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- PDB-3fax: The crystal structure of GBS pullulanase SAP in complex with malt... -

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Basic information

Entry
Database: PDB / ID: 3fax
TitleThe crystal structure of GBS pullulanase SAP in complex with maltotetraose
ComponentsReticulocyte binding protein
KeywordsHYDROLASE / TIM barrel / alpha amylase domain / pullulanase domain / Cell wall / Peptidoglycan-anchor / Secreted
Function / homology
Function and homology information


Immunoglobulin-like - #1220 / Golgi alpha-mannosidase II / Glycosidases / Immunoglobulins / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-maltotriose / :
Similarity search - Component
Biological speciesStreptococcus agalactiae COH1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsGourlay, L.J.
CitationJournal: J.Bacteriol. / Year: 2009
Title: Group B Streptococcus pullulanase crystal structures in the context of a novel strategy for vaccine development
Authors: Gourlay, L.J. / Santi, I. / Pezzicoli, A. / Grandi, G. / Soriani, M. / Bolognesi, M.
History
DepositionNov 18, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 14, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.label_asym_id ..._atom_site.auth_asym_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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.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.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_type.id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Reticulocyte binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2587
Polymers98,5581
Non-polymers7006
Water1,13563
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.214, 102.862, 171.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Reticulocyte binding protein


Mass: 98557.578 Da / Num. of mol.: 1
Fragment: N2, N3, A and C pullulanase domains, UNP residues 346-1215
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae COH1 (bacteria)
Gene: SAN_1346 / Plasmid: pET21-b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3DB05
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranose / beta-maltotriose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 504.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-maltotriose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 63 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9.8
Details: 30% PEG3K, 0.2M CaCl2, 0.05M CAPSO, pH9.8, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→40 Å / Num. obs: 34193 / % possible obs: 99.6 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.064 Å2 / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 11.9
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.7 / Num. unique all: 4926 / Rsym value: 0.351 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0053refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3FAW

3faw


Resolution: 2.4→40 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.886 / SU B: 24.663 / SU ML: 0.254 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.487 / ESU R Free: 0.302 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28259 1726 5.1 %RANDOM
Rwork0.22112 ---
obs0.22422 32409 99.5 %-
all-41610 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.488 Å2
Baniso -1Baniso -2Baniso -3
1-6.87 Å20 Å20 Å2
2---0.01 Å20 Å2
3----6.86 Å2
Refinement stepCycle: LAST / Resolution: 2.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6083 0 39 63 6185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0226250
X-RAY DIFFRACTIONr_bond_other_d0.0010.024201
X-RAY DIFFRACTIONr_angle_refined_deg1.0141.9588460
X-RAY DIFFRACTIONr_angle_other_deg0.787310281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6415768
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.54725.136294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.946151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.1631526
X-RAY DIFFRACTIONr_chiral_restr0.060.2946
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.026913
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021209
X-RAY DIFFRACTIONr_mcbond_it1.16523833
X-RAY DIFFRACTIONr_mcbond_other0.2421568
X-RAY DIFFRACTIONr_mcangle_it1.87536185
X-RAY DIFFRACTIONr_scbond_it1.12222417
X-RAY DIFFRACTIONr_scangle_it1.65832274
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.375 127 -
Rwork0.306 2337 -
obs--99.88 %
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)
14.53680.05491.56875.30740.25496.5304-0.0662-0.223-0.0513-0.00570.06760.30770.5924-0.44-0.00140.0648-0.03960.00520.0798-0.03230.05152.309683.766635.6913
20.7094-0.66290.73671.8875-0.02163.3906-0.0844-0.2855-0.01650.2440.09340.0343-0.012-0.2928-0.0090.0320.01030.00670.14230.00290.017128.391459.950942.8556
30.4648-0.0751-0.04980.72620.37793.81170.01410.00030.0011-0.06060.01860.00070.34760.1193-0.03270.0450.0101-0.00380.0076-0.01380.04432.71553.628711.526
40.5471-0.0952-0.29720.35540.00533.35750.09990.18120.0572-0.25550.0086-0.0329-0.22160.758-0.10850.2048-0.05370.05230.3092-0.03090.085343.512457.8736-18.1822
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A380 - 466
2X-RAY DIFFRACTION2A467 - 590
3X-RAY DIFFRACTION3A591 - 1056
4X-RAY DIFFRACTION4A1057 - 1160

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