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- PDB-3qwt: The crystal structure of a possible member of GH105 family from S... -

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Basic information

Entry
Database: PDB / ID: 3qwt
TitleThe crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
ComponentsPutative GH105 family protein
KeywordsUNKNOWN FUNCTION / structural genomics / PSI-Biology / protein structure initiative / midwest center for structural genomic s / MCSG / Hydrolase / GH105 / Midwest Center for Structural Genomics / alpha/alpha toroid
Function / homology
Function and homology information


catalytic activity / carbohydrate metabolic process
Similarity search - Function
: / Glycosyl hydrolase, family 88 / Glycosyl Hydrolase Family 88 / Glycosyltransferase - #10 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Mainly Alpha
Similarity search - Domain/homology
Glycoside hydrolase family 105 protein / Uncharacterized protein
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Paratyphi A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.183 Å
AuthorsTan, K. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a possible member of GH105 family from Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150
Authors: Tan, K. / Hatzos-Skintges, C. / Bearden, J. / Joachimiak, A.
History
DepositionFeb 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative GH105 family protein
B: Putative GH105 family protein
C: Putative GH105 family protein
D: Putative GH105 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,66315
Polymers179,6504
Non-polymers1,01311
Water6,413356
1
A: Putative GH105 family protein
B: Putative GH105 family protein
C: Putative GH105 family protein
D: Putative GH105 family protein
hetero molecules

A: Putative GH105 family protein
B: Putative GH105 family protein
C: Putative GH105 family protein
D: Putative GH105 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)361,32630
Polymers359,3008
Non-polymers2,02622
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area32700 Å2
ΔGint-56 kcal/mol
Surface area101260 Å2
MethodPISA
2
A: Putative GH105 family protein
hetero molecules

B: Putative GH105 family protein
C: Putative GH105 family protein
D: Putative GH105 family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,66315
Polymers179,6504
Non-polymers1,01311
Water724
TypeNameSymmetry operationNumber
crystal symmetry operation3_555-x,y,-z+1/21
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-16 kcal/mol
Surface area55470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.026, 159.361, 179.115
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
11B-405-

HOH

DetailsExperimentally Unknown. It is possilbe the molecule forms dimer. The chains A and B form a dimer. The chain C and its symmetry-related moleucle, by an operator -x,y,-z+1/2, form a dimer. The chain D and its symmtry-related molecule, by an operator, -x,y,-z+1/2, form a dimer.

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Components

#1: Protein
Putative GH105 family protein


Mass: 44912.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Paratyphi A (bacteria)
Gene: SPA0958 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q5PMY7, UniProt: A0A0H2WND1*PLUS
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 356 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M NaCl, 0.1M Tris.HCl, 25% (w/v) PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97942, 0.97951
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 31, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979421
20.979511
ReflectionResolution: 2.18→40 Å / Num. all: 87941 / Num. obs: 87941 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 20.7
Reflection shellResolution: 2.18→2.22 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.696 / Mean I/σ(I) obs: 2.02 / Num. unique all: 4188 / % possible all: 94.9

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: MAD / Resolution: 2.183→39.84 Å / SU ML: 0.35 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 4255 5.01 %random
Rwork0.1824 ---
all0.1851 84868 --
obs0.1851 84868 94.54 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.937 Å2 / ksol: 0.329 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7133 Å2-0 Å2-0 Å2
2---1.317 Å20 Å2
3----2.3963 Å2
Refinement stepCycle: LAST / Resolution: 2.183→39.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12396 0 66 356 12818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00812820
X-RAY DIFFRACTIONf_angle_d1.11717412
X-RAY DIFFRACTIONf_dihedral_angle_d15.7384616
X-RAY DIFFRACTIONf_chiral_restr0.0731816
X-RAY DIFFRACTIONf_plane_restr0.0052228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1829-2.26090.30243670.25146897X-RAY DIFFRACTION82
2.2609-2.35140.34863510.24897390X-RAY DIFFRACTION87
2.3514-2.45840.31734200.23377676X-RAY DIFFRACTION91
2.4584-2.5880.32034480.23057872X-RAY DIFFRACTION93
2.588-2.75020.31184200.22448161X-RAY DIFFRACTION96
2.7502-2.96240.26384430.2098317X-RAY DIFFRACTION98
2.9624-3.26040.26664140.20868484X-RAY DIFFRACTION99
3.2604-3.73190.22424640.18058507X-RAY DIFFRACTION100
3.7319-4.70060.17364790.13218542X-RAY DIFFRACTION100
4.7006-39.84690.19894490.14978767X-RAY DIFFRACTION99
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)
10.62280.0843-0.44750.50670.13940.4774-0.1255-0.38920.0450.2250.1547-0.05110.22480.2696-0.02120.22430.1867-0.06320.3437-0.00990.067117.960828.732379.1237
20.50580.2939-0.2940.2409-0.08530.9186-0.0788-0.02840.1084-0.01060.0958-0.10830.08920.3936-0.00860.03510.1675-0.030.2064-0.01780.150738.621833.491841.6826
30.85410.011-0.4280.2540.00060.7488-0.28880.152-0.17590.02550.0824-0.03520.727-0.04970.19350.64370.0180.10950.1019-0.06060.120512.4529-1.362327.2024
40.63170.20730.0290.37090.02390.4556-0.03080.12520.3409-0.0660.0768-0.0319-0.02930.025-0.03260.026-0.0292-0.00960.08640.07670.20998.278463.531524.9004
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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