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- PDB-4eiu: Crystal structure of a DUF3823 family protein (BACUNI_03093) from... -

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Basic information

Entry
Database: PDB / ID: 4eiu
TitleCrystal structure of a DUF3823 family protein (BACUNI_03093) from Bacteroides uniformis ATCC 8492 at 1.90 A resolution
Componentsuncharacterized hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PF12866 family protein / DUF3823 / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyImmunoglobulin-like - #2060 / Carboxypeptidase-like, regulatory domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / DUF3823 domain-containing protein
Function and homology information
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BACUNI_03093) from Bacteroides uniformis ATCC 8492 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 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 ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 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

Downloads & links

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Assembly

Deposited unit
A: uncharacterized hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,77714
Polymers28,3101
Non-polymers1,46813
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.895, 83.895, 112.365
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-516-

HOH

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Components

#1: Protein uncharacterized hypothetical protein


Mass: 28309.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: ATCC 8492 / Gene: BACUNI_03093 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V680
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 24-271) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 24-271) 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: 3.49 Å3/Da / Density % sol: 64.78 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.5
Details: 50.0% polyethylene glycol 200, 0.1M CHES pH 9.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL14-1 / Wavelength: 0.97915
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 13, 2012
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: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.9→29.661 Å / Num. all: 32310 / Num. obs: 32310 / % possible obs: 99.9 % / Redundancy: 11.9 % / Biso Wilson estimate: 33.31 Å2 / Rsym value: 0.095 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.9-1.9511.90.9722.62797723470.972100
1.95-2120.7421.12724422790.742100
2-2.06120.5561.42655822160.556100
2.06-2.12120.4521.72599321720.452100
2.12-2.19120.3592.12515020950.359100
2.19-2.27120.2952.52453720460.295100
2.27-2.36120.243.12341719500.24100
2.36-2.45120.2033.62288419050.203100
2.45-2.56120.184.12183918260.18100
2.56-2.69120.154.52091017470.15100
2.69-2.8311.90.1325.11979316650.132100
2.83-311.90.1135.71890515850.113100
3-3.2111.90.0986.31779214950.098100
3.21-3.4711.90.0797.81670014030.079100
3.47-3.811.80.0689.41526612940.068100
3.8-4.2511.70.06110.71386511850.061100
4.25-4.9111.60.0699.31212210460.06999.9
4.91-6.0111.40.0748.7103479110.074100
6.01-8.510.90.0729.279547280.072100
8.5-29.6619.30.06410.438694150.06494.9

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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
REFMAC5.6.0117refinement
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→29.661 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.168 / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.109 / ESU R Free: 0.106
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
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. 5.PEG200 FRAGMENTS (PEG AND PGE) FROM THE CRYSTALLIZATION SOLUTION HAVE BEEN MODELED IN THE SOLVENT STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.2065 1634 5.1 %RANDOM
Rwork0.1789 ---
obs0.1803 32242 99.88 %-
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: 157.29 Å2 / Biso mean: 59.1033 Å2 / Biso min: 30.35 Å2
Baniso -1Baniso -2Baniso -3
1-1.74 Å20 Å20 Å2
2--1.74 Å20 Å2
3----3.48 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.661 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 97 142 2150
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022058
X-RAY DIFFRACTIONr_bond_other_d0.0030.021460
X-RAY DIFFRACTIONr_angle_refined_deg1.6751.9652759
X-RAY DIFFRACTIONr_angle_other_deg0.94133524
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0915247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.48924.1100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.56615319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9661516
X-RAY DIFFRACTIONr_chiral_restr0.0940.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212256
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02424
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 109 -
Rwork0.277 2009 -
all-2118 -
obs--99.91 %
Refinement TLS params.Method: refined / Origin x: 17.2963 Å / Origin y: 34.9767 Å / Origin z: 19.7742 Å
111213212223313233
T0.033 Å20.0138 Å2-0.02 Å2-0.0775 Å2-0.0278 Å2--0.0358 Å2
L2.1775 °2-0.5931 °2-0.6425 °2-2.6842 °21.7956 °2--4.5264 °2
S-0.0154 Å °-0.3164 Å °0.019 Å °0.2912 Å °0.209 Å °-0.194 Å °0.1661 Å °0.4283 Å °-0.1936 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A30 - 134
2X-RAY DIFFRACTION1A135 - 271

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