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- PDB-4q69: Crystal structure of a SusD homolog (BT2259) from Bacteroides the... -

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Basic information

Entry
Database: PDB / ID: 4q69
TitleCrystal structure of a SusD homolog (BT2259) from Bacteroides thetaiotaomicron VPI-5482 at 2.50 A resolution
ComponentsPutative lipoprotein
KeywordsSUGAR BINDING PROTEIN / SusD-like_2 family / PF12771 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologySusD-like 2 / Starch-binding associating with outer membrane / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / Putative lipoprotein
Function and homology information
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a SusD homolog (BT2259) from Bacteroides thetaiotaomicron VPI-5482 at 2.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 25, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Feb 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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Putative lipoprotein
B: Putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,6266
Polymers105,4532
Non-polymers1744
Water5,260292
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-49 kcal/mol
Surface area33920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.124, 135.124, 139.567
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein Putative lipoprotein / SusD homolog


Mass: 52726.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: BT_2259 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q8A5I0
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 28-488 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: 3.49 Å3/Da / Density % sol: 64.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M sodium citrate pH 6.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.95369,0.97936,0.97918
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 13, 2014 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.953691
20.979361
30.979181
ReflectionResolution: 2.5→89.672 Å / Num. all: 51369 / Num. obs: 51369 / % possible obs: 100 % / Redundancy: 6.2 % / Rsym value: 0.155 / Net I/σ(I): 9
Reflection shell

Rmerge(I) obs: 0.01 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.566.31.92364337591.01100
2.56-2.646.32.12294136400.899100
2.64-2.716.32.42238735580.76100
2.71-2.86.32.92190734830.631100
2.8-2.896.33.82109833470.46100
2.89-2.996.34.32051632660.388100
2.99-3.16.35.41975731450.301100
3.1-3.236.36.81901630150.237100
3.23-3.376.38.21821129020.192100
3.37-3.546.310.31759527940.154100
3.54-3.736.312.41666726600.128100
3.73-3.956.314.51574725120.104100
3.95-4.236.316.11481723690.09100
4.23-4.566.218.61368621980.076100
4.56-56.218.91278720520.069100
5-5.596.217.11146418570.073100
5.59-6.466.216.41017516500.073100
6.46-7.916.118.1849714000.061100
7.91-11.185.924.4660911130.043100
11.18-89.6725.420.935056490.04398.1

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
MOSFLMdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→89.672 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 13.373 / SU ML: 0.145 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.277 / ESU R Free: 0.199
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 3. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 5. 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. 6. CHLORIDE ION (CL), SODIUM IONS (NA), AND GLYCEROL (GOL) MOLECULE FROM PURIFICATION/CRYSTALLIZATION/CRYOPROTECTION SOLUTIONS ARE MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.1989 2605 5.1 %RANDOM
Rwork0.172 ---
obs0.1733 51309 99.83 %-
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: 133 Å2 / Biso mean: 45.4606 Å2 / Biso min: 9.98 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20.42 Å2-0 Å2
2--0.42 Å2-0 Å2
3----1.37 Å2
Refinement stepCycle: LAST / Resolution: 2.5→89.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7188 0 9 292 7489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.027381
X-RAY DIFFRACTIONr_bond_other_d0.0020.026767
X-RAY DIFFRACTIONr_angle_refined_deg0.9981.97410037
X-RAY DIFFRACTIONr_angle_other_deg0.778315630
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7455911
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.8425.311354
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.221151121
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8481528
X-RAY DIFFRACTIONr_chiral_restr0.0570.21071
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218473
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021659
X-RAY DIFFRACTIONr_mcbond_it2.5886.683638
X-RAY DIFFRACTIONr_mcbond_other2.5896.6793637
X-RAY DIFFRACTIONr_mcangle_it4.01112.5154545
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.314 204 -
Rwork0.279 3545 -
all-3749 -
obs--99.87 %
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)
11.0533-0.086-0.5330.54510.10960.3826-0.12320.08020.02870.01430.07040.02650.0907-0.04260.05280.0761-0.03730.00730.0762-0.02590.05955.719-51.179-25.537
21.0582-0.0928-0.05730.9210.4130.26530.1430.10270.0675-0.082-0.15270.0368-0.0521-0.01870.00970.10170.04360.02030.07480.00540.05665.115-15.452-7.225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A33 - 488
2X-RAY DIFFRACTION2B36 - 488

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