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- PDB-3l22: CRYSTAL STRUCTURE OF A SUSD SUPERFAMILY PROTEIN (BF_0597) FROM BA... -

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Basic information

Entry
Database: PDB / ID: 3l22
TitleCRYSTAL STRUCTURE OF A SUSD SUPERFAMILY PROTEIN (BF_0597) FROM BACTEROIDES FRAGILIS AT 2.05 A RESOLUTION
ComponentsSusD superfamily protein
KeywordsSUGAR BINDING PROTEIN / SUSD SUPERFAMILY PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2
Function / homology
Function and homology information


cell outer membrane / metal ion binding
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / SusD-like, N-terminal / Starch-binding associating with outer membrane / RagB/SusD domain / SusD family / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Putative membrane protein
Similarity search - Component
Biological speciesBacteroides fragilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of SusD superfamily protein (YP_210307.1) from Bacteroides fragilis NCTC 9343 at 2.05 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 14, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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_alt_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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_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_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_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_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

Downloads & links

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Assembly

Deposited unit
A: SusD superfamily protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,69928
Polymers50,0201
Non-polymers1,67927
Water11,115617
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.034, 94.034, 201.581
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
DetailsCRYSTAL PACKING AND ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY ANALYSES SUPPORT THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION.

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Components

#1: Protein SusD superfamily protein / Putative membrane protein


Mass: 50020.285 Da / Num. of mol.: 1 / Fragment: sequence database residues 25-464
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides fragilis (bacteria) / Strain: ATCC 25285 / NCTC 9343 / Gene: BF0597 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q5LHN1
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 617 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT (25-464) WAS EXPRESSED WITH THE PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...THIS CONSTRUCT (25-464) WAS EXPRESSED WITH THE 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: 4.45 Å3/Da / Density % sol: 72.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.33
Details: 0.2000M zinc acetate, 22.5000% Ethanol, 0.1M MES pH 6.33, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.978930,0.979373,0.918370
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 3, 2009 / Details: Vertical focusing mirror
RadiationMonochromator: Single crystal Si(311) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.978931
20.9793731
30.918371
ReflectionResolution: 2.05→29.412 Å / Num. obs: 57591 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.12 % / Biso Wilson estimate: 26.653 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 11.52
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.05-2.120.7841.83716510104197.2
2.12-2.210.5762.44296611464199.8
2.21-2.310.4443.24054410769199.8
2.31-2.430.3234.34065510682199.8
2.43-2.580.2395.84084510701199.8
2.58-2.780.1777.64187710960199.8
2.78-3.060.11511.24151910849199.7
3.06-3.50.0717.44133710818199.7
3.5-4.40.04227.44090410798199.7
4.4-29.4120.03233.64198710974199.4

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.05→29.412 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / Occupancy max: 1 / Occupancy min: 0.19 / SU B: 4.648 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.099
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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. ZINC IONS (ZN), ACETATE (ACT), AND ETHYLENE GLYCOL (EDO) FROM THE CRYSTALLIZATION/CRYOPROTECTANT SOLUTIONS HAVE BEEN MODELED INTO THE SOLVENT STRUCTURE. 5. TLS GROUPS WERE ASSIGNED WITH THE AID OF THE TLSMD SERVER.
RfactorNum. reflection% reflectionSelection details
Rfree0.171 2921 5.1 %RANDOM
Rwork0.146 ---
obs0.148 57523 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 80.35 Å2 / Biso mean: 19.013 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.05→29.412 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3377 0 81 617 4075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0223618
X-RAY DIFFRACTIONr_bond_other_d0.0020.022421
X-RAY DIFFRACTIONr_angle_refined_deg1.61.9764912
X-RAY DIFFRACTIONr_angle_other_deg1.20335951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8155466
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90925.266169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.09615632
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.1671517
X-RAY DIFFRACTIONr_chiral_restr0.0980.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214051
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02691
X-RAY DIFFRACTIONr_mcbond_it0.7211.52221
X-RAY DIFFRACTIONr_mcbond_other0.2061.5885
X-RAY DIFFRACTIONr_mcangle_it1.27923587
X-RAY DIFFRACTIONr_scbond_it2.31831397
X-RAY DIFFRACTIONr_scangle_it3.364.51306
LS refinement shellResolution: 2.049→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 200 -
Rwork0.247 3902 -
all-4102 -
obs--98.3 %
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)
115.18043.5426-0.94518.2977.243810.74190.0242-0.5563-0.8150.90720.06710.07620.898-0.4553-0.09140.18730.02950.05720.27690.0960.122442.67848.92921.559
21.2564-0.2033-0.1380.5943-0.12170.6914-0.10630.0688-0.22-0.00090.03240.00720.0947-0.11250.07390.05790.00210.03470.0786-0.01390.052363.58844.1589.393
30.9266-0.3137-0.3750.97340.5380.9253-0.02910.2184-0.0996-0.0431-0.05630.052-0.0265-0.2320.08540.04930.00770.00720.1575-0.01830.036858.95551.6473.778
40.9866-0.0766-0.34010.51970.0040.7643-0.0170.01620.0558-0.00470.0086-0.1282-0.040.05750.00850.0550.01930.01140.07690.01110.055678.68858.71810.361
54.49711.6991-0.0941.45550.01871.0608-0.04230.2106-0.5174-0.0685-0.0359-0.09760.24280.01260.07810.10380.01460.07050.0677-0.05140.161976.26435.6330.62
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A35 - 43
2X-RAY DIFFRACTION2A44 - 177
3X-RAY DIFFRACTION3A178 - 236
4X-RAY DIFFRACTION4A237 - 425
5X-RAY DIFFRACTION5A426 - 464

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