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- PDB-3rcc: Crystal Structure of the Streptococcus agalactiae Sortase A -

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Basic information

Entry
Database: PDB / ID: 3rcc
TitleCrystal Structure of the Streptococcus agalactiae Sortase A
ComponentsSortase SrtA
KeywordsHYDROLASE / Sortase fold / Beta-barrel / Housekeeping sortase / Surface protein anchoring / Pili anchoring / Pili biogenesis
Function / homology
Function and homology information


cysteine-type peptidase activity / metal ion binding
Similarity search - Function
Sortase A / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesStreptococcus agalactiae serogroup V (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement-SAD / Resolution: 3.1 Å
AuthorsKhare, B. / Narayana, S.V.L.
CitationJournal: Plos One / Year: 2011
Title: Structural differences between the Streptococcus agalactiae housekeeping and pilus-specific sortases: SrtA and SrtC1.
Authors: Khare, B. / Krishnan, V. / Rajashankar, K.R. / I-Hsiu, H. / Xin, M. / Ton-That, H. / Narayana, S.V.
History
DepositionMar 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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.value / _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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortase SrtA
B: Sortase SrtA
C: Sortase SrtA
D: Sortase SrtA
E: Sortase SrtA
F: Sortase SrtA
G: Sortase SrtA
H: Sortase SrtA
I: Sortase SrtA
J: Sortase SrtA
K: Sortase SrtA
L: Sortase SrtA
M: Sortase SrtA
N: Sortase SrtA
O: Sortase SrtA
P: Sortase SrtA
Q: Sortase SrtA
R: Sortase SrtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)315,91591
Polymers311,14118
Non-polymers4,77573
Water97354
1
A: Sortase SrtA
B: Sortase SrtA
C: Sortase SrtA
D: Sortase SrtA
E: Sortase SrtA
F: Sortase SrtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,41432
Polymers103,7146
Non-polymers1,70126
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
G: Sortase SrtA
H: Sortase SrtA
I: Sortase SrtA
J: Sortase SrtA
K: Sortase SrtA
L: Sortase SrtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,21829
Polymers103,7146
Non-polymers1,50423
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
M: Sortase SrtA
N: Sortase SrtA
O: Sortase SrtA
P: Sortase SrtA
Q: Sortase SrtA
R: Sortase SrtA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,28330
Polymers103,7146
Non-polymers1,57024
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)237.674, 167.759, 97.536
Angle α, β, γ (deg.)90.00, 93.55, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A66 - 115
2114G66 - 115
3114M66 - 115
1214A66 - 184
2214G66 - 184
3214M66 - 184
1314A66 - 205
2314G66 - 205
3314M66 - 205
1414B66 - 115
2414H66 - 115
3414N66 - 115
1514B66 - 184
2514H66 - 184
3514N66 - 184
1614B66 - 205
2614H66 - 205
3614N66 - 205
1714C66 - 115
2714I66 - 115
3714O66 - 115
1814C66 - 184
2814I66 - 184
3814O66 - 184
1914C66 - 205
2914I66 - 205
3914O66 - 205
11014D66 - 115
21014J66 - 115
31014P66 - 115
11114D66 - 184
21114J66 - 184
31114P66 - 184
11214D66 - 205
21214J66 - 205
31214P66 - 205
11314E66 - 115
21314K66 - 115
31314Q66 - 115
11414E66 - 184
21414K66 - 184
31414Q66 - 184
11514E66 - 205
21514K66 - 205
31514Q66 - 205
11614F66 - 115
21614L66 - 115
31614R66 - 115
11714F66 - 184
21714L66 - 184
31714R66 - 184
11814F66 - 205
21814L66 - 205
31814R66 - 205

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Components

#1: Protein
Sortase SrtA


Mass: 17285.590 Da / Num. of mol.: 18 / Fragment: UNP residues 82-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae serogroup V (bacteria)
Strain: SAG2603 V/R / Gene: SAG0961, srtA, srtA (SAG0961) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q8DZY1
#2: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 73 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 3.12 Å3/Da / Density % sol: 60.56 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 8% PEG8000, 0.1 M imidazole, 0.2 M zinc sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. obs: 68853 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 16.4
Reflection shellResolution: 3.1→3.2 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.841 / Mean I/σ(I) obs: 1.85 / % possible all: 99.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: molecular replacement-SAD / Resolution: 3.1→39.23 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.834 / SU B: 23.095 / SU ML: 0.407 / Cross valid method: THROUGHOUT / ESU R Free: 0.493 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29907 3478 5.1 %RANDOM
Rwork0.23166 ---
obs0.23507 65303 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.573 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20.02 Å2
2--0.03 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.1→39.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17680 0 73 54 17807
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02218031
X-RAY DIFFRACTIONr_angle_refined_deg1.5851.96824495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04552289
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.09825.683681
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.581152985
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8631518
X-RAY DIFFRACTIONr_chiral_restr0.0980.22914
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02113222
X-RAY DIFFRACTIONr_mcbond_it0.7851.511598
X-RAY DIFFRACTIONr_mcangle_it1.458218764
X-RAY DIFFRACTIONr_scbond_it1.37436433
X-RAY DIFFRACTIONr_scangle_it2.5184.55731
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 4844 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.580.5
Bmedium positional0.580.5
Cmedium positional0.580.5
Dmedium positional0.580.5
Emedium positional0.580.5
Fmedium positional0.580.5
Gmedium positional0.670.5
Hmedium positional0.670.5
Imedium positional0.670.5
Jmedium positional0.670.5
Kmedium positional0.670.5
Lmedium positional0.670.5
Mmedium positional0.810.5
Nmedium positional0.810.5
Omedium positional0.810.5
Pmedium positional0.810.5
Qmedium positional0.810.5
Rmedium positional0.810.5
Amedium thermal0.852
Bmedium thermal0.852
Cmedium thermal0.852
Dmedium thermal0.852
Emedium thermal0.852
Fmedium thermal0.852
Gmedium thermal1.122
Hmedium thermal1.122
Imedium thermal1.122
Jmedium thermal1.122
Kmedium thermal1.122
Lmedium thermal1.122
Mmedium thermal1.052
Nmedium thermal1.052
Omedium thermal1.052
Pmedium thermal1.052
Qmedium thermal1.052
Rmedium thermal1.052
LS refinement shellResolution: 3.098→3.178 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.381 252 -
Rwork0.316 4556 -
obs--94.46 %

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