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- PDB-3tc9: Crystal structure of an auxiliary nutrient binding protein (BT_34... -

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Basic information

Entry
Database: PDB / ID: 3tc9
TitleCrystal structure of an auxiliary nutrient binding protein (BT_3476) from Bacteroides thetaiotaomicron VPI-5482 at 2.23 A resolution
ComponentsHypothetical hydrolase
KeywordsHYDROLASE / 6-bladed beta-propeller / Immunoglobulin-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homology
Function and homology information


TolB, C-terminal domain / IPT/TIG domain / IPT domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins ...TolB, C-terminal domain / IPT/TIG domain / IPT domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Prokaryotic membrane lipoprotein lipid attachment site profile. / Immunoglobulin E-set / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
PHOSPHATE ION / IPT/TIG domain-containing protein
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.23 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a Hypothetical hydrolase (BT_3476) from Bacteroides thetaiotaomicron VPI-5482 at 2.23 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionAug 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 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

Downloads & links

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Assembly

Deposited unit
A: Hypothetical hydrolase
B: Hypothetical hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,29723
Polymers97,9812
Non-polymers1,31621
Water6,810378
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Hypothetical hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,86615
Polymers48,9901
Non-polymers87514
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Hypothetical hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4318
Polymers48,9901
Non-polymers4417
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)239.670, 51.250, 75.990
Angle α, β, γ (deg.)90.000, 93.610, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Hypothetical hydrolase


Mass: 48990.422 Da / Num. of mol.: 2 / Fragment: UNP residues 29-457
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: BT_3476 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8A230
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 378 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 29-457 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: 2.38 Å3/Da / Density % sol: 48.25 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 20.00% polyethylene glycol 3350, 0.20M sodium dihydrogen phosphate, 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: 0.91837,0.97932,0.97913
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 22, 2011 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
30.979131
ReflectionResolution: 2.23→29.899 Å / Num. obs: 45197 / % possible obs: 97.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 42.202 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.31
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.23-2.310.5261.4129448551197.9
2.31-2.40.4361.7127458391197.9
2.4-2.510.3532.1132948740198
2.51-2.640.2822.5129368497198.2
2.64-2.810.2153.3135588887197.9
2.81-3.020.1425128368397198.2
3.02-3.330.0848.2134058767197.8
3.33-3.810.04514.1132098618197.6
3.81-4.780.02821.3130708475197.2
4.78-29.8990.02523.4134168651196.6

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 6, 2010data scaling
BUSTER-TNT2.8.0refinement
XDSdata reduction
SHELXDphasing
BUSTER2.8.0refinement
RefinementMethod to determine structure: MAD / Resolution: 2.23→29.899 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.9374 / Occupancy max: 1 / Occupancy min: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 3. A MET-INHIBITION ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS 2. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 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. 1,2 ETHANEDIOL (EDO) AND PHOSPATE (PO4) FROM THE CRYSTALLIZATION CONDITIONS AND CHLORIDE (CL)FROM THE EXPRESSION OR PURIFICATION BUFFERS HAVE BEEN MODELED IN THE SOLVENT STRUCTURE. 5. NCS RESTRAINTS WERE APPLIED USING BUSTER'S LSSR RESTRAINT REPRESENTATION (-AUTONCS). 6. THE REFINEMENT WAS RESTRAINED AGAINST THE MAD PHASES.
RfactorNum. reflection% reflectionSelection details
Rfree0.2055 2308 5.11 %RANDOM
Rwork0.161 ---
obs0.1632 45151 --
Displacement parametersBiso max: 117.08 Å2 / Biso mean: 43.4784 Å2 / Biso min: 9.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.2395 Å20 Å21.3969 Å2
2---2.648 Å20 Å2
3---2.8875 Å2
Refinement stepCycle: LAST / Resolution: 2.23→29.899 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6741 0 80 378 7199
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3217SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes204HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1033HARMONIC5
X-RAY DIFFRACTIONt_it7043HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion877SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7753SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7043HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg9509HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.69
X-RAY DIFFRACTIONt_other_torsion3.01
LS refinement shellResolution: 2.23→2.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2252 173 5.27 %
Rwork0.2011 3111 -
all0.2024 3284 -
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)
10.367-0.04910.10730.2624-0.00580.58650.00330.03710.0013-0.009500.0148-0.0020.1052-0.0032-0.0298-0.01790.0019-0.01630.0044-0.091871.02329.341627.5152
20.77680.19770.38560.60660.28651.3061-0.0057-0.07460.16740.08210.00560.0113-0.19130.02850.0001-0.1044-0.00050.0162-0.05090.0167-0.1261100.182745.10858.9429
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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