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- PDB-4r8o: Crystal structure of a DUF3836 family protein (BVU_1206) from Bac... -

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Basic information

Entry
Database: PDB / ID: 4r8o
TitleCrystal structure of a DUF3836 family protein (BVU_1206) from Bacteroides vulgatus ATCC 8482 at 2.50 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF12930 family (DUF3836) / single layer beta sheet protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyLipocalin - #720 / Protein of unknown function DUF3836 / Family of unknown function (DUF3836) / Lipocalin / Beta Barrel / Mainly Beta / DUF3836 domain-containing protein
Function and homology information
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Protein Sci. / Year: 2019
Title: Structures of single-layer beta-sheet proteins evolved from beta-hairpin repeats.
Authors: Xu, Q. / Biancalana, M. / Grant, J.C. / Chiu, H.J. / Jaroszewski, L. / Knuth, M.W. / Lesley, S.A. / Godzik, A. / Elsliger, M.A. / Deacon, A.M. / Wilson, I.A.
History
DepositionSep 2, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 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 1.4Apr 22, 2020Group: Database references / Derived calculations / Category: citation / citation_author / struct_conn
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Feb 1, 2023Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Oct 9, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
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: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)25,2442
Polymers25,2442
Non-polymers00
Water30617
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,6221
Polymers12,6221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)12,6221
Polymers12,6221
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-16 kcal/mol
Surface area13040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.080, 98.080, 89.240
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 12622.137 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / Gene: BVU_1206 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6KZN2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 26-128 OF 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: 4.91 Å3/Da / Density % sol: 74.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25.0% Glycerol 1.50M ammonium sulfate, 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: 0.97905
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2014
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: 0.97905 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.499
11-h,-k,l20.501
ReflectionResolution: 2.5→49.04 Å / Num. obs: 17436 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 9.79 % / Biso Wilson estimate: 84.846 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 16.06
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.5-2.578.922.4390.7511180125498.3
2.57-2.641.0991.712458122599.6
2.64-2.710.7442.612588122399.7
2.71-2.80.5773.311941116399.7
2.8-2.890.5223.611662115599.7
2.89-2.990.3495.410810109299.7
2.99-3.10.2976.610022106199.8
3.1-3.230.18210.59734102398.9
3.23-3.370.11516.71014499399.9
3.37-3.540.09420.5957494499.8
3.54-3.730.07825.2905290799.9
3.73-3.950.07228.68334851100
3.95-4.230.06531.1734880698.8
4.23-4.570.05435.9771876699.9
4.57-50.05236.8697369399.9
5-5.590.06235.2608063299.7
5.59-6.460.06832.8490655597.5
6.46-7.910.06336.8486949099.8
7.91-11.180.05637.8346238199
11.18-49.040.04336.5187022295.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
XSCALEJanuary 10, 2014 BUILT=20140307data scaling
REFMAC5.8.0073refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→49.04 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.922 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 10.521 / SU ML: 0.114 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.039 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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. 4.ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2444 881 5.1 %RANDOM
Rwork0.1768 ---
obs0.18 17387 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 152.31 Å2 / Biso mean: 79.4772 Å2 / Biso min: 34.55 Å2
Baniso -1Baniso -2Baniso -3
1--41.18 Å2-0 Å2-0 Å2
2---41.18 Å2-0 Å2
3---82.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→49.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1648 0 0 17 1665
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021682
X-RAY DIFFRACTIONr_bond_other_d0.0060.021532
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9442270
X-RAY DIFFRACTIONr_angle_other_deg1.46433524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.51225.65292
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75315280
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.678156
X-RAY DIFFRACTIONr_chiral_restr0.10.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021916
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02406
X-RAY DIFFRACTIONr_mcbond_it4.1816.282782
X-RAY DIFFRACTIONr_mcbond_other4.1826.278781
X-RAY DIFFRACTIONr_mcangle_it6.4239.41974
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.456 56 -
Rwork0.412 1150 -
all-1206 -
obs--94.59 %
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)
10.6237-0.1264-0.09871.03710.4750.9903-0.1819-0.0651-0.00530.13370.20290.0085-0.0089-0.0145-0.0210.21210.0854-0.02020.1479-0.00310.005423.921840.47310.2369
22.2859-1.59990.31522.1168-0.18360.8805-0.2035-0.2029-0.06160.370.2123-0.07760.0454-0.0603-0.00870.31290.15310.00030.10880.00990.018532.112124.142819.3875
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 127
2X-RAY DIFFRACTION2B30 - 127

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