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- PDB-8d4o: Crystal Structure of the Neutrophil Serine Protease Inhibitor Eap... -

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Basic information

Entry
Database: PDB / ID: 8d4o
TitleCrystal Structure of the Neutrophil Serine Protease Inhibitor Eap1 from S. aureus
ComponentsExtracellular Adherence Protein
KeywordsPROTEIN BINDING / Protease Inhibitor / Immune Evasion / Neutrophil / S. aureus
Function / homologyMAP domain / MAP domain / MAP repeat profile. / Protein map
Function and homology information
Biological speciesStaphylococcus aureus subsp. aureus Mu50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.45 Å
AuthorsGido, C.D. / Geisbrecht, B.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R35GM140852 United States
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Characterization of two distinct neutrophil serine protease-binding modes within a Staphylococcus aureus innate immune evasion protein family.
Authors: Gido, C.D. / Herdendorf, T.J. / Geisbrecht, B.V.
History
DepositionJun 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Apr 3, 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

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Assembly

Deposited unit
A: Extracellular Adherence Protein
B: Extracellular Adherence Protein
C: Extracellular Adherence Protein
D: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,8348
Polymers44,7424
Non-polymers924
Water9,278515
1
A: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2323
Polymers11,1861
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2092
Polymers11,1861
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Extracellular Adherence Protein


Theoretical massNumber of molelcules
Total (without water)11,1861
Polymers11,1861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Extracellular Adherence Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2092
Polymers11,1861
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.623, 48.091, 55.161
Angle α, β, γ (deg.)84.260, 89.920, 72.960
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Extracellular Adherence Protein


Mass: 11185.606 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus subsp. aureus Mu50 (bacteria)
Strain: Mu50 / ATCC 700699 / Gene: map, SAV1938 / Plasmid: pT7HMT / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q99QS1
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 515 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.12 Å3/Da / Density % sol: 42.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate trihydrate, 2.0 M sodium chloride
PH range: 4.0-5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97243 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97243 Å / Relative weight: 1
ReflectionResolution: 1.45→50 Å / Num. obs: 57248 / % possible obs: 88 % / Redundancy: 3.4 % / Biso Wilson estimate: 10.5 Å2 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.041 / Rrim(I) all: 0.078 / Χ2: 1.005 / Net I/σ(I): 16.5 / Num. measured all: 195869
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.45-1.52.10.25948440.8930.1890.3231.0774.4
1.5-1.562.70.24354880.9030.1660.2961.06184.5
1.56-1.633.20.21852430.9350.140.260.99380.6
1.63-1.723.60.19460590.9560.1180.2271.02392.9
1.72-1.833.70.16560290.9720.0990.1920.99592.9
1.83-1.973.70.12259840.9830.0740.1430.99191.4
1.97-2.173.70.08957230.9890.0540.1040.95488.5
2.17-2.483.70.06957650.9930.0410.080.95588.2
2.48-3.123.70.05261710.9960.0310.061.05694.9
3.12-503.70.03659420.9710.0220.0421.01191.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YN3_A

Resolution: 1.45→37.08 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0.35 / Phase error: 21.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1974 1970 3.5 %
Rwork0.1686 54359 -
obs0.1696 56329 86.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.08 Å2 / Biso mean: 13.8341 Å2 / Biso min: 4.35 Å2
Refinement stepCycle: final / Resolution: 1.45→37.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3132 0 4 515 3651
Biso mean--26.52 22.82 -
Num. residues----396
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.45-1.490.28721030.23192974307767
1.49-1.530.26241310.20593520365178
1.53-1.570.23761350.18953718385382
1.57-1.620.20771260.17443400352676
1.62-1.680.22841500.16714092424291
1.68-1.750.24031470.17624065421291
1.75-1.830.241500.17394114426491
1.83-1.920.2381450.17274105425091
1.92-2.040.20051450.16044050419590
2.04-2.20.18731380.15683773391184
2.2-2.420.17461440.16593988413289
2.42-2.770.20671560.17444299445595
2.77-3.490.19141520.16694196434893
3.49-37.080.14641480.15484065421391

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