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- PDB-7o61: Crystal structure of the C-terminal PASTA domains of Staphylococc... -

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Basic information

Entry
Database: PDB / ID: 7o61
TitleCrystal structure of the C-terminal PASTA domains of Staphylococcus aureus PBP1
ComponentsPenicillin-binding protein 1
KeywordsPROTEIN BINDING / Penicillin binding protein / PASTA domain / penicillin-binding protein and serine/threonine kinase associated domain / peptidoglycan binding
Function / homology
Function and homology information


penicillin binding / cell wall organization / plasma membrane
Similarity search - Function
PASTA domain / PASTA domain / PASTA domain profile. / PASTA / Penicillin-binding protein, dimerisation domain / Penicillin-binding Protein dimerisation domain / Penicillin-binding protein, dimerisation domain superfamily / : / Penicillin-binding protein, transpeptidase / Penicillin binding protein transpeptidase domain / Beta-lactamase/transpeptidase-like
Similarity search - Domain/homology
Penicillin-binding protein 1
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsRao, V.A. / Lewis, R.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N002679/1 United Kingdom
CitationJournal: To Be Published
Title: Crystal structure of the C-terminal PASTA domains of Staphylococcus aureus PBP1
Authors: Rao, V.A. / Lewis, R.J.
History
DepositionApr 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Penicillin-binding protein 1
B: Penicillin-binding protein 1


Theoretical massNumber of molelcules
Total (without water)32,7922
Polymers32,7922
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1260 Å2
ΔGint-2 kcal/mol
Surface area11520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.782, 81.393, 89.617
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Penicillin-binding protein 1


Mass: 16396.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325 / PS 47) (bacteria)
Strain: NCTC 8325 / PS 47 / Gene: SAOUHSC_01145 / Plasmid: pOPINRSF
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q2FZ94
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.24 Å3/Da / Density % sol: 45.04 % / Description: Orthorhombic
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M NaCl, 0.1 M sodium/potassium phosphate pH 6.2, 50 % (v/v) PEG 200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.3513 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3513 Å / Relative weight: 1
ReflectionResolution: 1.78→44.81 Å / Num. obs: 28660 / % possible obs: 99.9 % / Redundancy: 7.7 % / Biso Wilson estimate: 32.27 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.03 / Rrim(I) all: 0.067 / Χ2: 0.9 / Net I/σ(I): 14.2
Reflection shellResolution: 1.78→1.82 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.663 / Mean I/σ(I) obs: 2 / Num. unique obs: 1610 / CC1/2: 0.923 / Rpim(I) all: 0.391 / Rrim(I) all: 0.774 / Χ2: 0.66 / % possible all: 99.8

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHENIX1.18.2_3874refinement
PHASER2.8.3phasing
Coot0.8model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5oau

5oau


Resolution: 1.78→44.81 Å / SU ML: 0.2194 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5921
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.21 1368 4.79 %
Rwork0.1877 27200 -
obs0.1888 28568 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.66 Å2
Refinement stepCycle: LAST / Resolution: 1.78→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1739 0 0 123 1862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451785
X-RAY DIFFRACTIONf_angle_d0.75462419
X-RAY DIFFRACTIONf_chiral_restr0.0517289
X-RAY DIFFRACTIONf_plane_restr0.0033313
X-RAY DIFFRACTIONf_dihedral_angle_d5.6365241
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.840.40991320.33972663X-RAY DIFFRACTION99.61
1.84-1.920.25121370.27272661X-RAY DIFFRACTION99.5
1.92-20.26751300.22742687X-RAY DIFFRACTION99.68
2-2.110.23851190.20262702X-RAY DIFFRACTION99.68
2.11-2.240.23681490.19782678X-RAY DIFFRACTION99.82
2.24-2.420.19621370.19172696X-RAY DIFFRACTION99.89
2.42-2.660.24881420.19192735X-RAY DIFFRACTION99.86
2.66-3.040.23161340.20652730X-RAY DIFFRACTION100
3.04-3.830.19121330.17732758X-RAY DIFFRACTION99.62
3.83-44.810.18421550.16322890X-RAY DIFFRACTION99.38
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)
13.6580162844-1.05461220913-4.638996344284.81554743947-0.7777870114568.11007903338-0.1372210104510.299858308579-0.1692888667280.2477151024750.006308657724080.4222480997970.506609147321-0.4499923791740.09091523407140.469450824112-0.0556014765665-0.0006375374286140.310336175741-0.01259286571590.35508566776-12.7484087091-17.8564300583-5.41828727021
28.71265015209-0.2393287071-2.804574272034.694995486721.615172202346.98991990463-0.02205318362780.49670225421-0.1332266647620.0414348385811-0.125273992220.5028052884460.0286288088561-0.7316129996180.1023228810620.342863837801-0.0105420978724-0.0270245887970.272182568205-0.01231730847420.240749064574-12.1449474157-13.3741603333-12.1519862852
32.47670748793-0.0153693339184-2.145129076726.10227025194-2.685634149626.351301418590.167818835965-0.0371532795973-0.0201643893606-0.0769411780218-0.0834184870907-0.181464871796-0.1077116986520.385397082557-0.03912156091090.336830788944-0.0330023994320.01233102038950.2807056292520.02568893516790.27559720678-0.975181683083-12.8606300427-10.8910958038
47.34201631466.0265074672-2.657430205595.57513764948-3.291632168584.720638787270.288377076496-0.889778550472-0.5064845682350.481804403617-0.838152425575-0.1597779917660.1077342838050.531297298820.4361486037120.523101260613-0.0649728481870.09415786738130.269579465312-0.04421768419520.353265114111-10.7689137378-15.7951099590.872957703996
59.35416297650.639992300654-4.162285115063.96850259414-1.337883061845.400292665980.2881628239260.5890640752650.3989694123810.251559796409-0.03600333036060.318448685149-0.481332768938-0.369665620383-0.2723637430840.35799345353-0.01485904114960.01689484714480.223618089434-0.01949975371550.251594951987-13.7912519827-10.1759859406-4.84199143084
66.68777976753-2.25538660518-0.999271540334.68550470942-0.2167706051115.477669831410.254777668295-0.2078008372240.01010688668270.685877822715-0.1822767712770.126571414202-0.191751513356-0.0701729572915-0.05569478103350.542861093714-0.1056112332220.0225312654170.294783984795-0.00151174158970.359177823588-5.73585344285-1.66479858647-5.06812186375
74.87986570642-2.12132804034-4.795197821516.755948918675.243857851326.424883896750.075276993478-0.798887566874-0.3958743112710.932329363061-0.152347309562-0.0729374080405-0.1901401112870.5650978357920.001078571492320.744187886898-0.04818498225740.09240447732890.385970129267-0.0619541547810.353133453904-2.522463646124.52913703521.0798399172
89.644487238760.840684004657-3.102795722495.912075153221.668253805785.189986419330.342261330335-0.2951459520590.620070067260.350668770422-0.03678756031880.270825587655-0.4705291058460.0895721341579-0.3540800135540.629069582037-0.05813298981460.07602469677360.3067350282080.01332423536020.388329808358-3.165243528735.30785616494-7.31161587313
90.352482468610.946190581552-0.4362392048113.566177414711.591464121298.007801256720.2094730421010.181021646751.771420151150.5902091980440.3386017643260.421664154518-1.37530624354-0.449861866761-0.5570855804860.754007528288-0.01238800736330.2663848951970.375273559832-0.0293418090590.717881482904-10.18536582699.40272091837-2.37781784576
108.37420034529-0.770787038896-4.472539690876.724641330320.3543733577598.02242724671-0.1942742943130.218893011547-0.9136966668140.297093126534-0.0940440870696-0.7801779284420.7749466521690.8097763862650.06775550301870.4216739679970.0303604493582-0.02553108533630.40158760788-0.03556300101770.451581886803-15.5823535131-17.815097300415.1083271648
117.68955022879-0.675879015022-1.049254557067.378057657710.1096071189089.240900455130.181800064432-0.464764133628-0.2455021102291.04708522598-0.307242877618-0.638100587530.03333561974830.652606188050.06396076380390.397360541838-0.0207770268833-0.08936345055650.335146047035-0.009696454729860.303554825186-14.2087527722-13.331153104122.3438057583
123.510546800181.53968408213-0.8212173723826.320394388122.932956306616.89896431457-0.0307712155107-0.0957991818808-0.264463480072-0.0307940381368-0.041149352492-0.252361164038-0.0618715102840.108375267140.1628541371490.290658554312-0.0040539409961-0.02177639457730.2049804289180.03570506804360.237033538845-16.6167655872-11.847612132815.2640376534
135.606136949590.269762984433-0.897895981636.873492568120.6782579363665.860598636780.1186931814120.08335895275270.416575991563-0.9026916411870.00867843568117-0.348354328348-0.1979924611220.286552346401-0.1812339445070.5017041382640.002847985159110.04640015808630.334512904962-0.05117484611520.330113076136-13.29920492531.1113099458914.7445980858
145.64430476723-1.52646055339-4.724591250378.794615274930.6786774849644.675451048650.427499366380.5660900603970.772805328699-0.6622114216410.234098746013-0.162303204257-0.722337203916-0.334827827152-0.6827572326390.721957628794-0.04444593036610.01864679839180.43227137068-0.01687078184180.431355844501-14.08678864638.3259429135217.4054454664
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 16 )AA5 - 161 - 12
22chain 'A' and (resid 17 through 34 )AA17 - 3413 - 30
33chain 'A' and (resid 35 through 43 )AA35 - 4331 - 39
44chain 'A' and (resid 44 through 49 )AA44 - 4940 - 45
55chain 'A' and (resid 50 through 61 )AA50 - 6146 - 57
66chain 'A' and (resid 62 through 85 )AA62 - 8558 - 83
77chain 'A' and (resid 86 through 92 )AA86 - 9284 - 92
88chain 'A' and (resid 93 through 113 )AA93 - 11393 - 113
99chain 'A' and (resid 114 through 120 )AA114 - 120114 - 120
1010chain 'B' and (resid 4 through 16 )BB4 - 161 - 13
1111chain 'B' and (resid 17 through 34 )BB17 - 3414 - 31
1212chain 'B' and (resid 35 through 55 )BB35 - 5532 - 52
1313chain 'B' and (resid 56 through 100 )BB56 - 10053 - 101
1414chain 'B' and (resid 101 through 120 )BB101 - 120102 - 121

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