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- PDB-4puc: Crystal structure of a SusD homolog (BACUNI_02643) from Bacteroid... -

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Basic information

Entry
Database: PDB / ID: 4puc
TitleCrystal structure of a SusD homolog (BACUNI_02643) from Bacteroides uniformis ATCC 8492 at 2.00 A resolution
ComponentsSusD homolog
KeywordsSUGAR BINDING PROTEIN / SusD-like family / PF12741 / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


SusD-like / Susd and RagB outer membrane lipoprotein / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / SusD/RagB family nutrient-binding outer membrane lipoprotein
Similarity search - Component
Biological speciesBacteroides uniformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a SusD homolog (BACUNI_02643) from Bacteroides uniformis ATCC 8492 at 2.00 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMar 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 4, 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_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 homolog
B: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,10212
Polymers112,4732
Non-polymers62910
Water14,502805
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3290 Å2
ΔGint-174 kcal/mol
Surface area34160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.540, 112.190, 150.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SusD homolog


Mass: 56236.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides uniformis (bacteria) / Strain: ATCC 8492 / Gene: BACUNI_02643 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: A7V4Y5
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 805 / 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 27-529 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: 2.49 Å3/Da / Density % sol: 50.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.2M zinc acetate, 10.0% polyethylene glycol 8000, 0.1M MES pH 6.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91162,0.97959,0.97889
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 26, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979591
30.978891
ReflectionResolution: 2→89.858 Å / Num. obs: 59887 / % possible obs: 75.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 25.719 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 9.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2-2.050.5471.411266664561.4
2.05-2.110.3721.72109138113
2.11-2.170.3412.417776990496.5
2.17-2.240.32.713764788479.2
2.24-2.310.23333266208721.4
2.31-2.390.213.716102898896
2.39-2.480.1754.516065881097.3
2.48-2.580.155.315231838897
2.58-2.70.1365.86372359443.1
2.7-2.830.17.212101725490.8
2.83-2.980.0799.313270732196.7
2.98-3.160.0611.812783697096.7
3.16-3.380.04615.211708646096.2
3.38-3.650.036186078361457.5
3.65-40.03120.76211348760.7
4-4.470.02724.69274501995.9
4.47-5.160.02625.67758430493.5
5.16-6.320.02922.96392362093.7
6.32-8.940.02227.65215288396.3
8.940.01536.42730152892.3

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEdata scaling
REFMAC5.7.0032refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2→89.858 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 7.249 / SU ML: 0.108 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.229 / ESU R Free: 0.171
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. ANOMALOUS DIFFERENCE FOURIERS AND PRESENCE OF ZINC ACETATE IN CRYSTALLIZATION SOLUTION SUPPORT THE MODELING OF ZINC IONS. 7. ACETATE (ACT) FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 8. THE NOMINAL RESOLUTION IS 2.20 A WITH 12238 OBSERVED REFLECTIONS BETWEEN 2.20-2.00 (65.2% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.1998 3009 5 %RANDOM
Rwork0.1681 ---
obs0.1697 59881 78.08 %-
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: 97.48 Å2 / Biso mean: 29.7957 Å2 / Biso min: 10.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.83 Å2-0 Å2-0 Å2
2---1.88 Å2-0 Å2
3----1.95 Å2
Refinement stepCycle: LAST / Resolution: 2→89.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7658 0 22 805 8485
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.027966
X-RAY DIFFRACTIONr_bond_other_d0.0020.027271
X-RAY DIFFRACTIONr_angle_refined_deg1.0381.94710870
X-RAY DIFFRACTIONr_angle_other_deg0.799316754
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.13751020
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.15624.844384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55151220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2781541
X-RAY DIFFRACTIONr_chiral_restr0.0590.21174
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219311
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021874
X-RAY DIFFRACTIONr_mcbond_it1.5193.1313964
X-RAY DIFFRACTIONr_mcbond_other1.5023.1253959
X-RAY DIFFRACTIONr_mcangle_it2.385.8464957
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 198 -
Rwork0.266 3493 -
all-3691 -
obs--66.25 %
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)
10.5259-0.12420.08890.4324-0.03850.2614-0.0134-0.0157-0.00650.03150.0178-0.0106-0.0188-0.0162-0.00440.00620.00120.00140.1624-0.00090.173859.956-10.74680.452
20.133-0.1479-0.02420.55670.03190.50170.01960.0271-0.00760.0123-0.00610.0027-0.0765-0.0473-0.01350.05730.0273-0.00580.16670.00810.162835.51415.74151.126
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A42 - 529
2X-RAY DIFFRACTION2B38 - 529

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