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- PDB-2y1v: Full length structure of RrgB Pilus protein from Streptococcus pn... -

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Basic information

Entry
Database: PDB / ID: 2y1v
TitleFull length structure of RrgB Pilus protein from Streptococcus pneumoniae
ComponentsCELL WALL SURFACE ANCHOR FAMILY PROTEIN
KeywordsSTRUCTURAL PROTEIN / MAJOR PILIN / PILUS ASSEMBLY
Function / homology
Function and homology information


membrane => GO:0016020 / membrane
Similarity search - Function
Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Collagen-binding surface protein Cna, B-type domain / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif ...Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 3, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Gram-positive pilin backbone subunit 2, Cna-B-like domain / Collagen-binding surface protein Cna, B-type domain / Fimbrial isopeptide formation D2 domain / Immunoglobulin-like - #740 / Prealbumin-like fold domain / Prealbumin-like fold domain / LPXTG cell wall anchor motif / LPXTG cell wall anchor domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
NICKEL (II) ION / Cell wall surface anchor family protein / Cell wall surface anchor family protein
Similarity search - Component
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.39 Å
AuthorsEl-Mortaji, L. / Contreras-Martel, C. / Manzano, C. / Vernet, T. / Dessen, A. / DiGuilmi, A.M.
CitationJournal: Biochem.J. / Year: 2012
Title: The Full-Length Streptococcus Pneumoniae Major Pilin Rrgb Crystallizes in a Fibre-Like Structure, which Presents the D1 Isopeptide Bond and Provides Details on the Mechanism of Pilus Polymerization.
Authors: El Mortaji, L. / Contreras-Martel, C. / Moschioni, M. / Ferlenghi, I. / Manzano, C. / Vernet, T. / Dessen, A. / Di Guilmi, A.M.
History
DepositionDec 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
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
Item: _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_database_status.status_code_sf / _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
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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
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.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_ncs_dom_lim.beg_auth_comp_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 / _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
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)196,60412
Polymers196,0763
Non-polymers5289
Water7,746430
1
A: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5354
Polymers65,3591
Non-polymers1763
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)65,5354
Polymers65,3591
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: CELL WALL SURFACE ANCHOR FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5354
Polymers65,3591
Non-polymers1763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.619, 74.619, 340.527
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12B
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLYGLYGLYGLY5AA29 - 6321 - 604
211GLYGLYGLYGLY5BB29 - 6321 - 604
121NINININI6AD - F800 - 802
221NINININI6BG - I800 - 802
112GLYGLYGLYGLY5BB29 - 6321 - 604
212GLYGLYGLYGLY5CC29 - 6321 - 604
122NINININI6BG - I800 - 802
222NINININI6CJ - L800 - 802

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(0.999991, 0.000886, -0.004114), (0.000896, -0.999997, 0.002454), (-0.004111, -0.002457, -0.999988)-37.2583, 21.8341, 0.38649
2given(0.442967, 0.896182, -0.025255), (0.883768, -0.441221, -0.155812), (-0.150779, 0.0467, -0.987464)34.50905, -19.01812, -15.20364

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Components

#1: Protein CELL WALL SURFACE ANCHOR FAMILY PROTEIN / RRGB


Mass: 65358.672 Da / Num. of mol.: 3 / Fragment: RESIDUES 30-633
Source method: isolated from a genetically manipulated source
Details: ISOPEPTIDE BONDS K41 AND N184, K193 AND N318, K349 AND N428, K453 AND N623
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: TIGR4 / Plasmid: PLIM (PROTEIN EXPERT, GRENOBLE) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)-RIL (INVITROGEN) / References: UniProt: Q97SC2, UniProt: A0A0H2UNM7*PLUS
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Ni
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57 % / Description: NONE
Crystal growpH: 7.5 / Details: 23% PEG 8000, 0.1M TRIS PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97485
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97485 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.592
11K, H, -L20.408
ReflectionResolution: 2.39→20 Å / Num. obs: 164140 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 4 % / Biso Wilson estimate: 47.736 Å2 / Rsym value: 0.06 / Net I/σ(I): 25.7
Reflection shellResolution: 2.39→2.54 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 4.9 / Rsym value: 0.49 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2X9W

2x9w


Resolution: 2.39→113.53 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.918 / SU B: 18.266 / SU ML: 0.186 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2335 8548 10.3 %RANDOM
Rwork0.18704 ---
obs0.1919 74075 98.65 %-
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: 53.737 Å2
Baniso -1Baniso -2Baniso -3
1-30.78 Å20 Å20 Å2
2--30.78 Å20 Å2
3----61.57 Å2
Refinement stepCycle: LAST / Resolution: 2.39→113.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13728 0 9 430 14167
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02213965
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.95618990
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.36451809
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62326.915603
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.84152349
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8861524
X-RAY DIFFRACTIONr_chiral_restr0.0710.22229
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02110530
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.151.59006
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.035214547
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7434959
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.6484.54443
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

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A2416medium positional0.140.5
12B2416medium positional0.140.5
21B2416medium positional0.340.5
22C2416medium positional0.340.5
11A2163loose positional0.285
12B2163loose positional0.285
21B2163loose positional0.445
22C2163loose positional0.445
11A2416medium thermal1.992
12B2416medium thermal1.992
21B2416medium thermal3.542
22C2416medium thermal3.542
11A2163loose thermal2.9810
12B2163loose thermal2.9810
21B2163loose thermal3.9810
22C2163loose thermal3.9810
LS refinement shellResolution: 2.392→2.454 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 528 -
Rwork0.264 4801 -
obs--86.45 %
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)
10.3894-0.1012-0.0688-0.0075-0.08690.56930.01090.052-0.0541-0.0528-0.04550.00550.08110.08380.03460.07340.05670.01480.2568-0.00190.431916.7127-0.1029-11.6597
20.0353-0.06410.06690.104-0.04180.27180.0518-0.0333-0.0362-0.055-0.0594-0.04770.08520.1510.00750.00790.0214-0.00280.2905-0.01680.374424.2252.69660.491
30.3198-0.0552-0.25550.2503-0.06790.53860.01120.0568-0.0325-0.06240.02560.00880.1359-0.0446-0.0367-0.002-0.0201-0.050.2222-0.03990.33666.5504-3.31261.0343
40.1720.054-0.11580.0857-0.15550.25280.0816-0.06710.0027-0.0418-0.0575-0.00070.07420.0753-0.02410.2098-0.0003-0.00640.20850.00430.209321.84951.310114.2856
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 188
2X-RAY DIFFRACTION1B29 - 188
3X-RAY DIFFRACTION1C29 - 188
4X-RAY DIFFRACTION2A189 - 329
5X-RAY DIFFRACTION2A433 - 446
6X-RAY DIFFRACTION2B189 - 329
7X-RAY DIFFRACTION2B433 - 446
8X-RAY DIFFRACTION2C189 - 329
9X-RAY DIFFRACTION2C433 - 446
10X-RAY DIFFRACTION3A330 - 432
11X-RAY DIFFRACTION3B330 - 432
12X-RAY DIFFRACTION3C330 - 432
13X-RAY DIFFRACTION4A447 - 633
14X-RAY DIFFRACTION4B447 - 633
15X-RAY DIFFRACTION4C447 - 633

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