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- PDB-5c0p: The crystal structure of endo-arabinase from Bacteroides thetaiot... -

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Basic information

Entry
Database: PDB / ID: 5c0p
TitleThe crystal structure of endo-arabinase from Bacteroides thetaiotaomicron VPI-5482
ComponentsEndo-arabinase
KeywordsHYDROLASE / endo-arabinase / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
: / Glycoside hydrolase, family 43 / Glycosyl hydrolases family 43 / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Mainly Beta
Similarity search - Domain/homology
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.532 Å
AuthorsTan, K. / Cuff, M. / Joachimiak, G. / Endres, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM094585 United States
CitationJournal: To Be Published
Title: The crystal structure of endo-arabinase from Bacteroides thetaiotaomicron VPI-5482
Authors: Tan, K. / Cuff, M. / Joachimiak, G. / Endres, M. / Joachimiak, A.
History
DepositionJun 12, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Derived calculations / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_audit_support ...entity_src_gen / pdbx_audit_support / pdbx_struct_assembly / pdbx_struct_oper_list / pdbx_validate_symm_contact / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.2Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Nov 20, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endo-arabinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,32810
Polymers33,7181
Non-polymers6109
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.804, 83.804, 43.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Endo-arabinase


Mass: 33718.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (strain ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482) (bacteria)
Strain: ATCC 29148 / DSM 2079 / NCTC 10582 / E50 / VPI-5482 / Gene: BT_1873 / Plasmid: pMCSG68 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)Magic / References: UniProt: Q8A6K8

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Non-polymers , 5 types, 302 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 293 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.16M MgCl2, 0.08M Tris:HCl, 24% (w/v) PEG4000, 15(v/v)Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.53→50 Å / Num. obs: 45139 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 18.7
Reflection shellResolution: 1.53→1.56 Å / Redundancy: 2 % / Rmerge(I) obs: 0.486 / Mean I/σ(I) obs: 1.3 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-3000data reduction
HKL-3000data scaling
MLPHAREphasing
RefinementMethod to determine structure: SAD / Resolution: 1.532→30.133 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 16.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1638 2120 4.97 %Random selection
Rwork0.1491 ---
obs0.1498 42629 93.64 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.532→30.133 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2256 0 35 293 2584
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062371
X-RAY DIFFRACTIONf_angle_d1.1613222
X-RAY DIFFRACTIONf_dihedral_angle_d11.977852
X-RAY DIFFRACTIONf_chiral_restr0.083340
X-RAY DIFFRACTIONf_plane_restr0.005406
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5321-1.56770.2417510.21721084X-RAY DIFFRACTION38
1.5677-1.60690.2747770.21452077X-RAY DIFFRACTION71
1.6069-1.65040.1951490.19032741X-RAY DIFFRACTION96
1.6504-1.69890.18331760.1752818X-RAY DIFFRACTION100
1.6989-1.75380.1831290.15312898X-RAY DIFFRACTION100
1.7538-1.81640.23251410.15482865X-RAY DIFFRACTION100
1.8164-1.88920.16171350.14372898X-RAY DIFFRACTION100
1.8892-1.97510.16551700.13962846X-RAY DIFFRACTION100
1.9751-2.07920.17071640.14392847X-RAY DIFFRACTION100
2.0792-2.20950.17011620.14462872X-RAY DIFFRACTION100
2.2095-2.380.16581490.14552883X-RAY DIFFRACTION100
2.38-2.61940.15771630.15842895X-RAY DIFFRACTION100
2.6194-2.99810.18281400.15842900X-RAY DIFFRACTION100
2.9981-3.77610.13491560.13792913X-RAY DIFFRACTION100
3.7761-30.13930.14171580.13612972X-RAY DIFFRACTION100
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)
10.73620.07520.04141.6121-0.80161.5103-0.00370.046-0.0647-0.0404-0.0601-0.16020.06680.09880.07310.07450.00570.00370.0838-0.00360.09631.720610.081836.6534
21.6303-0.0595-0.1842.1324-0.31151.70040.02690.18120.073-0.1042-0.0527-0.1057-0.0220.02510.01640.0695-0.0068-0.00990.09410.00550.046523.444618.006327.3108
30.87880.39090.61452.92761.9761.975-0.03080.10040.1104-0.14610.0249-0.0595-0.11640.02270.01950.09920.00760.00240.09720.02370.097118.286230.035333.3053
41.1761-0.35430.22180.7003-0.29410.5394-0.0545-0.15560.00430.10440.0496-0.0083-0.0136-0.05850.0040.10030.0028-0.00170.1062-0.00260.069118.806421.7747.162
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 40 through 115 )
2X-RAY DIFFRACTION2chain 'A' and (resid 116 through 171 )
3X-RAY DIFFRACTION3chain 'A' and (resid 172 through 226 )
4X-RAY DIFFRACTION4chain 'A' and (resid 227 through 323 )

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