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- PDB-8fha: Intramolecular ester bond-containing repeat domain 1 from Suiprao... -

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Basic information

Entry
Database: PDB / ID: 8fha
TitleIntramolecular ester bond-containing repeat domain 1 from Suipraoptans intestinalis adhesin
ComponentsAdhesin
KeywordsCELL ADHESION / bacterial adhesin domain / Ig-like domain / intramolecular ester bond
Function / homology
Function and homology information


extracellular region / metal ion binding / membrane
Similarity search - Function
T-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
Similarity search - Domain/homology
VaFE repeat-containing surface-anchored protein
Similarity search - Component
Biological speciesSuipraeoptans intestinalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 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
DepositionDec 13, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)64,53314
Polymers64,2354
Non-polymers29810
Water4,234235
1
A: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1223
Polymers16,0591
Non-polymers632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1454
Polymers16,0591
Non-polymers863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1454
Polymers16,0591
Non-polymers863
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1223
Polymers16,0591
Non-polymers632
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.051, 104.712, 52.587
Angle α, β, γ (deg.)90.000, 91.810, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Adhesin


Mass: 16058.631 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Suipraeoptans intestinalis (bacteria) / Gene: FYJ34_05395 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6N7UZI9
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.06 Å3/Da / Density % sol: 40.25 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, 70% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.49→48.09 Å / Num. obs: 81829 / % possible obs: 96.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 18.9 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.5
Reflection shellResolution: 1.49→1.52 Å / Redundancy: 5.4 % / Num. unique obs: 3553 / CC1/2: 0.35 / % possible all: 84.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.49→48.027 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.621 / SU ML: 0.058 / Cross valid method: FREE R-VALUE / ESU R: 0.087 / ESU R Free: 0.078
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 4090 4.979 %random selection
Rwork0.1664 78050 --
all0.169 ---
obs-78050 97.023 %-
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: 21.476 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20 Å20.098 Å2
2---0.451 Å2-0 Å2
3---0.135 Å2
Refinement stepCycle: LAST / Resolution: 1.49→48.027 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4164 0 10 235 4409
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0134328
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164034
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.6455808
X-RAY DIFFRACTIONr_angle_other_deg1.3381.5969361
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1825582
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.52927.308156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.57815717
X-RAY DIFFRACTIONr_chiral_restr0.0540.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024842
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02762
X-RAY DIFFRACTIONr_nbd_refined0.1830.2588
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.23517
X-RAY DIFFRACTIONr_nbtor_refined0.1480.22051
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.22090
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2170
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.5450.26
X-RAY DIFFRACTIONr_nbd_other0.1420.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1220.212
X-RAY DIFFRACTIONr_mcbond_it1.8392.0452309
X-RAY DIFFRACTIONr_mcbond_other1.8292.0422304
X-RAY DIFFRACTIONr_mcangle_it2.3463.072871
X-RAY DIFFRACTIONr_mcangle_other2.3463.0712872
X-RAY DIFFRACTIONr_scbond_it2.3242.4372019
X-RAY DIFFRACTIONr_scbond_other2.2972.4342002
X-RAY DIFFRACTIONr_scangle_it2.8133.4692930
X-RAY DIFFRACTIONr_scangle_other2.8123.4692930
X-RAY DIFFRACTIONr_lrange_it3.13824.8534303
X-RAY DIFFRACTIONr_lrange_other3.12724.7964291
X-RAY DIFFRACTIONr_rigid_bond_restr1.1938362
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
1.49-1.5290.32720.27956390.2862200.7270.7595.03220.267
1.529-1.570.3112850.23955470.24361050.8020.83195.52830.223
1.57-1.6160.2722390.21154250.21459150.8560.87195.75650.193
1.616-1.6660.252600.18952380.19157460.8870.90295.6840.169
1.666-1.720.242640.17251220.17655930.90.92396.29890.152
1.72-1.780.2432660.14949340.15353820.9130.94296.61840.13
1.78-1.8480.2162400.14147820.14552040.9320.9596.50270.124
1.848-1.9230.2062460.1446040.14349920.9440.95897.15540.126
1.923-2.0080.1892350.1344430.13348260.9540.96596.93330.119
2.008-2.1060.2042350.14642130.14945540.950.96197.67240.136
2.106-2.220.1922170.14640510.14843720.9470.96297.62120.137
2.22-2.3540.1992070.14738430.14941400.950.96297.82610.14
2.354-2.5160.2192290.16936130.17239100.940.94798.26090.164
2.516-2.7170.2491890.18633600.1936050.920.94198.44660.182
2.717-2.9760.2461470.17931520.18133430.9260.94898.68380.181
2.976-3.3250.2131390.17628390.17830130.9430.95598.83840.183
3.325-3.8370.1881570.16625010.16726840.960.96599.03130.178
3.837-4.6910.1731090.1421410.14122660.9730.97699.29390.159
4.691-6.6030.2131020.1716560.17317670.9640.97199.49070.189
6.603-48.0270.175520.2049480.20310040.9640.95899.60160.224

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