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_00967 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A7LT28
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 23-456) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 23-456) 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Description
12.4850.5THREE-WAVELENGTH MAD PHASES WERE OBTAINED FROM TWO CRYSTALS. THE PEAK DATA WERE FROM ONE CRYSTAL DIFFRACTING TO 2.08 A. THE INFLECTION AND REMOTE DATA WERE FROM ANOTHER CRYSTAL DIFFRACTING TO 2.6 A. THE PEAK DATA (FROM THE HIGHER RESOLUTION CRYSTAL) WERE USED FOR REFINEMENT.
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2771vapor diffusion, sitting drop80.2M Ca(OAc)2, 20.0% PEG-1000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
2772vapor diffusion, sitting drop80.2M Ca(OAc)2, 20.0% PEG-1000, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL9-210.97903
SYNCHROTRONSSRL BL9-220.97918,0.91837
Detector
TypeIDDetectorDateDetails
MARMOSAIC 325 mm CCD1CCDJul 22, 2010Flat collimating mirror, toroid focusing mirror
MARMOSAIC 325 mm CCD2CCDJul 22, 2010Flat collimating mirror, toroid focusing mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double crystal monochromatorMADMx-ray1
2Double crystal monochromatorMADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.979031
20.979181
30.918371
ReflectionResolution: 2.08→44.623 Å / Num. obs: 28606 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Biso Wilson estimate: 27.02 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 9.31
Reflection shell

Diffraction-ID: 1,2

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.08-2.153.70.5672.110236272299.9
2.15-2.243.80.4412.711288299599.5
2.24-2.343.80.3823.210326277299.5
2.34-2.473.80.3243.811427301699.5
2.47-2.623.80.2644.6103952749100
2.62-2.823.80.1976.110711282199.6
2.82-3.13.80.13910811284799.6
3.1-3.553.70.07114.910893288499.4
3.55-4.473.80.04821.210788287499.2
4.47-44.63.80.0462510884292199.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
BUSTER-TNTBUSTER 2.8.0refinement
XSCALEdata processing
PDB_EXTRACT3.1data extraction
XDSdata reduction
XSCALEdata scaling
SHELXDphasing
autoSHARPphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.08→25.75 Å / Cor.coef. Fo:Fc: 0.9493 / Cor.coef. Fo:Fc free: 0.9287 / 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. CALCIUM (CA), ACETATE, POLYETHYLENE GLYCOL FRAGMENTS (PGE) MODELED ARE PRESENT PROTEIN/CRYSTALLIZATION/CRYO BUFFER. 4. RAMACHANDRAN OUTLIERS (A66 AND A210) ARE SUPPORTED BY DENSITY. 5. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2039 1449 5.07 %RANDOM
Rwork0.161 ---
obs0.1633 28586 --
Displacement parametersBiso mean: 31.81 Å2
Baniso -1Baniso -2Baniso -3
1-5.1771 Å20 Å2-3.8575 Å2
2---3.7928 Å20 Å2
3----1.3843 Å2
Refinement stepCycle: LAST / Resolution: 2.08→25.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3223 0 25 301 3549
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013328HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.084517HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1539SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes95HARMONIC2
X-RAY DIFFRACTIONt_gen_planes478HARMONIC5
X-RAY DIFFRACTIONt_it3328HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.93
X-RAY DIFFRACTIONt_other_torsion2.91
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion431SEMIHARMONIC5
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_contact4072SEMIHARMONIC4
LS refinement shellResolution: 2.08→2.16 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2556 130 4.32 %
Rwork0.1848 2881 -
all0.1876 3011 -
Refinement TLS params.Method: refined / Origin x: 11.7092 Å / Origin y: -0.349 Å / Origin z: 25.9619 Å
111213212223313233
T-0.1042 Å20.0044 Å20.0103 Å2-0.015 Å20.005 Å2---0.0997 Å2
L1.4399 °20.2403 °2-0.0677 °2-0.4378 °20.0674 °2--0.3739 °2
S0.0192 Å °-0.1222 Å °-0.0968 Å °0.0286 Å °-0.0233 Å °-0.0755 Å °0.0376 Å °0.0136 Å °0.0042 Å °
Refinement TLS groupSelection details: { A| 40 - 456 }

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