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- PDB-3ihv: Crystal structure of SusD homolog (NP_813570.1) from Bacteroides ... -

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Basic information

Entry
Database: PDB / ID: 3ihv
TitleCrystal structure of SusD homolog (NP_813570.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.70 A resolution
ComponentsSusD homolog
KeywordsSUGAR BINDING PROTEIN / NP_813570.1 / SusD homolog / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 / RagB / SusD and hypothetical proteins
Function / homology
Function and homology information


cell outer membrane
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #890 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #900 / 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
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of SusD homolog (NP_813570.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJul 30, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 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_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_seq_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_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.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)124,11930
Polymers122,6442
Non-polymers1,47528
Water22,4831248
1
A: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,06015
Polymers61,3221
Non-polymers73814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,06015
Polymers61,3221
Non-polymers73814
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.908, 72.318, 131.629
Angle α, β, γ (deg.)90.000, 97.310, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1116A0 - 557
2116B0 - 557

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Components

#1: Protein SusD homolog


Mass: 61322.000 Da / Num. of mol.: 2 / Fragment: sequence database residues 24-557
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Strain: VPI-548 / Gene: BT_4659, NP_813570.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q89YS2
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1248 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT (RESIDUES 24-557) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 24-557) 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: 2.42 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.1
Details: 0.2000M Na2HPO4, 20.0000% PEG-3350, No Buffer pH 9.1, 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: 0.91837,0.97864,0.97806
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 15, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.978641
30.978061
ReflectionResolution: 1.7→29.748 Å / Num. obs: 128297 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.275 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 7.57
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.7-1.760.4611.84412023936195.7
1.76-1.830.3512.34520224282196.2
1.83-1.910.2782.94467223755196.5
1.91-2.020.2013.95082026752197
2.02-2.140.1475.34501923331197.3
2.14-2.310.1116.74981625505197.8
2.31-2.540.0898.14900724696198.6
2.54-2.90.06610.34906724579198.4
2.9-3.660.03914.85067225266198.4
3.66-29.7480.02719.25019124922198

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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
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→29.748 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / Occupancy max: 1 / Occupancy min: 0.37 / SU B: 4.314 / SU ML: 0.063 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.098 / ESU R Free: 0.096
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 ...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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. (3). SODIUM IONS (NA) AND AND CHLORIDES (CL) FROM THE CRYSTALLIZATION SOLUTION WERE MODELED INTO THE STRUCTURE. (4). ETHYLENE GLYCOLS (EDO) FROM THE CRYOPROTECTION WERE MODELED INTO THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 6461 5 %RANDOM
Rwork0.162 ---
obs0.163 128277 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.52 Å2 / Biso mean: 11.531 Å2 / Biso min: 2.32 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å2-0.9 Å2
2---0.62 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.7→29.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8554 0 88 1248 9890
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0228999
X-RAY DIFFRACTIONr_bond_other_d0.0020.026070
X-RAY DIFFRACTIONr_angle_refined_deg1.5231.9412247
X-RAY DIFFRACTIONr_angle_other_deg1.032314739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.16651128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08324.311450
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.357151465
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.631556
X-RAY DIFFRACTIONr_chiral_restr0.1010.21310
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210177
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021905
X-RAY DIFFRACTIONr_mcbond_it0.7431.55413
X-RAY DIFFRACTIONr_mcbond_other0.2571.52199
X-RAY DIFFRACTIONr_mcangle_it1.21828745
X-RAY DIFFRACTIONr_scbond_it2.06433586
X-RAY DIFFRACTIONr_scangle_it3.1854.53471
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 7182 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
LOOSE POSITIONAL0.185
LOOSE THERMAL1.0110
LS refinement shellResolution: 1.7→1.743 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 493 -
Rwork0.253 8837 -
all-9330 -
obs--98.29 %
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)
10.43780.08790.09130.64750.10150.7275-0.01390.03020.0163-0.05480.0277-0.018-0.03780.0231-0.01380.0393-0.0032-0.00080.02720.00190.022349.1480.74839.997
20.4733-0.20110.15650.999-0.19070.7023-0.0223-0.042-0.01240.14580.06230.021-0.051-0.0363-0.040.0470.00670.00280.02830.00540.012468.935-35.425.114
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 557
2X-RAY DIFFRACTION2B0 - 557

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