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- PDB-3myv: Crystal structure of a SusD superfamily protein (BVU_0732) from B... -

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Basic information

Entry
Database: PDB / ID: 3myv
TitleCrystal structure of a SusD superfamily protein (BVU_0732) from Bacteroides vulgatus ATCC 8482 at 1.80 A resolution
ComponentsSusD superfamily protein
KeywordsSACCHARIDE BINDING PROTEIN / RagB / SusD and hypothetical proteins / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / Polysaccharide Binding Protein
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Anthopleurin-A - #130 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #900 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Anthopleurin-A / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Single Sheet / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...Anthopleurin-A - #130 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #900 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Anthopleurin-A / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Single Sheet / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / Putative outer membrane protein, probably involved in nutrient binding
Similarity search - Component
Biological speciesBacteroides vulgatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a SusD superfamily protein (BVU_0732) from Bacteroides vulgatus ATCC 8482 at 1.80 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 11, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_asym_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.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_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: SusD superfamily protein
B: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,33722
Polymers103,1022
Non-polymers1,23520
Water22,1941232
1
A: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,07010
Polymers51,5511
Non-polymers5209
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,26612
Polymers51,5511
Non-polymers71611
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.136, 83.639, 223.303
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A SIGNIFICANT OLIGMERIZATION STATE IN SOLUTION.

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Components

#1: Protein SusD superfamily protein / Putative outer membrane protein


Mass: 51550.832 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides vulgatus (bacteria) / Strain: ATCC 8482 / DSM 1447 / NCTC 11154 / Gene: BVU_0732 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6KYC4
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1232 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 28-480) WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG ...THE CONSTRUCT (RESIDUES 28-480) WAS EXPRESSED WITH AN N-TERMINAL 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: 2.5 Å3/Da / Density % sol: 50.74 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 22.5000% polyethylene glycol 3350, 0.2000M di-sodium hydrogen phosphate, 0.1M HEPES pH 6.7, 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: 0.91837,0.97954,0.97934
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 6, 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
10.918371
20.979541
30.979341
ReflectionResolution: 1.8→74.434 Å / Num. obs: 96603 / % possible obs: 99.9 % / Redundancy: 3.7 % / Biso Wilson estimate: 18.505 Å2 / Rsym value: 0.112 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.8-1.93.70.591.951786139610.5999.9
1.9-2.013.70.4122.648873131630.412100
2.01-2.153.70.2723.846407124680.272100
2.15-2.323.70.24.843356116350.2100
2.32-2.553.70.1496.239910107120.149100
2.55-2.853.70.1137.73619997240.113100
2.85-3.293.70.0859.93205586310.085100
3.29-4.023.70.06613.42723473440.06699.8
4.02-5.693.70.05814.52106257310.05899.5
5.69-74.433.50.06313.41147832340.06397.8

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
SCALA3.3.15data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→74.434 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.953 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 4.355 / SU ML: 0.071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.106
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. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. WATERS WERE EXCLUDED FROM TLS GROUPS. 5. RAMACHANDRAN OUTLIERS (A61 AND B61) ARE SUPPORTED BY CLEAR DENSITY. 5. SODIUM ION (NA), PHOSPHATE ION (PO4), AND ETHYLENE GLYCOL (EDO) MODELED WERE PRESENT IN CRYSTLLIZATION/CRYO CONDITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19 4830 5 %RANDOM
Rwork0.151 ---
obs0.153 96490 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 67.32 Å2 / Biso mean: 22.387 Å2 / Biso min: 6.11 Å2
Baniso -1Baniso -2Baniso -3
1-1.33 Å20 Å20 Å2
2---0.56 Å20 Å2
3----0.77 Å2
Refinement stepCycle: LAST / Resolution: 1.8→74.434 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7018 0 78 1232 8328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0227435
X-RAY DIFFRACTIONr_bond_other_d0.0010.025050
X-RAY DIFFRACTIONr_angle_refined_deg1.2721.96110093
X-RAY DIFFRACTIONr_angle_other_deg0.882312295
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7515949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81524.636371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.674151225
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0031539
X-RAY DIFFRACTIONr_chiral_restr0.0790.21059
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028448
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021547
X-RAY DIFFRACTIONr_mcbond_it1.45534496
X-RAY DIFFRACTIONr_mcbond_other0.45431852
X-RAY DIFFRACTIONr_mcangle_it2.16557217
X-RAY DIFFRACTIONr_scbond_it3.77882939
X-RAY DIFFRACTIONr_scangle_it5.268112844
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 356 -
Rwork0.254 6704 -
all-7060 -
obs--99.8 %
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)
10.15170.0206-0.03660.51950.00120.27220.0144-0.0130.00570.0175-0.0123-0.00450.00580.011-0.00210.0122-0.0026-0.00220.0025-0.00230.00718.260239.749710.215
20.4406-0.1099-0.07680.39020.08050.32110.04250.1393-0.0384-0.0644-0.0320.0067-0.0196-0.0139-0.01050.03450.021-0.01640.0537-0.01630.012421.324641.6833-41.917
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A36 - 480
2X-RAY DIFFRACTION2B36 - 479

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