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- PDB-4k61: Crystal structure of a DUF2874 family protein (BACUNI_01296) from... -

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Basic information

Entry
Database: PDB / ID: 4k61
TitleCrystal structure of a DUF2874 family protein (BACUNI_01296) from Bacteroides uniformis ATCC 8492 at 1.70 A resolution
ComponentsUncharacterized protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / DUF2874 / PF11396 family protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyNuclear Transport Factor 2; Chain: A, - #360 / Putative beta-lactamase-inhibitor-like, PepSY-like / Putative beta-lactamase-inhibitor-like, PepSY-like / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / PepSY_like domain-containing protein
Function and homology information
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACUNI_01296) from Bacteroides uniformis ATCC 8492 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 15, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2013Provider: 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
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)32,1382
Polymers32,1382
Non-polymers00
Water4,684260
1
A: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,0691
Polymers16,0691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)16,0691
Polymers16,0691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.773, 86.773, 85.633
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Uncharacterized protein


Mass: 16068.989 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: ATCC 8492 / Gene: BACUNI_01296 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V158
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 22-160 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: 2.51 Å3/Da / Density % sol: 50.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.05M calcium acetate, 40% 1,2-propanediol, 0.1M sodium acetate pH 4.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97926,0.91837
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979261
20.918371
ReflectionResolution: 1.7→27.44 Å / Num. obs: 34782 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.537 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13.29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.760.7881.517932634193.2
1.76-1.830.594219269673497.9
1.83-1.910.3633.218109646497.7
1.91-2.020.2314.719326736597.4
2.02-2.140.1547.219152641498
2.14-2.310.1089.920323690898.3
2.31-2.540.07413.619520677399
2.54-2.90.0521817480666597.9
2.9-3.660.0330.820449685198.4
3.660.02241.219168677597.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEJuly 4, 2012data scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→27.44 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.573 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.11 / ESU R Free: 0.102
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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.
RfactorNum. reflection% reflectionSelection details
Rfree0.212 1745 5 %RANDOM
Rwork0.1897 ---
obs0.1909 34780 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 131.05 Å2 / Biso mean: 37.9645 Å2 / Biso min: 16.14 Å2
Baniso -1Baniso -2Baniso -3
1-1.55 Å20 Å20 Å2
2--1.55 Å2-0 Å2
3----3.09 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 0 260 2480
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022365
X-RAY DIFFRACTIONr_bond_other_d0.0040.022118
X-RAY DIFFRACTIONr_angle_refined_deg1.3921.9263253
X-RAY DIFFRACTIONr_angle_other_deg1.01234868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3755296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.97125118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43315309
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.117156
X-RAY DIFFRACTIONr_chiral_restr0.0860.2341
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212764
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02592
X-RAY DIFFRACTIONr_mcbond_it2.3932.6391130
X-RAY DIFFRACTIONr_mcbond_other2.3932.6391129
X-RAY DIFFRACTIONr_mcangle_it3.8894.9151414
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 129 -
Rwork0.293 2397 -
all-2526 -
obs--99.18 %
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)
10.330.1082-0.98611.13611.37266.852-0.02660.0267-0.0427-0.0374-0.13110.0229-0.197-0.57910.15770.05160.04020.00570.10090.00510.235615.85110.72514
21.22-0.06780.93592.37110.59955.1688-0.1961-0.01730.25-0.4450.00210.0924-0.2793-0.44620.1940.163-0.0299-0.0870.0962-0.01370.288513.93431.82228.31
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 160
2X-RAY DIFFRACTION2B23 - 160

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