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- PDB-8f90: Intramolecular ester bond-containing repeat domain 2 from Suiprao... -

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Basic information

Entry
Database: PDB / ID: 8f90
TitleIntramolecular ester bond-containing repeat domain 2 from Suipraoptans intestinalis adhesin
ComponentsAdhesin
KeywordsCELL ADHESION / bacterial adhesin domain / Ig-like domain / intramolecular ester bond
Function / homologyT-Q ester bond containing domain / T-Q ester bond containing domain / Prealbumin-like fold domain / Prealbumin-like fold domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / Immunoglobulin-like fold / membrane / VaFE repeat-containing surface-anchored protein
Function and homology information
Biological speciesSuipraeoptans intestinalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsJin, S. / Young, P.G. / Squire, C.J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Intramolecular ester bond-containing repeat domain from Suipraoptans intestinalis adhesin
Authors: Jin, S. / Young, P.G. / Squire, C.J.
History
DepositionNov 22, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adhesin
B: Adhesin
C: Adhesin
D: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,5908
Polymers63,4934
Non-polymers974
Water8,269459
1
A: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8982
Polymers15,8731
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8982
Polymers15,8731
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8982
Polymers15,8731
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,8982
Polymers15,8731
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.075, 90.603, 89.686
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Adhesin / VaFE repeat-containing surface-anchored protein


Mass: 15873.245 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suipraeoptans intestinalis (bacteria) / Plasmid: pPROEXHTa / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6N7UZI9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / 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: 2.63 Å3/Da / Density % sol: 53.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2 M MgCl2, 0.1 M Bis-Tris, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953739 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953739 Å / Relative weight: 1
ReflectionResolution: 1.46→45.301 Å / Num. obs: 114397 / % possible obs: 99.6 % / Redundancy: 13.6 % / CC1/2: 0.999 / Net I/σ(I): 10.6
Reflection shellResolution: 1.46→1.49 Å / Redundancy: 12.1 % / Mean I/σ(I) obs: 1 / Num. unique obs: 5159 / CC1/2: 0.211 / % possible all: 92.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→45.301 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.962 / WRfactor Rfree: 0.192 / WRfactor Rwork: 0.151 / SU B: 3.864 / SU ML: 0.058 / Average fsc free: 0.9143 / Average fsc work: 0.9296 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.077
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1981 4410 4.969 %random selection
Rwork0.1572 84347 --
all0.159 ---
obs-88757 99.972 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.769 Å2
Baniso -1Baniso -2Baniso -3
1--0.317 Å20 Å2-0 Å2
2--0.135 Å20 Å2
3---0.182 Å2
Refinement stepCycle: LAST / Resolution: 1.6→45.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 4 459 4809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0134482
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154087
X-RAY DIFFRACTIONr_angle_refined_deg1.2791.6586101
X-RAY DIFFRACTIONr_angle_other_deg1.3041.589500
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1135600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.7726.284183
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.41915695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.711158
X-RAY DIFFRACTIONr_chiral_restr0.0530.2639
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025141
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02831
X-RAY DIFFRACTIONr_nbd_refined0.1860.2597
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.23663
X-RAY DIFFRACTIONr_nbtor_refined0.1460.22097
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.22008
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2292
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.180.210
X-RAY DIFFRACTIONr_nbd_other0.1570.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0890.220
X-RAY DIFFRACTIONr_mcbond_it1.4782.1872382
X-RAY DIFFRACTIONr_mcbond_other1.4472.1852381
X-RAY DIFFRACTIONr_mcangle_it1.8793.2872976
X-RAY DIFFRACTIONr_mcangle_other1.8833.2882977
X-RAY DIFFRACTIONr_scbond_it2.0032.5172100
X-RAY DIFFRACTIONr_scbond_other2.0012.5182097
X-RAY DIFFRACTIONr_scangle_it2.4853.6413121
X-RAY DIFFRACTIONr_scangle_other2.4843.6413122
X-RAY DIFFRACTIONr_lrange_it2.92827.0024555
X-RAY DIFFRACTIONr_lrange_other2.83426.7094498
X-RAY DIFFRACTIONr_rigid_bond_restr0.98438569
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.6-1.6420.2993570.28361280.28464930.7690.77299.87680.246
1.642-1.6860.3053730.25159430.25463190.7730.80699.95250.215
1.686-1.7350.2713080.21358130.21661240.8550.8799.9510.174
1.735-1.7890.2133120.16756850.1759990.9180.92699.96670.133
1.789-1.8470.2062800.14755210.1558010.9370.9461000.118
1.847-1.9120.1892860.13853200.14156060.9450.9561000.11
1.912-1.9840.1882400.12751630.1354040.9540.96499.98150.105
1.984-2.0650.182460.12649920.12952390.9540.96799.98090.107
2.065-2.1560.2062390.12847730.13150120.9480.9671000.112
2.156-2.2610.172650.13145620.13348270.9610.9671000.116
2.261-2.3830.192080.13943590.14145670.9560.9671000.124
2.383-2.5270.2222190.14741270.15143460.950.9621000.135
2.527-2.7010.2061920.14638930.14940850.9560.9661000.138
2.701-2.9170.1851520.15236800.15338320.9580.9651000.149
2.917-3.1940.1971790.15933360.16135150.9540.9641000.159
3.194-3.5690.21500.1730590.17132090.960.9621000.176
3.569-4.1170.1981270.16527420.16628690.9620.9671000.177
4.117-5.0310.1451460.13822770.13924230.9790.9791000.16
5.031-7.0720.199840.16718430.16919270.9710.9731000.187
7.072-45.3010.216460.1911130.19111610.9530.97199.82770.205

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