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- PDB-2xtl: Structure of the major pilus backbone protein from Streptococcus ... -

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Basic information

Entry
Database: PDB / ID: 2xtl
TitleStructure of the major pilus backbone protein from Streptococcus Agalactiae
ComponentsCELL WALL SURFACE ANCHOR FAMILY PROTEIN
KeywordsSTRUCTURAL PROTEIN / GRAM-POSITIVE PILI PROTEIN / BP-2A 515 ALLELE / IMMUNOGLOBULIN-LIKE DOMAINS
Function / homology
Function and homology information


Collagen-binding surface protein Cna, B-type domain / Immunoglobulin-like - #740 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #90 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSTREPTOCOCCUS AGALACTIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRinauda, D. / Gourlay, L.J. / Soriano, M. / Grandi, G. / Bolognesi, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structure-Based Approach to Rationally Design a Chimeric Protein for an Effective Vaccine Against Group B Streptococcus Infections.
Authors: Nuccitelli, A. / Cozzi, R. / Gourlay, L.J. / Donnarumma, D. / Necchi, F. / Norais, N. / Telford, J.L. / Rappuoli, R. / Bolognesi, M. / Maione, D. / Grandi, G. / Rinaudo, C.D.
History
DepositionOct 11, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_conn_angle ...pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id ..._pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Jun 5, 2024Group: Advisory / Derived calculations / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact ...pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_auth_seq_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
B: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,9435
Polymers98,8262
Non-polymers1173
Water16,123895
1
A: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4913
Polymers49,4131
Non-polymers782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4522
Polymers49,4131
Non-polymers391
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.863, 104.681, 159.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: THR / End label comp-ID: THR / Refine code: 4

Dom-IDBeg auth comp-IDBeg label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1GLUGLUAA192 - 6403 - 451
2ASNASNBB190 - 6401 - 451

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Components

#1: Protein CELL WALL SURFACE ANCHOR FAMILY PROTEIN / MAJOR BACKBONE PILUS PROTEIN BP-2A


Mass: 49412.926 Da / Num. of mol.: 2 / Fragment: RESIDUES 190-641
Source method: isolated from a genetically manipulated source
Details: ISOPEPTIDE BONDS BETWEEN K199 AND N325, K437 AND N355, K463 AND N636
Source: (gene. exp.) STREPTOCOCCUS AGALACTIAE (bacteria) / Strain: 515 / Plasmid: PET-21B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q3DMP5
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 895 / 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: 2.63 Å3/Da / Density % sol: 53.24 % / Description: NONE
Crystal growpH: 7.2
Details: 25% PEG4K, 0.1M HEPES PH 7.2, 90 MM POTASSIUM SODIUM TARTRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9475
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9475 Å / Relative weight: 1
ReflectionResolution: 1.75→40 Å / Num. obs: 108305 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 9.6 % / Biso Wilson estimate: 18.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.9
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X9W

2x9w


Resolution: 1.75→40 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.935 / SU B: 4.55 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.21588 5403 5 %RANDOM
Rwork0.18489 ---
obs0.1864 102811 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.831 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2--0.58 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.75→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6929 0 3 895 7827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0227213
X-RAY DIFFRACTIONr_bond_other_d0.0010.024794
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.9579793
X-RAY DIFFRACTIONr_angle_other_deg0.745311924
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9975964
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83626.899316
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.672151336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.5091512
X-RAY DIFFRACTIONr_chiral_restr0.0640.21131
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028100
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021280
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3791.54564
X-RAY DIFFRACTIONr_mcbond_other0.0931.51871
X-RAY DIFFRACTIONr_mcangle_it0.72527403
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.23732647
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.0814.52357
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 5616 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Amedium positional0.440.5
2Bmedium positional0.440.5
1Amedium thermal0.342
2Bmedium thermal0.342
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 358 -
Rwork0.215 7508 -
obs--100 %
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)
12.75560.0166-0.46770.6221-0.12150.8304-0.04130.1128-0.0366-0.0259-0.0146-0.0620.06320.15560.05590.06870.00410.0010.08910.01090.0458-13.5682.129.202
20.5471-0.0634-0.32020.75920.01421.77560-0.02590.1169-0.0149-0.0336-0.0062-0.08610.07420.03370.0572-0.0204-0.01390.0489-0.00550.0348-25.67919.00122.428
32.24230.1579-0.50330.4161-0.0190.7183-0.08890.1019-0.35620.00190.00240.02460.1193-0.14440.08650.0914-0.028-0.00050.0480.01130.1083-47.904-9.50140.388
41.7405-0.3438-0.46210.84270.30310.9161-0.04670.0136-0.15570.0562-0.0090.08370.0887-0.09140.05580.0773-0.010.00910.0602-0.01940.0518-50.436-0.302-4.388
50.93670.2099-0.24880.540.01560.8174-0.01930.01290.0248-0.0032-0.0086-0.0016-0.0436-0.01610.02790.0480.0087-0.00880.0199-0.00730.0054-38.68517.4690.354
61.8824-0.7186-0.58040.69180.31440.5046-0.0797-0.1141-0.2220.07490.0835-0.06780.14270.1809-0.00380.11120.0543-0.02820.1259-0.07280.1438-15.499-12.494-15.271
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A190 - 332
2X-RAY DIFFRACTION2A333 - 446
3X-RAY DIFFRACTION3A447 - 640
4X-RAY DIFFRACTION4B190 - 332
5X-RAY DIFFRACTION5B333 - 446
6X-RAY DIFFRACTION6B447 - 640

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