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- PDB-4qvs: 2.1 Angstrom resolution crystal structure of S-layer domain-conta... -

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Basic information

Entry
Database: PDB / ID: 4qvs
Title2.1 Angstrom resolution crystal structure of S-layer domain-containing protein (residues 221-444) from Clostridium thermocellum ATCC 27405
ComponentsS-layer domain-containing protein
KeywordsUNKNOWN FUNCTION / Human Microbiome / Midwest Center for Structural Genomics / MCSG / PSI-Biology
Function / homology
Function and homology information


cellulose binding / membrane => GO:0016020 / carbohydrate metabolic process
Similarity search - Function
Cadherin-like beta sandwich domain / Cadherin-like beta sandwich domain / LamG-like jellyroll fold / LamG-like jellyroll fold domain / Concanavalin A-like lectin/glucanases superfamily / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Cellulose binding domain / Cellulose binding domain ...Cadherin-like beta sandwich domain / Cadherin-like beta sandwich domain / LamG-like jellyroll fold / LamG-like jellyroll fold domain / Concanavalin A-like lectin/glucanases superfamily / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Cellulose binding domain / Cellulose binding domain / Carbohydrate-binding module 3 / Carbohydrate-binding module 3 superfamily / CBM3 (carbohydrate binding type-3) domain profile. / CBM2/CBM3, carbohydrate-binding domain superfamily / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
S-layer domain-containing protein
Similarity search - Component
Biological speciesRuminiclostridium thermocellum ATCC 27405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsHalavaty, A.S. / Wawrzak, Z. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: 2.1 Angstrom resolution crystal structure of S-layer domain-containing protein (residues 221-444) from Clostridium thermocellum ATCC 27405
Authors: Halavaty, A.S. / Wawrzak, Z. / Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Shuvalova, L. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F.
History
DepositionJul 15, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: S-layer domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0223
Polymers24,9641
Non-polymers582
Water79344
1
A: S-layer domain-containing protein
hetero molecules

A: S-layer domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0446
Polymers49,9272
Non-polymers1174
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_557x,-y,-z+21
Buried area16780 Å2
ΔGint-149 kcal/mol
Surface area17470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.958, 74.813, 98.398
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-603-

HOH

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Components

#1: Protein S-layer domain-containing protein


Mass: 24963.666 Da / Num. of mol.: 1 / Fragment: UNP residues 221-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminiclostridium thermocellum ATCC 27405 (bacteria)
Strain: ATCC 27405 / DSM 1237 / Gene: Cthe_2506 / Plasmid: pMCSG68 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: A3DIC9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: protein: 9.35 mg/mL in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME, crystallization: The PEGs II Suite G11 (83): 0.5 M Lithium chloride, 0.1 M Tris pH 8.5. 28% (w/v) PEG 6000, cyo: well ...Details: protein: 9.35 mg/mL in 10 mM Tris-HCl pH 8.3, 500 mM NaCl, 5 mM BME, crystallization: The PEGs II Suite G11 (83): 0.5 M Lithium chloride, 0.1 M Tris pH 8.5. 28% (w/v) PEG 6000, cyo: well solution, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 4, 2014 / Details: Beryllium lenses
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 14480 / Num. obs: 14480 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 48.6 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 43.56
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 2.6 / Num. unique all: 668 / % possible all: 95.3

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.7.0029refinement
xia2data reduction
MOSFLMdata reduction
pointlessdata scaling
Aimlessdata scaling
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→27.35 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.949 / SU B: 12.957 / SU ML: 0.162 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24878 721 5 %RANDOM
Rwork0.20802 ---
obs0.20994 13697 99.01 %-
all-13697 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.661 Å2
Baniso -1Baniso -2Baniso -3
1--5.6 Å20 Å2-0 Å2
2---0.74 Å2-0 Å2
3---6.34 Å2
Refinement stepCycle: LAST / Resolution: 2.1→27.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1673 0 2 44 1719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021725
X-RAY DIFFRACTIONr_bond_other_d0.0010.021525
X-RAY DIFFRACTIONr_angle_refined_deg1.8141.9422340
X-RAY DIFFRACTIONr_angle_other_deg0.83333518
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.3265217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.24625.11984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.69315251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1154
X-RAY DIFFRACTIONr_chiral_restr0.1090.2250
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022015
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02413
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 47 -
Rwork0.319 968 -
obs-968 95.75 %
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)
11.86440.47470.42661.3275-0.89051.07770.0465-0.29510.19720.2173-0.11490.0245-0.2017-0.03840.06840.3095-0.00690.01940.1329-0.03250.02298.995522.905181.8999
22.02030.0013-0.09722.40970.27071.12340.0144-0.1943-0.30790.135-0.0215-0.20110.10670.04040.00710.29920.0068-0.02270.15710.04470.065516.28865.795582.4876
34.855-1.14032.74361.7001-0.55182.94750.00720.36540.1665-0.45540.0424-0.3695-0.2866-0.1293-0.04960.3161-0.01060.10730.20270.0340.099420.8405-8.4474107.7386
41.8757-0.2453-0.54872.46510.28370.7886-0.01470.20660.1318-0.1182-0.064-0.01150.0798-0.04380.07870.30470.00980.01130.16470.020.031214.8677-12.2684113.5942
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A221 - 285
2X-RAY DIFFRACTION2A286 - 345
3X-RAY DIFFRACTION3A346 - 389
4X-RAY DIFFRACTION4A390 - 438

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