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- PDB-6uax: Crystal structure of a GH128 (subgroup II) endo-beta-1,3-glucanas... -

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Basic information

Entry
Database: PDB / ID: 6uax
TitleCrystal structure of a GH128 (subgroup II) endo-beta-1,3-glucanase from Sorangium cellulosum (ScGH128_II)
ComponentsHypothetical serine rich protein
KeywordsHYDROLASE / Glycosyl hydrolase / CARBOHYDRATE
Function / homologyUncharacterised protein family, glycosyl hydrolase catalytic domain / Glycosyl hydrolase catalytic core / Glycoside hydrolase superfamily / Hypothetical serine rich protein
Function and homology information
Biological speciesSorangium cellulosum So ce56 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsSantos, C.R. / Costa, P.A.C.R. / Domingues, M.N. / Lima, E.A. / Mandelli, F. / Vieira, P.S. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)15/26982-0 Brazil
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Structural insights into beta-1,3-glucan cleavage by a glycoside hydrolase family.
Authors: Santos, C.R. / Costa, P.A.C.R. / Vieira, P.S. / Gonzalez, S.E.T. / Correa, T.L.R. / Lima, E.A. / Mandelli, F. / Pirolla, R.A.S. / Domingues, M.N. / Cabral, L. / Martins, M.P. / Cordeiro, R.L. ...Authors: Santos, C.R. / Costa, P.A.C.R. / Vieira, P.S. / Gonzalez, S.E.T. / Correa, T.L.R. / Lima, E.A. / Mandelli, F. / Pirolla, R.A.S. / Domingues, M.N. / Cabral, L. / Martins, M.P. / Cordeiro, R.L. / Junior, A.T. / Souza, B.P. / Prates, E.T. / Gozzo, F.C. / Persinoti, G.F. / Skaf, M.S. / Murakami, M.T.
History
DepositionSep 11, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 5, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_conn_angle / struct_conn
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.3Oct 11, 2023Group: 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: Hypothetical serine rich protein
B: Hypothetical serine rich protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,92510
Polymers73,2512
Non-polymers6748
Water13,890771
1
A: Hypothetical serine rich protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1026
Polymers36,6261
Non-polymers4765
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Hypothetical serine rich protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8234
Polymers36,6261
Non-polymers1983
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.756, 65.628, 86.551
Angle α, β, γ (deg.)90.000, 95.960, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Hypothetical serine rich protein


Mass: 36625.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sorangium cellulosum So ce56 (bacteria)
Strain: So ce56 / Gene: sce3275 / Production host: Escherichia coli (E. coli) / References: UniProt: A9GMG4

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Non-polymers , 5 types, 779 molecules

#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 771 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.8 Å3/Da / Density % sol: 31.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18% PEG3350 4% isopropanol 0.1 M calcium chloride 0.1 M HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.3→46.55 Å / Num. obs: 123123 / % possible obs: 97.7 % / Redundancy: 6.59 % / CC1/2: 0.999 / Net I/σ(I): 14.91
Reflection shellResolution: 1.31→1.39 Å / Redundancy: 6.56 % / Mean I/σ(I) obs: 2.93 / Num. unique obs: 18875 / CC1/2: 0.858 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6UAQ

6uaq


Resolution: 1.3→46.55 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.867 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.044 / ESU R Free: 0.045
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1672 6235 5 %RANDOM
Rwork0.1291 ---
obs0.1309 119559 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 123.72 Å2 / Biso mean: 12.768 Å2 / Biso min: 4.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å2-0.49 Å2
2--1.94 Å20 Å2
3----1.14 Å2
Refinement stepCycle: final / Resolution: 1.3→46.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 36 771 4781
Biso mean--32.37 27.18 -
Num. residues----514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0134233
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173653
X-RAY DIFFRACTIONr_angle_refined_deg2.0771.6335790
X-RAY DIFFRACTIONr_angle_other_deg1.6531.5848477
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.5555540
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.80922.814231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.54815590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8081522
X-RAY DIFFRACTIONr_chiral_restr0.1210.2508
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024958
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02960
X-RAY DIFFRACTIONr_rigid_bond_restr9.39137886
LS refinement shellResolution: 1.3→1.334 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 451 -
Rwork0.26 8532 -
all-8983 -
obs--95.58 %

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