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- PDB-4jhy: Crystal structure of a TBP-like protein (BDI_3606) from Parabacte... -

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Basic information

Entry
Database: PDB / ID: 4jhy
TitleCrystal structure of a TBP-like protein (BDI_3606) from Parabacteroides distasonis ATCC 8503 at 1.90 A resolution
Componentshypothetical protein
KeywordsStructural Genomics / Unknown Function / DUF4468 with TBP-like fold / PF14730 family protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyAlpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 - #80 / Domain of unknown function DUF4468 with TBP-like fold / Domain of unknown function (DUF4468) with TBP-like fold / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / 2-Layer Sandwich / Alpha Beta / DUF4468 domain-containing protein
Function and homology information
Biological speciesParabacteroides distasonis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (BDI_3606) from Parabacteroides distasonis ATCC 8503 at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 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

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Assembly

Deposited unit
A: hypothetical protein


Theoretical massNumber of molelcules
Total (without water)18,9901
Polymers18,9901
Non-polymers00
Water1,36976
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.670, 82.344, 40.543
Angle α, β, γ (deg.)90.000, 106.830, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein hypothetical protein /


Mass: 18989.957 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Parabacteroides distasonis (bacteria) / Strain: ATCC 8503 / Gene: BDI_3606, YP_001304926.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A6LHZ0
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 76 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (RESIDUES 19-184) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 19-184) 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: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M ammonium chloride, 20.0% polyethylene glycol 3350, 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: 0.97939, 0.91837, 0.97895
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 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
10.979391
20.918371
30.978951
ReflectionResolution: 1.9→28.239 Å / Num. obs: 12093 / % possible obs: 84.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.307 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 7.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.9-1.970.3581.83368212780.5
1.97-2.050.2792.63622228284.6
2.05-2.140.2073.23189203083.1
2.14-2.250.164.13303208980.5
2.25-2.390.1294.93627229687.7
2.39-2.580.115.73656233187.4
2.58-2.840.0787.43270210781.1
2.84-3.250.05910.23574232988.3
3.25-4.080.0414.23344218784.1
4.080.03216.53546235888.3

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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
CCP45.7.0032model building
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.9→28.239 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.929 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.522 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.172 / ESU R Free: 0.154
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. 4.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 5.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2261 590 4.9 %RANDOM
Rwork0.1832 ---
obs0.1853 12073 91.02 %-
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: 93.92 Å2 / Biso mean: 30.148 Å2 / Biso min: 14.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å2-0.8 Å2
2--1.38 Å2-0 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.239 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1245 0 0 76 1321
LS refinement shellResolution: 1.898→1.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 53 -
Rwork0.239 791 -
all-844 -
obs--88.56 %
Refinement TLS params.Method: refined / Origin x: 8.6767 Å / Origin y: 18.4004 Å / Origin z: 24.8252 Å
111213212223313233
T0.0762 Å20.0071 Å20.0258 Å2-0.0806 Å20.0074 Å2--0.105 Å2
L1.5341 °20.4898 °20.5979 °2-1.2645 °20.7073 °2--2.0034 °2
S-0.001 Å °0.0312 Å °-0.0994 Å °0.0014 Å °0.0137 Å °-0.0435 Å °0.0647 Å °-0.0294 Å °-0.0127 Å °

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