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- PDB-4lfd: Staphylococcus aureus sortase B-substrate complex -

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Basic information

Entry
Database: PDB / ID: 4lfd
TitleStaphylococcus aureus sortase B-substrate complex
Components
  • (CBZ)NPQ(B27) PEPTIDE
  • Sortase B
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Transpeptidase / IsdC / Membrane / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


Sortase B, Firmicutes / Sortase B family / Sortase; Chain: A; / Sortase / Sortase family / Sortase domain superfamily / Sortase domain / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
(CBZ)NPQ(B27) peptide / Sortase B / Sortase B
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsJacobitz, A.W. / Sawaya, M.R. / Yi, S.W. / Amer, B.R. / Huang, G.L. / Nguyen, A.V. / Jung, M.E. / Clubb, R.T.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural and Computational Studies of the Staphylococcus aureus Sortase B-Substrate Complex Reveal a Substrate-stabilized Oxyanion Hole.
Authors: Jacobitz, A.W. / Wereszczynski, J. / Yi, S.W. / Amer, B.R. / Huang, G.L. / Nguyen, A.V. / Sawaya, M.R. / Jung, M.E. / McCammon, J.A. / Clubb, R.T.
History
DepositionJun 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Apr 16, 2014Group: Database references
Revision 1.3Sep 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_ref_seq_dif / 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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Sortase B
E: (CBZ)NPQ(B27) PEPTIDE
B: Sortase B
F: (CBZ)NPQ(B27) PEPTIDE
C: Sortase B
G: (CBZ)NPQ(B27) PEPTIDE
D: Sortase B
H: (CBZ)NPQ(B27) PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,47816
Polymers105,7098
Non-polymers7698
Water48627
1
A: Sortase B
E: (CBZ)NPQ(B27) PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5233
Polymers26,4272
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area950 Å2
ΔGint-16 kcal/mol
Surface area10950 Å2
MethodPISA
2
B: Sortase B
F: (CBZ)NPQ(B27) PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7155
Polymers26,4272
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1290 Å2
ΔGint-42 kcal/mol
Surface area11090 Å2
MethodPISA
3
C: Sortase B
G: (CBZ)NPQ(B27) PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6194
Polymers26,4272
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-26 kcal/mol
Surface area10990 Å2
MethodPISA
4
D: Sortase B
H: (CBZ)NPQ(B27) PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6194
Polymers26,4272
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-29 kcal/mol
Surface area11010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.600, 59.120, 72.490
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Sortase B /


Mass: 25814.129 Da / Num. of mol.: 4 / Fragment: UNP Residues 31-244
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: USA300 / Gene: srtB, SAUSA300_1034 / Plasmid: pE-SUMO / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS
References: UniProt: Q2FHU6, UniProt: A0A0H2XI76*PLUS, sortase B
#2: Protein/peptide
(CBZ)NPQ(B27) PEPTIDE


Type: Peptide-like / Class: Inhibitor / Mass: 613.125 Da / Num. of mol.: 4 / Source method: obtained synthetically / References: (CBZ)NPQ(B27) peptide
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.08 Å3/Da / Density % sol: 40.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 150 uM SrtB-NPQT in 2.8 M Ammonium Sulfate, 70 mM Sodium Citrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.964 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 2.49→72.49 Å / Num. all: 29837 / Num. obs: 30889 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 56.2 Å2 / Rmerge(I) obs: 0.244
Reflection shellResolution: 2.49→2.58 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 3.8 / % possible all: 89.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1NG5

1ng5


Resolution: 2.49→72.49 Å / Cor.coef. Fo:Fc: 0.9477 / Cor.coef. Fo:Fc free: 0.9002 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1402 4.98 %RANDOM
Rwork0.215 ---
obs0.2177 28147 91.39 %-
all-30889 --
Displacement parametersBiso mean: 72.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.3326 Å20 Å22.4729 Å2
2--3.2197 Å20 Å2
3----5.5523 Å2
Refine analyzeLuzzati coordinate error obs: 0.524 Å
Refinement stepCycle: LAST / Resolution: 2.49→72.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7384 0 40 27 7451
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017556HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.2610156HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2856SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes260HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1044HARMONIC5
X-RAY DIFFRACTIONt_it7556HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.44
X-RAY DIFFRACTIONt_other_torsion18.9
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion956SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8414SEMIHARMONIC4
LS refinement shellResolution: 2.49→2.58 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2772 137 4.8 %
Rwork0.2371 2718 -
all0.2389 2855 -
obs--91.39 %
Refinement TLS params.

T33: 0.6079 Å2 / 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)Origin x (Å)Origin y (Å)Origin z (Å)
13.611-0.4726-0.61463.55860.57192.00530.00260.0914-0.0185-0.23230.10870.13220.0636-0.0658-0.1114-0.5634-0.0388-0.0395-0.53120.017814.3841.81551.0205
23.4375-0.13490.25892.37950.24071.77460.03540.09840.0673-0.12930.1409-0.00990.02610.0954-0.1763-0.5011-0.00380.0521-0.45770.002536.917127.54071.2349
33.2567-0.0701-0.12143.35750.02181.75860.01150.1187-0.0901-0.15310.11830.1551-0.0121-0.0916-0.1298-0.579-0.0146-0.0281-0.5710.00214.383524.451337.4819
43.72840.0840.30653.363-0.20111.7524-0.02370.090.0862-0.14350.1444-0.0344-0.01240.1022-0.1207-0.6079-0.02420.0546-0.6079-0.008736.886650.181137.2554
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A29 - 244
2X-RAY DIFFRACTION2{ B|* }B29 - 244
3X-RAY DIFFRACTION3{ C|* }C29 - 244
4X-RAY DIFFRACTION4{ D|* }D29 - 244

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