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- PDB-4gt6: Crystal structure of a leucine rich cell surface protein (FAEPRAA... -

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Basic information

Entry
Database: PDB / ID: 4gt6
TitleCrystal structure of a leucine rich cell surface protein (FAEPRAA2165_01021) from Faecalibacterium prausnitzii A2-165 at 1.80 A resolution
ComponentsCell surface protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Leucine rich repeats / putative protein binding / extracellular protein / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyBspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat domain superfamily / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesFaecalibacterium prausnitzii A2-165 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of a leucine rich cell surface protein (FAEPRAA2165_01021) from Faecalibacterium prausnitzii A2-165 at 1.80 A resolution (CASP Target)
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
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_alt_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_alt_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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_conn.ptnr2_auth_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

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Assembly

Deposited unit
A: Cell surface protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,00718
Polymers42,9911
Non-polymers1,01617
Water9,530529
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)119.538, 119.538, 77.568
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Cell surface protein


Mass: 42991.203 Da / Num. of mol.: 1 / Fragment: UNP residues 28-420
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Faecalibacterium prausnitzii A2-165 (bacteria)
Gene: FAEPRAA2165_01021 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: C7H408
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 529 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 28-420 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: 3.72 Å3/Da / Density % sol: 66.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 30.00% polyethylene glycol 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: BL12-2 / Wavelength: 0.9794
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.8→26.927 Å / Num. all: 58422 / Num. obs: 58422 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 20.427 Å2 / Rsym value: 0.118 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.857.10.7322.73027242840.73299.9
1.85-1.98.10.5983.53399542160.598100
1.9-1.958.10.4494.63294940870.449100
1.95-2.017.80.3495.53065439490.349100
2.01-2.087.50.2716.62839938060.27199.9
2.08-2.157.10.2217.72668237420.22199.9
2.15-2.2370.1848.72508336020.184100
2.23-2.328.10.16710.32790434460.167100
2.32-2.4380.14811.32643633210.148100
2.43-2.5580.13312.12538631800.133100
2.55-2.687.80.118132341430110.118100
2.68-2.856.80.10313.61943228730.10399.9
2.85-3.048.40.096172230126670.096100
3.04-3.298.30.0918.72074524950.09100
3.29-3.68.20.08420.61898823210.084100
3.6-4.027.20.08120.81509720870.08199.8
4.02-4.657.60.07722.71418118580.077100
4.65-5.698.30.08822.61308115830.088100
5.69-8.057.10.10119.9865512140.10199.9
8.05-26.9278.50.06923.857906800.06997.4

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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
BUSTER-TNT2.10.0refinement
MOSFLMdata reduction
SHELXDphasing
BUSTER2.10.0refinement
RefinementMethod to determine structure: SAD / Resolution: 1.8→26.927 Å / Cor.coef. Fo:Fc: 0.9648 / Cor.coef. Fo:Fc free: 0.9535 / Occupancy max: 1 / Occupancy min: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1741 2954 5.06 %RANDOM
Rwork0.1506 ---
obs0.1517 58367 99.92 %-
Displacement parametersBiso max: 159.01 Å2 / Biso mean: 27.1026 Å2 / Biso min: 7.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.8486 Å20 Å20 Å2
2--0.8486 Å20 Å2
3----1.6973 Å2
Refine analyzeLuzzati coordinate error obs: 0.168 Å
Refinement stepCycle: LAST / Resolution: 1.8→26.927 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2886 0 65 529 3480
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1513SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes81HARMONIC2
X-RAY DIFFRACTIONt_gen_planes493HARMONIC5
X-RAY DIFFRACTIONt_it3214HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion468SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance3HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4477SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3214HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg4394HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion4.25
X-RAY DIFFRACTIONt_other_torsion2.51
LS refinement shellResolution: 1.8→1.85 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2204 216 5.05 %
Rwork0.1979 4063 -
all0.199 4279 -
obs--99.92 %
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)
10.71750.1308-0.10940.5302-0.30850.4690.0471-0.0402-0.01210.068-0.00360.0062-0.06230.0289-0.0435-0.05280.0024-0.0101-0.0371-0.0058-0.041967.741651.015672.2041
20.94920.1372-0.03891.2460.56632.02370.06240.1840.049-0.1528-0.07650.1135-0.2114-0.19310.0141-0.05190.0113-0.00390.01850.02950.001580.660966.793243.1306
32.9306-0.65651.29386.27383.38865.4137-0.08830.3822-0.0599-0.30860.17710.1581-0.1953-0.526-0.08890.04030.0434-0.05380.02220.0065-0.125378.489764.505826.6218
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 274
2X-RAY DIFFRACTION2A275 - 383
3X-RAY DIFFRACTION3A384 - 406

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