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- PDB-4c0z: The N-terminal domain of the Streptococcus pyogenes pilus tip adh... -

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Basic information

Entry
Database: PDB / ID: 4c0z
TitleThe N-terminal domain of the Streptococcus pyogenes pilus tip adhesin Cpa
ComponentsANCILLARY PROTEIN 2
KeywordsCELL ADHESION / THIOESTER-DOMAIN / PILUS
Function / homology
Function and homology information


DNA polymerase; domain 1 - #480 / Thioester domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / SH3 type barrels. / DNA polymerase; domain 1 / Roll ...DNA polymerase; domain 1 - #480 / Thioester domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / SH3 type barrels. / DNA polymerase; domain 1 / Roll / Immunoglobulin-like fold / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / SPERMIDINE / Pilus tip adhesin Cpa
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsLinke-Winnebeck, C. / Paterson, N. / Baker, E.N.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural Model for the Covalent Adhesion of the Streptococcus Pyogenes Pilus Through a Thioester Bond.
Authors: Linke-Winnebeck, C. / Paterson, N.G. / Young, P.G. / Middleditch, M.J. / Greenwood, D.R. / Witte, G. / Baker, E.N.
History
DepositionAug 8, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references / Structure summary
Revision 1.2Jan 15, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ANCILLARY PROTEIN 2
B: ANCILLARY PROTEIN 2
C: ANCILLARY PROTEIN 2
D: ANCILLARY PROTEIN 2
E: ANCILLARY PROTEIN 2
F: ANCILLARY PROTEIN 2
G: ANCILLARY PROTEIN 2
H: ANCILLARY PROTEIN 2
I: ANCILLARY PROTEIN 2
J: ANCILLARY PROTEIN 2
K: ANCILLARY PROTEIN 2
L: ANCILLARY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,47238
Polymers298,54312
Non-polymers1,92926
Water17,745985
1
I: ANCILLARY PROTEIN 2
J: ANCILLARY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0305
Polymers49,7572
Non-polymers2733
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-11.9 kcal/mol
Surface area18680 Å2
MethodPISA
2
A: ANCILLARY PROTEIN 2
B: ANCILLARY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1398
Polymers49,7572
Non-polymers3826
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-48.2 kcal/mol
Surface area18770 Å2
MethodPISA
3
C: ANCILLARY PROTEIN 2
D: ANCILLARY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1256
Polymers49,7572
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3400 Å2
ΔGint-15.6 kcal/mol
Surface area18690 Å2
MethodPISA
4
E: ANCILLARY PROTEIN 2
F: ANCILLARY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0686
Polymers49,7572
Non-polymers3114
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3320 Å2
ΔGint-24.6 kcal/mol
Surface area18480 Å2
MethodPISA
5
G: ANCILLARY PROTEIN 2
H: ANCILLARY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0447
Polymers49,7572
Non-polymers2875
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-36.6 kcal/mol
Surface area18840 Å2
MethodPISA
6
K: ANCILLARY PROTEIN 2
L: ANCILLARY PROTEIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0656
Polymers49,7572
Non-polymers3084
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3260 Å2
ΔGint-18 kcal/mol
Surface area18520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.220, 132.220, 136.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
ANCILLARY PROTEIN 2 / CPA


Mass: 24878.572 Da / Num. of mol.: 12 / Fragment: N-TERMINAL DOMAIN, RESIDUES 8-222
Source method: isolated from a genetically manipulated source
Details: COVALENT SPERMIDINE CROSS-LINK BETWEEN Q211 OF A AND B, C AND D, E AND F, G AND H, I AND J, K AND L
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Strain: 90/306S / Description: NEW ZEALAND / Plasmid: PPROEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: S5FV19

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Non-polymers , 5 types, 1011 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-SPD / SPERMIDINE / N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE / PA(34)


Mass: 145.246 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H19N3
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 985 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsSPERMIDINE (SPD): COVALENT LINK WITH GLN 211

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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: 2.26 Å3/Da / Density % sol: 42.4 %
Description: STRUCTURE WAS SOLVED USING MAD USING A SELENOMETHIONINE-DERIVATIVE. INITIAL MODEL WAS USED TO SOLVE THE NATIVE DATASET USED FOR BUILDING OF FINAL MODEL.
Crystal growpH: 7.4 / Details: 16 % PEG3350, 0.3 M KH2PO4, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 13, 2013 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→47.91 Å / Num. obs: 1069788 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 36.14 Å2 / Rmerge(I) obs: 0.16 / Net I/σ(I): 4.94
Reflection shellResolution: 2→2 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 0.5 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
autoSHARPphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2→47.5 Å / Cor.coef. Fo:Fc: 0.9477 / Cor.coef. Fo:Fc free: 0.9277 / SU R Cruickshank DPI: 0.193 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.186 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.16
Details: CHAINS A, B, C, D, E, F, G, H IN RELIABLE ELECTRON DENSITY. CHAINS K, L LESS SO. CHAINS K, L WERE MODELLED BASED ON CHAIN A.
RfactorNum. reflection% reflectionSelection details
Rfree0.232 9223 5.12 %RANDOM
Rwork0.2013 ---
obs0.2026 180308 99.96 %-
Displacement parametersBiso mean: 49.57 Å2
Baniso -1Baniso -2Baniso -3
1--2.1959 Å20 Å20 Å2
2---2.1959 Å20 Å2
3---4.3919 Å2
Refine analyzeLuzzati coordinate error obs: 0.307 Å
Refinement stepCycle: LAST / Resolution: 2→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20385 0 107 985 21477
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0121104HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0528594HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d7391SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes685HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2913HARMONIC5
X-RAY DIFFRACTIONt_it21104HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.18
X-RAY DIFFRACTIONt_other_torsion18.12
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion2637SEMIHARMONIC5
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_contact24168SEMIHARMONIC4
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2417 1131 8.54 %
Rwork0.2206 12116 -
all0.2224 13247 -
obs--99.96 %
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)
11.6757-0.38660.26591.4944-0.21882.10680.01790.1338-0.1186-0.0508-0.0531-0.07930.22940.30410.0352-0.05180.07980.00640.0101-0.0398-0.1339-47.50123.029367.1496
22.58980.5874-0.58662.613-1.15983.1185-0.3599-0.2037-0.5335-0.0147-0.0583-0.34690.2799-0.11720.4182-0.12590.06480.1191-0.2060.03-0.0116-24.4325-3.374943.8526
31.4742-0.5486-0.01511.92630.00653.80680.01510.24250.2555-0.097-0.06370.0813-0.4574-0.69610.0486-0.25540.0354-0.05020.0287-0.0323-0.0642-16.606616.783599.4152
41.3172-0.00931.18181.2905-0.08653.43790.19860.1691-0.22870.03010.1248-0.10680.59970.4216-0.3235-0.02360.0783-0.0617-0.08-0.0967-0.1257-47.096823.141-1.7722
53.78140.36740.48131.28210.48432.5049-0.04520.0653-0.20240.1441-0.11830.2180.3712-0.26380.1635-0.182-0.02310.0487-0.1066-0.1206-0.0115-23.2977-4.5918114.601
62.16340.4565-0.52114.6108-1.86452.7976-0.24480.08640.01320.0223-0.1766-0.5565-0.32430.05480.4214-0.111-0.0074-0.0523-0.22080.0339-0.1081-16.58618.128329.7719
72.2916-0.7265-0.71952.16280.49462.92450.22250.09020.3656-0.2012-0.0339-0.3804-0.54890.3506-0.1886-0.0525-0.07340.0332-0.1146-0.0085-0.1318-43.177845.260381.8208
82.1453-0.1009-0.12752.3729-0.22642.0840.07370.0798-0.13310.01070.0740.4647-0.2418-0.1852-0.1477-0.06430.007-0.0471-0.14250.0482-0.0599-23.613971.5419108.23
94.14580.4244-0.01991.47040.70493.34830.1363-0.6551-1.21050.2453-0.0591-0.07990.64570.0455-0.0772-0.1416-0.0106-0.1057-0.24230.23920.0278-9.378853.583153.9036
102.1620.12770.50821.1250.15212.3543-0.1480.10270.15160.04220.1537-0.1795-0.17730.3644-0.0057-0.1016-0.0282-0.0161-0.0177-0.0407-0.0929-42.883745.530812.7708
112.9549-0.2832-0.88651.89691.18943.74450.19390.0492-0.1057-0.1099-0.27850.2256-0.5088-0.41790.0845-0.06190.0791-0.0583-0.1137-0.0079-0.1504-23.818771.038239.5648
122.07540.24120.22272.29970.60082.7208-0.0020.0475-0.35520.01190.10860.09450.23610.3353-0.1065-0.14410.0398-0.0053-0.07060.0481-0.0622-9.561654.201123.38
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L

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