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- PDB-4qrl: Crystal structure of a lipocalin-like protein (BACUNI_01346) from... -

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Basic information

Entry
Database: PDB / ID: 4qrl
TitleCrystal structure of a lipocalin-like protein (BACUNI_01346) from Bacteroides uniformis ATCC 8492 at 1.79 A resolution
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Lipocalin-like protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyLipocalin-like domain / Lipocalin - #280 / Lipocalin-like domain / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta / Lipocalin-like domain-containing protein
Function and homology information
Biological speciesBacteroides uniformis ATCC 8492 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.79 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein (BACUNI_01346) from Bacteroides uniformis ATCC 8492 at 1.79 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,2994
Polymers13,1131
Non-polymers1863
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.851, 48.851, 78.451
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-308-

HOH

31A-350-

HOH

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Components

#1: Protein Hypothetical protein


Mass: 13112.521 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis ATCC 8492 (bacteria)
Gene: BACUNI_01346, ZP_02069929.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V1A8
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN
Sequence detailsTHE CONSTRUCT (21-135) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (21-135) 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: 2.06 Å3/Da / Density % sol: 40.31 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M calcium chloride, 20.0% 2-propanol, 10.0% 1,2-butanediol, 0.1M sodium acetate pH 4.6, 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: 0.91837
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2013
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: 0.91837 Å / Relative weight: 1
ReflectionResolution: 1.79→39.225 Å / Num. obs: 10664 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 6.34 % / Biso Wilson estimate: 28.043 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 18.23
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.79-1.856.670.7252.43657898699.9
1.85-1.930.4613.77411113499.6
1.93-2.020.3145.36622105599.4
2.02-2.120.2098630299599.9
2.12-2.250.16310.568431023100
2.25-2.430.12913.17233110099.9
2.43-2.670.09117.96294103698.4
2.67-3.060.05828.27206109199.8
3.06-3.850.037416283107999.5
3.85-39.230.02747.56816116599.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
XSCALEdata scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→39.225 Å / Cor.coef. Fo:Fc: 0.9636 / Cor.coef. Fo:Fc free: 0.9302 / Occupancy max: 1 / Occupancy min: 0.35 / 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. EDO MODELED WAS PRESENT IN CRYO CONDITION. 4. THE STRUCTURE WAS SOLVED BY MOLECULAR REPLACEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2199 505 4.75 %RANDOM
Rwork0.1703 ---
obs0.1727 10638 99.62 %-
Displacement parametersBiso max: 98.29 Å2 / Biso mean: 33.9279 Å2 / Biso min: 18.16 Å2
Baniso -1Baniso -2Baniso -3
1-3.2953 Å20 Å20 Å2
2--3.2953 Å20 Å2
3----6.5906 Å2
Refine analyzeLuzzati coordinate error obs: 0.207 Å
Refinement stepCycle: LAST / Resolution: 1.79→39.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms888 0 12 112 1012
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d431SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes23HARMONIC2
X-RAY DIFFRACTIONt_gen_planes138HARMONIC5
X-RAY DIFFRACTIONt_it939HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion114SEMIHARMONIC5
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_contact1137SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d939HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1263HARMONIC21
X-RAY DIFFRACTIONt_omega_torsion3.72
X-RAY DIFFRACTIONt_other_torsion2.7
LS refinement shellResolution: 1.79→2 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2026 137 4.63 %
Rwork0.1948 2820 -
all0.1952 2957 -
obs--99.62 %
Refinement TLS params.Method: refined / Origin x: 9.5385 Å / Origin y: 27.6457 Å / Origin z: 12.1177 Å
111213212223313233
T-0.0563 Å2-0.0036 Å20.0256 Å2--0.0561 Å20.0013 Å2---0.0058 Å2
L1.8105 °20.2281 °2-0.0593 °2-1.8675 °2-0.4246 °2--1.084 °2
S0.015 Å °-0.1303 Å °0.0333 Å °0.0115 Å °-0.0087 Å °0.0265 Å °-0.0227 Å °-0.0767 Å °-0.0063 Å °
Refinement TLS groupSelection details: {A|26 - 135}

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