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- PDB-6q75: The structure of GH26A from Muricauda sp. MAR_2010_75 -

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Basic information

Entry
Database: PDB / ID: 6q75
TitleThe structure of GH26A from Muricauda sp. MAR_2010_75
ComponentsGH26A
KeywordsHYDROLASE / GH26 / glycoside hydrolase
Biological speciesMuricauda sp. MAR_2010_75 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRobb, C.S. / Hehemann, J.H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research FoundationHE 7217/1-1 Germany
CitationJournal: To Be Published
Title: The structure of GH26A from Muricauda sp. MAR_2010_75
Authors: Robb, C.S. / Hehemann, J.H.
History
DepositionDec 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GH26A
B: GH26A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8655
Polymers77,5592
Non-polymers3063
Water7,710428
1
A: GH26A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9943
Polymers38,7801
Non-polymers2142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GH26A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8722
Polymers38,7801
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.524, 49.342, 71.711
Angle α, β, γ (deg.)78.00, 89.83, 69.64
Int Tables number1
Space group name H-MP1

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Components

#1: Protein GH26A


Mass: 38779.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Muricauda sp. MAR_2010_75 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 428 / 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: 1.98 Å3/Da / Density % sol: 37.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.15M Magnesium chloride 0.1M TRIS pH 8.5 21% PEG4000 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.75→45.12 Å / Num. obs: 58106 / % possible obs: 96.7 % / Redundancy: 4.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.2
Reflection shellResolution: 1.75→1.84 Å / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 8362 / CC1/2: 0.885 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3wdq

3wdq


Resolution: 1.75→44.428 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 21.01
RfactorNum. reflection% reflection
Rfree0.1899 2969 5.11 %
Rwork0.1521 --
obs0.1541 58069 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.75→44.428 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4970 0 20 428 5418
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095159
X-RAY DIFFRACTIONf_angle_d0.9327043
X-RAY DIFFRACTIONf_dihedral_angle_d7.7032942
X-RAY DIFFRACTIONf_chiral_restr0.061712
X-RAY DIFFRACTIONf_plane_restr0.007898
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.77870.26511460.20672558X-RAY DIFFRACTION95
1.7787-1.80940.2441200.20462592X-RAY DIFFRACTION95
1.8094-1.84230.25831290.19412617X-RAY DIFFRACTION95
1.8423-1.87770.24161350.18882586X-RAY DIFFRACTION96
1.8777-1.9160.25941590.18542585X-RAY DIFFRACTION95
1.916-1.95770.24641360.17552618X-RAY DIFFRACTION96
1.9577-2.00320.2321320.16272593X-RAY DIFFRACTION96
2.0032-2.05330.2091440.1532648X-RAY DIFFRACTION96
2.0533-2.10880.19321230.14762592X-RAY DIFFRACTION97
2.1088-2.17090.19871540.14412597X-RAY DIFFRACTION96
2.1709-2.2410.17621520.14852608X-RAY DIFFRACTION96
2.241-2.32110.22271310.15032662X-RAY DIFFRACTION97
2.3211-2.4140.20171470.15832592X-RAY DIFFRACTION97
2.414-2.52380.18611250.16192677X-RAY DIFFRACTION97
2.5238-2.65690.19551500.15172646X-RAY DIFFRACTION97
2.6569-2.82330.16581430.15312622X-RAY DIFFRACTION98
2.8233-3.04130.17831410.1512643X-RAY DIFFRACTION98
3.0413-3.34720.19891410.15112662X-RAY DIFFRACTION98
3.3472-3.83130.1831470.13792659X-RAY DIFFRACTION98
3.8313-4.82620.15991670.12692653X-RAY DIFFRACTION98
4.8262-44.44180.16191470.15432690X-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)
11.35530.20810.68851.67380.16211.8646-0.0276-0.00950.04520.2008-0.0214-0.1768-0.18870.04610.05360.229-0.026-0.03040.18370.00620.1985-10.2918-17.6513-47.2325
20.84260.010.38861.11-0.171.53790.14780.0067-0.15630.2654-0.1211-0.37140.1670.1696-0.030.27950.0015-0.09420.21180.00710.2588-7.1545-33.2324-41.939
30.82430.05640.15431.41120.01151.10310.0706-0.1186-0.01980.3214-0.0854-0.02230.073-0.15570.00650.2626-0.0246-0.01540.1918-0.00450.1435-19.8508-30.9107-41.8939
41.68020.19210.04031.25430.20531.6309-0.035-0.02630.1356-0.0004-0.07060.0823-0.3387-0.12510.09750.27040.038-0.01880.2065-0.01160.1713-22.2672-15.17-53.9258
50.8258-0.77010.00471.7597-0.18451.68670.1310.09480.0135-0.4259-0.1423-0.04840.13620.06190.00450.18490.02250.02590.16260.0010.1642-30.499-34.4145-87.0034
61.0137-0.70250.27182.301-0.21081.58990.05550.039-0.0085-0.2927-0.01260.1556-0.1155-0.1642-0.0350.14170.018-0.00690.16980.00490.1612-41.6353-23.5979-83.2606
71.2733-0.25330.04022.0379-0.51361.8812-0.0062-0.0645-0.02790.01930.0202-0.11580.18050.1053-0.01570.13640.01090.00050.16780.00220.1763-28.3234-38.6726-73.4932
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 24 through 87 )
2X-RAY DIFFRACTION2chain 'A' and (resid 88 through 165 )
3X-RAY DIFFRACTION3chain 'A' and (resid 166 through 251 )
4X-RAY DIFFRACTION4chain 'A' and (resid 252 through 333 )
5X-RAY DIFFRACTION5chain 'B' and (resid 24 through 87 )
6X-RAY DIFFRACTION6chain 'B' and (resid 88 through 251 )
7X-RAY DIFFRACTION7chain 'B' and (resid 252 through 329 )

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