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- PDB-3ckc: B. thetaiotaomicron SusD -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 3ckc
TitleB. thetaiotaomicron SusD
ComponentsSusDLunca, Bihor
KeywordsSUGAR BINDING PROTEIN / TPR repeat / carbohydrate binding / starch binding
Function / homology
Function and homology information


starch metabolic process / starch catabolic process / starch binding / outer membrane / cell outer membrane / calcium ion binding / identical protein binding
Similarity search - Function
TPR-like / SusD-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / RagB/SusD domain / SusD family / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily ...TPR-like / SusD-like / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #390 / RagB/SusD domain / SusD family / Tetratricopeptide repeat domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Horseshoe / Tetratricopeptide-like helical domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Starch-binding protein SusD
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å
AuthorsKoropatkin, N.M. / Martens, E.C. / Gordon, J.I. / Smith, T.J.
CitationJournal: Structure / Year: 2008
Title: Starch catabolism by a prominent human gut symbiont is directed by the recognition of amylose helices.
Authors: Koropatkin, N.M. / Martens, E.C. / Gordon, J.I. / Smith, T.J.
History
DepositionMar 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 6, 2013Group: Data collection
Revision 1.3Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SusD
B: SusD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,83119
Polymers119,5992
Non-polymers1,23217
Water22,0321223
1
A: SusD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3898
Polymers59,7991
Non-polymers5907
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SusD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,44211
Polymers59,7991
Non-polymers64310
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.196, 68.056, 83.050
Angle α, β, γ (deg.)111.090, 93.170, 109.170
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein SusD / Lunca, Bihor


Mass: 59799.340 Da / Num. of mol.: 2 / Fragment: UNP residues 26-551
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Strain: VPI-5482 / Gene: SusD / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q8A1G2

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Non-polymers , 5 types, 1240 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1223 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTHE ORIGINAL SUSD GENE SEQUENCE DEPOSITED BY WASHINGTON UNIVERSITY (FROM JEFFREY I. GORDON'S ...THE ORIGINAL SUSD GENE SEQUENCE DEPOSITED BY WASHINGTON UNIVERSITY (FROM JEFFREY I. GORDON'S LABORATORY) IS INCORRECT. THE SAME LAB HAS SUBSEQUENTLY RE-SEQUENCED THE GENE AND CONFIRMED THAT LYS IS THE CORRECT AMINO ACID AT THIS POSITION.

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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: 2.54 Å3/Da / Density % sol: 51.57 %
Crystal growTemperature: 298 K / Method: seeding in batch / pH: 6
Details: 50mM MES, 50mM NaCl, 14% PEG 8000, pH 6.0, seeding in batch, temperature 298K

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97167 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 30, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97167 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. all: 190539 / Num. obs: 190539 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rsym value: 0.045 / Net I/σ(I): 54
Reflection shellResolution: 1.47→1.52 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 19.7 / Num. unique all: 17881 / Rsym value: 0.084 / % possible all: 90

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-3000data collection
HKL-3000data reduction
RefinementResolution: 1.5→50 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21 18043 9.6 %random
Rwork0.192 ---
all0.192 181457 --
obs0.192 181457 96.2 %-
Solvent computationBsol: 43.532 Å2
Displacement parametersBiso mean: 17.429 Å2
Baniso -1Baniso -2Baniso -3
1--0.594 Å24.22 Å2-2.383 Å2
2--4.652 Å21.559 Å2
3----4.058 Å2
Refinement stepCycle: LAST / Resolution: 1.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8048 0 76 1223 9347
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.21
X-RAY DIFFRACTIONc_mcbond_it0.9521.5
X-RAY DIFFRACTIONc_scbond_it1.5832
X-RAY DIFFRACTIONc_mcangle_it1.2632
X-RAY DIFFRACTIONc_scangle_it2.1742.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION5eg.parameg.top

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