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- PDB-4ecn: Crystal structure of a leucine-rich repeat protein (BT_0210) from... -

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Basic information

Entry
Database: PDB / ID: 4ecn
TitleCrystal structure of a leucine-rich repeat protein (BT_0210) from Bacteroides thetaiotaomicron VPI-5482 at 2.80 A resolution
ComponentsLeucine-rich repeat protein
KeywordsUNKNOWN FUNCTION / leucine-rich repeats / DUF4458 domain / protein binding / extracellular protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


membrane => GO:0016020
Similarity search - Function
Domain of unknown function DUF4458 / Domain of unknown function DUF4458 / Leucine Rich repeat protein, N-terminal domain superfamily / DUF4458 domain-containing protein, leucine-rich repeat / Domain of unknown function (DUF4458) / Leucine-rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily ...Domain of unknown function DUF4458 / Domain of unknown function DUF4458 / Leucine Rich repeat protein, N-terminal domain superfamily / DUF4458 domain-containing protein, leucine-rich repeat / Domain of unknown function (DUF4458) / Leucine-rich repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Leucine-rich repeat protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a leucine-rich repeat protein (BT_0210) from Bacteroides thetaiotaomicron VPI-5482 at 2.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 26, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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: Leucine-rich repeat protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,5413
Polymers99,4831
Non-polymers582
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.399, 105.463, 161.196
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 Leucine-rich repeat protein /


Mass: 99482.820 Da / Num. of mol.: 1 / Fragment: UNP residues 30-904
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_0210 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8ABA0
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 30-904) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 30-904) 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: 3.65 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 20.00% PEG-6000, 0.1M Bicine pH 9.0, 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: 0.97894,0.97949,0.92522
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 8, 2012
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
10.978941
20.979491
30.925221
ReflectionResolution: 2.8→47.876 Å / Num. obs: 36526 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 78.337 Å2 / Rmerge(I) obs: 0.138 / Net I/σ(I): 13.97
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.8-2.870.0121.6159132668199.5
2.87-2.950.0122.4243882616199.9
2.95-3.040.0123.42682025131100
3.04-3.130.01242593024391100
3.13-3.230.0125.82540024061100
3.23-3.350.0127.52412923101100
3.35-3.470.0129.72307222341100
3.47-3.610.01211.8221612158199.9
3.61-3.780.01214.2207042087199.9
3.78-3.960.01216.5186321967199.8
3.96-4.170.01218.6156001847198.7
4.17-4.430.01221.7187741811199.9
4.43-4.730.01225.7177471693199.9
4.73-5.110.01226.6162441578199.9
5.11-5.60.01224.51496714611100
5.6-6.260.01223.9132011340199.7
6.26-7.230.01224.6109361179199.6
7.23-8.850.01229.78425986196.7
8.85-12.520.01242.38054809199.9
12.52-47.8760.01245.54203481197.2

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
BUSTER-TNT2.10.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.8→47.876 Å / Cor.coef. Fo:Fc: 0.9363 / Cor.coef. Fo:Fc free: 0.9004 / Occupancy max: 1 / Occupancy min: 0.75 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. 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 ...Details: 1. 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. 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT. 4. RAMACHANDRAN OUTLIER (GLY229) IS LOCATED AT A REGION WITH POOR DENSITY. 5. SODIUM AND CHLORIDE MODELED WERE PRESENT IN THE CRYSTALLIZATION CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2317 1826 5.01 %RANDOM
Rwork0.1819 ---
obs0.1844 36444 99.61 %-
Displacement parametersBiso max: 147.49 Å2 / Biso mean: 61.4038 Å2 / Biso min: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.8022 Å20 Å20 Å2
2---9.2945 Å20 Å2
3---13.0967 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.8→47.876 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6594 0 2 85 6681
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3128SINUSOIDAL6
X-RAY DIFFRACTIONt_trig_c_planes193HARMONIC2
X-RAY DIFFRACTIONt_gen_planes955HARMONIC5
X-RAY DIFFRACTIONt_it6720HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion900SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7481SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6720HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9115HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion3.45
X-RAY DIFFRACTIONt_other_torsion2.49
LS refinement shellResolution: 2.8→2.88 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2968 149 5.1 %
Rwork0.2403 2770 -
all0.2433 2919 -
obs--99.61 %
Refinement TLS params.Method: refined / Origin x: 6.0875 Å / Origin y: 11.0669 Å / Origin z: 140.648 Å
111213212223313233
T-0.1507 Å20.0613 Å2-0.0441 Å2--0.0181 Å20.0163 Å2---0.1098 Å2
L0.2483 °2-0.1667 °2-0.1767 °2-0.664 °20.5455 °2--0.9936 °2
S-0.0555 Å °-0.09 Å °0.024 Å °0.1389 Å °0.0737 Å °-0.0636 Å °0.119 Å °-0.0644 Å °-0.0183 Å °

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