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- PDB-3no2: Crystal structure of a protein of unknown function (BACCAC_01654)... -

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Basic information

Entry
Database: PDB / ID: 3no2
TitleCrystal structure of a protein of unknown function (BACCAC_01654) from Bacteroides caccae at 1.35 A resolution
Componentsuncharacterized protein
KeywordsUNKNOWN FUNCTION / six-bladed beta-propeller / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyWD40/YVTN repeat-like-containing domain superfamily / CITRIC ACID / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesBacteroides caccae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.35 Å
AuthorsJoint Center for Structural Genomics / Joint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a protein of unknown function (BACCAC_01654) from Bacteroides caccae at 1.35 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 24, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1165
Polymers30,6761
Non-polymers4404
Water6,630368
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.173, 63.798, 105.600
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein uncharacterized protein


Mass: 30676.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides caccae (bacteria) / Strain: ATCC 43185 / Gene: BACCAC_01654, ZP_01960044.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A5ZFJ0
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 368 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (20-294) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THE CONSTRUCT (20-294) 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: 2.54 Å3/Da / Density % sol: 51.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 40.000000000% PEG-600, 0.1M Citrate pH 5.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97941,0.97894
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 8, 2010 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979411
30.978941
ReflectionResolution: 1.35→27.993 Å / Num. obs: 68533 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 10.556 Å2 / Rmerge F obs: 0.164 / Rmerge(I) obs: 0.058 / Rrim(I) all: 0.075 / Net I/σ(I): 10.61 / Num. measured all: 297194
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.35-1.40.8610.5051.92847113740130870.65795.2
1.4-1.450.6840.3962.42525211841114100.51696.4
1.45-1.520.5310.3083.13050714080136420.40196.9
1.52-1.60.3730.2224.22931813271129630.28897.7
1.6-1.70.2920.1685.52951513174129210.21998.1
1.7-1.830.1970.1187.63005313197129440.15398.1
1.83-2.020.1240.07511.53149313629134320.09898.6
2.02-2.310.0750.0516.53050813094129300.06598.7
2.31-2.910.0520.038213093413209130820.04999
2.910.0270.02531.63114313253130790.03298.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
SHELXphasing
REFMAC5.5.0110refinement
XSCALEdata scaling
PDB_EXTRACT3.1data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.35→27.993 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / Occupancy max: 1 / Occupancy min: 0.11 / SU B: 1.292 / SU ML: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.045
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. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. (3). A MET- ...Details: (1). HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. (2). ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. (3). 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (4). CL AND CITRATE (CIT) IONS, AND PEG-600 FRAGMENTS (PEG) FROM CRYSTALLIZATION CONDITION WERE MODELED INTO THE STRUCTURE. (5). RAMACHANDRAN OUTLIER OF RESIDUE GLN144 IS SUPPORTED BY ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.1595 3466 5.1 %RANDOM
Rwork0.1468 65006 --
obs0.1475 68472 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 64.22 Å2 / Biso mean: 14.9537 Å2 / Biso min: 2.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å20 Å20 Å2
2---0.28 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.35→27.993 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 0 28 368 2501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222460
X-RAY DIFFRACTIONr_bond_other_d0.0010.021667
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9573355
X-RAY DIFFRACTIONr_angle_other_deg0.91234096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0365328
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.60225.234107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.36515419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.711511
X-RAY DIFFRACTIONr_chiral_restr0.1030.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212874
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02482
X-RAY DIFFRACTIONr_mcbond_it1.54431543
X-RAY DIFFRACTIONr_mcbond_other0.3883628
X-RAY DIFFRACTIONr_mcangle_it2.63152504
X-RAY DIFFRACTIONr_scbond_it3.8748917
X-RAY DIFFRACTIONr_scangle_it6.15411851
LS refinement shellResolution: 1.35→1.385 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 241 -
Rwork0.254 4702 -
all-4943 -
obs--97.02 %
Refinement TLS params.Method: refined / Origin x: 40.1053 Å / Origin y: 9.5309 Å / Origin z: 16.8778 Å
111213212223313233
T0.0014 Å2-0.0042 Å2-0.0023 Å2-0.0086 Å20.0027 Å2--0.0051 Å2
L0.0357 °2-0.13 °20.0578 °2-0.3007 °2-0.0513 °2--0.2346 °2
S0.0037 Å °-0.0088 Å °-0.0065 Å °-0.0125 Å °0.002 Å °0.0102 Å °0.0045 Å °-0.0193 Å °-0.0057 Å °

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