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- PDB-3jys: Crystal structure of SusD superfamily protein (YP_001298690.1) fr... -

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Basic information

Entry
Database: PDB / ID: 3jys
TitleCrystal structure of SusD superfamily protein (YP_001298690.1) from Bacteroides vulgatus ATCC 8482 at 2.00 A resolution
ComponentsSusD superfamily protein
KeywordsSUGAR BINDING PROTEIN / YP_001298690.1 / SusD superfamily protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / RagB / SusD and hypothetical proteins / unknown function
Function / homology
Function and homology information


cell outer membrane / metal ion binding
Similarity search - Function
TPR-like / SusD-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe ...TPR-like / SusD-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative outer membrane protein, probably involved in nutrient binding
Similarity search - Component
Biological speciesBacteroides vulgatus ATCC 8482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of SusD superfamily protein (YP_001298690.1) from Bacteroides vulgatus ATCC 8482 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionSep 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_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

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Assembly

Deposited unit
A: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8392
Polymers56,8151
Non-polymers241
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.929, 63.929, 266.398
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein SusD superfamily protein / Putative outer membrane protein / probably involved in nutrient binding


Mass: 56814.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus ATCC 8482 (bacteria)
Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_1379, YP_001298690.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6L054
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSEQUENCE THIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THIS CONSTRUCT 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: 2.4 Å3/Da / Density % sol: 48.65 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.2000M MgCl2, 20.0000% PEG-3350, No Buffer pH 5.8, 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: 0.91162,0.97936
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 15, 2009 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979361
ReflectionResolution: 2→29.111 Å / Num. obs: 38690 / % possible obs: 100 % / Redundancy: 7.1 % / Biso Wilson estimate: 32.57 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2-2.057.30.6431.22023027860.643100
2.05-2.117.30.4891.61964727060.489100
2.11-2.177.30.37921921126450.379100
2.17-2.247.30.3252.31887125920.325100
2.24-2.317.30.2722.81827825130.272100
2.31-2.397.20.2163.51761024340.216100
2.39-2.487.30.18641701623390.186100
2.48-2.587.20.14851641522700.148100
2.58-2.77.20.1275.71577821900.127100
2.7-2.837.20.1027.11504820890.102100
2.83-2.987.20.0868.11432819900.086100
2.98-3.167.20.0798.21355218950.079100
3.16-3.387.10.0728.81280218050.072100
3.38-3.6570.0668.81176716710.066100
3.65-470.05410.51100615640.054100
4-4.4770.04513.6986214140.045100
4.47-5.166.80.04214.1865312650.042100
5.16-6.326.70.04314.5744911070.043100
6.32-8.946.40.03914.856528900.039100
8.94-29.65.60.03616.729565250.03696.7

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2→29.111 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 8.817 / SU ML: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.136
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. MAGNESIUM ION IS MODELED FROM CRYSTALLIZATION CONDITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.198 1931 5 %RANDOM
Rwork0.178 ---
obs0.179 38586 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 63.02 Å2 / Biso mean: 32.083 Å2 / Biso min: 20.18 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2--1.33 Å20 Å2
3----2.66 Å2
Refinement stepCycle: LAST / Resolution: 2→29.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3814 0 1 266 4081
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224001
X-RAY DIFFRACTIONr_bond_other_d0.0010.022667
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.9355460
X-RAY DIFFRACTIONr_angle_other_deg0.96736480
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1455505
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.63224.766214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.61815645
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.3071524
X-RAY DIFFRACTIONr_chiral_restr0.0930.2575
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024593
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02850
X-RAY DIFFRACTIONr_mcbond_it0.7241.52422
X-RAY DIFFRACTIONr_mcbond_other0.1981.5988
X-RAY DIFFRACTIONr_mcangle_it1.2523902
X-RAY DIFFRACTIONr_scbond_it2.04631579
X-RAY DIFFRACTIONr_scangle_it3.0594.51543
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 138 -
Rwork0.259 2644 -
all-2782 -
obs--100 %
Refinement TLS params.Method: refined / Origin x: 57.311 Å / Origin y: 25.77 Å / Origin z: 119.806 Å
111213212223313233
T0.1833 Å2-0.1092 Å20.0318 Å2-0.1264 Å2-0.0427 Å2--0.1262 Å2
L2.0743 °2-0.0264 °21.0421 °2-0.635 °2-0.0783 °2--2.2126 °2
S0.0462 Å °-0.2403 Å °0.197 Å °0.1126 Å °-0.1133 Å °0.046 Å °-0.2615 Å °-0.1743 Å °0.067 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 62
2X-RAY DIFFRACTION1A79 - 535

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