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- PDB-3fdh: Crystal structure of a susd/ragb family protein (bt_2033) from ba... -

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Basic information

Entry
Database: PDB / ID: 3fdh
TitleCrystal structure of a susd/ragb family protein (bt_2033) from bacteroides thetaiotaomicron vpi-5482 at 1.75 A resolution
ComponentsSusD homolog
KeywordsSUGAR BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologySusD-like 2 / Starch-binding associating with outer membrane / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Prokaryotic membrane lipoprotein lipid attachment site profile. / Tetratricopeptide-like helical domain superfamily / Mainly Alpha / SusD homolog
Function and homology information
Biological speciesBacteroides thetaiotaomicron VPI-5482 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be Published
Title: Crystal structure of SusD homolog (NP_810946.1) from BACTEROIDES THETAIOTAOMICRON VPI-5482 at 1.75 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionNov 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SusD homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6972
Polymers55,5021
Non-polymers1941
Water11,403633
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.854, 116.708, 118.964
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
DetailsAUTHORS STATE THAT RYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A MONOMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein SusD homolog


Mass: 55502.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron VPI-5482 (bacteria)
Gene: BT_2033, NP_810946.1 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A653
#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 633 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT (RESIDUE 23-520) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUE 23-520) 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 30.0000% PEG-6000, 0.1M HEPES pH 7.0, 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: 0.91162,0.97871,0.97799
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 13, 2008 / 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
10.911621
20.978711
30.977991
ReflectionResolution: 1.75→29.553 Å / Num. obs: 58982 / % possible obs: 99.9 % / Redundancy: 4.1 % / Biso Wilson estimate: 21.042 Å2 / Rmerge(I) obs: 0.118 / Rsym value: 0.118 / Net I/σ(I): 4.449
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.75-1.84.10.6861.11787643360.686100
1.8-1.844.10.5741.31721941740.574100
1.84-1.94.10.5061.51695241120.506100
1.9-1.964.10.4161.71642839790.416100
1.96-2.024.10.3482.11593438690.348100
2.02-2.094.10.2892.41538437410.289100
2.09-2.174.10.2512.81491436250.251100
2.17-2.264.10.2133.21427834730.213100
2.26-2.364.10.1843.61362933200.184100
2.36-2.474.10.1624.21318432190.162100
2.47-2.614.10.1424.81250030420.142100
2.61-2.774.10.1255.21182028800.125100
2.77-2.964.10.1056.21119227280.105100
2.96-3.24.10.096.91044325560.09100
3.2-3.54.10.0768.3947923300.076100
3.5-3.914.10.0698.5870421300.069100
3.91-4.5240.0718759318900.071100
4.52-5.5340.0817.6644516130.08199.8
5.53-7.8340.0787.8497712560.07899.4
7.83-29.5533.80.0619.626857090.06196.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.4.0067refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
SCALA3.2.5data scaling
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.75→29.553 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 4.864 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.094 / ESU R Free: 0.094
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. RAMACHANDRAN OUTLIER RESIDUE 330 IS SUPPORTED BY DENSITY. 5. PEG-200 MOLECULE FROM THE CRYO SOLUTION IS MODELED.
RfactorNum. reflection% reflectionSelection details
Rfree0.189 2984 5.1 %RANDOM
Rwork0.158 ---
obs0.159 58982 99.89 %-
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: 74.96 Å2 / Biso mean: 32.826 Å2 / Biso min: 17.89 Å2
Baniso -1Baniso -2Baniso -3
1--2.65 Å20 Å20 Å2
2--2.82 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.75→29.553 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3646 0 13 633 4292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223787
X-RAY DIFFRACTIONr_bond_other_d0.0020.022511
X-RAY DIFFRACTIONr_angle_refined_deg1.631.9495148
X-RAY DIFFRACTIONr_angle_other_deg1.52736117
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9835486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.37624.757185
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.20815599
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2291520
X-RAY DIFFRACTIONr_chiral_restr0.1040.2556
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024341
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02790
X-RAY DIFFRACTIONr_mcbond_it1.18422371
X-RAY DIFFRACTIONr_mcbond_other0.2652963
X-RAY DIFFRACTIONr_mcangle_it1.97343797
X-RAY DIFFRACTIONr_scbond_it3.47261416
X-RAY DIFFRACTIONr_scangle_it4.75681343
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 205 -
Rwork0.251 4126 -
all-4331 -
obs--99.93 %
Refinement TLS params.Method: refined / Origin x: 25.6668 Å / Origin y: 34.461 Å / Origin z: 39.4628 Å
111213212223313233
T-0.0979 Å2-0.0031 Å2-0.0203 Å2--0.1245 Å2-0.0296 Å2---0.093 Å2
L0.94 °20.0796 °2-0.11 °2-0.5093 °2-0.0726 °2--0.8877 °2
S0.0178 Å °-0.1165 Å °0.0131 Å °0.0433 Å °-0.0273 Å °-0.0206 Å °0.0118 Å °0.0248 Å °0.0095 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A39 - 157
2X-RAY DIFFRACTION1A168 - 520

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