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- PDB-4dqa: Crystal structure of a putative carbohydrate binding protein (BAC... -

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Basic information

Entry
Database: PDB / ID: 4dqa
TitleCrystal structure of a putative carbohydrate binding protein (BACOVA_03559) from Bacteroides ovatus ATCC 8483 at 1.50 A resolution
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / Two domains structure / DUF 1735 / laminin_G_3 concanavalin A-like lectin/glucanases superfamily domain / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


hypothetical protein (bacova_03559) / Domain of unknown function DUF1735 / BT_3987-like, N-terminal domain / Concanavalin A-like lectin/glucanases superfamily / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DUF1735 domain-containing protein
Similarity search - Component
Biological speciesBacteroides ovatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACOVA_03559) from Bacteroides ovatus ATCC 8483 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionFeb 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 21, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)39,5321
Polymers39,5321
Non-polymers00
Water7,891438
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.131, 94.131, 156.273
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein uncharacterized protein


Mass: 39531.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus (bacteria) / Strain: ATCC 8483 / Gene: BACOVA_03559 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7M0D0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 27-380) WAS EXPRESSED WITH AN N- TERMINAL PURIFICATION TAG ...THE CONSTRUCT (RESIDUES 27-380) WAS EXPRESSED WITH AN N- TERMINAL 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: 2.53 Å3/Da / Density % sol: 51.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M sodium chloride, 1.0M sodium citrate, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97916
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 1, 2011
Details: Vertical focusing mirror; double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 1.5→29.183 Å / Num. all: 65989 / Num. obs: 65989 / % possible obs: 100 % / Redundancy: 9 % / Rsym value: 0.088 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.5-1.548.90.8480.94300648100.848100
1.54-1.5890.7191.14169546460.719100
1.58-1.6390.5481.44099845660.548100
1.63-1.6890.4391.83973244090.439100
1.68-1.7390.3572.23864242860.357100
1.73-1.7990.282.83776141830.28100
1.79-1.8690.223.53632940210.22100
1.86-1.949.10.1694.43503438650.169100
1.94-2.029.10.1415.23369737210.141100
2.02-2.1290.1265.53232335790.126100
2.12-2.2490.1185.73075134060.118100
2.24-2.3790.1185.72924532330.118100
2.37-2.5490.1076.12757830510.107100
2.54-2.7490.0927.22559228340.092100
2.74-390.0778.62385526500.077100
3-3.358.90.0669.92145824040.066100
3.35-3.878.90.05811.21897921440.058100
3.87-4.748.70.05312.51600618450.053100
4.74-6.718.40.0610.91235714730.0699.9
6.71-29.1837.40.0659.963788630.06597.4

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
PHENIX1.7.3refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→29.183 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 15.3 / Stereochemistry target values: MLHL
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
RfactorNum. reflection% reflection
Rfree0.1764 3343 5.07 %
Rwork0.1558 --
obs0.1569 65902 99.96 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.188 Å2 / ksol: 0.41 e/Å3
Displacement parametersBiso max: 111.81 Å2 / Biso mean: 26.3022 Å2 / Biso min: 8.01 Å2
Baniso -1Baniso -2Baniso -3
1--1.3211 Å2-0 Å20 Å2
2---1.3211 Å20 Å2
3---2.6422 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2681 0 0 438 3119
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012884
X-RAY DIFFRACTIONf_angle_d1.2843955
X-RAY DIFFRACTIONf_chiral_restr0.079442
X-RAY DIFFRACTIONf_plane_restr0.007512
X-RAY DIFFRACTIONf_dihedral_angle_d12.9341061
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52140.29791280.25825722700100
1.5214-1.54410.26841370.239825692706100
1.5441-1.56830.24741380.224325742712100
1.5683-1.5940.23681440.21525182662100
1.594-1.62150.24411550.198125502705100
1.6215-1.65090.221220.186525872709100
1.6509-1.68270.18921350.166825742709100
1.6827-1.7170.19821570.163625462703100
1.717-1.75440.17391260.156825912717100
1.7544-1.79520.19561310.160425642695100
1.7952-1.84010.19241550.148325612716100
1.8401-1.88980.1711330.150425882721100
1.8898-1.94540.17851280.141726052733100
1.9454-2.00820.16851230.142526062729100
2.0082-2.07990.15011570.138525672724100
2.0799-2.16320.14961340.136726022736100
2.1632-2.26160.17571380.136626152753100
2.2616-2.38080.16251390.140225952734100
2.3808-2.52990.16671500.144626222772100
2.5299-2.72510.17831400.142526372777100
2.7251-2.99910.18411310.150626612792100
2.9991-3.43240.15551550.151726582813100
3.4324-4.32230.15861500.143127152865100
4.3223-29.18870.18721370.17642882301999
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)
11.2582-0.5293-0.041.95881.01921.1540.062-0.0281-0.0607-0.00320.09720.01230.13310.2127-0.08430.12950.033-0.04230.1099-0.02310.14281.064370.123120.495
21.0297-0.1969-0.2971.74060.10210.48520.05850.1318-0.0146-0.2332-0.08760.1510.0331-0.03360.0110.08250.0242-0.02490.09070.01040.0489-6.984725.91321.3118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 32:159)A32 - 159
2X-RAY DIFFRACTION2(chain A and resid 160:380)A160 - 380

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