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- PDB-6xi3: Crystal structure of tetra-tandem repeat in extending region of l... -

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Basic information

Entry
Database: PDB / ID: 6xi3
TitleCrystal structure of tetra-tandem repeat in extending region of large adhesion protein
ComponentsLarge adhesion protein (Lap) involved in biofilm formation
KeywordsMETAL BINDING PROTEIN / Adhesion protein / bacterial adhesin / Calcium-binding protein / beta-sandwich domains / Ig-like domain
Function / homology
Function and homology information


calcium ion binding
Similarity search - Function
Hemolysin-type calcium-binding conserved site / Hemolysin-type calcium-binding region signature. / RTX calcium-binding nonapeptide repeat / RTX calcium-binding nonapeptide repeat (4 copies) / PA14/GLEYA domain / PA14 domain profile. / PA14 domain / PA14 / PA14 domain / Serralysin-like metalloprotease, C-terminal / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-EDT / DI(HYDROXYETHYL)ETHER / Putative large adhesion protein (Lap) involved in biofilm formation
Similarity search - Component
Biological speciesMarinobacter hydrocarbonoclasticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsYe, Q. / Vance, T.D.R. / Davies, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)RGPIN-2016-04810 Canada
CitationJournal: J Struct Biol X / Year: 2020
Title: Essential role of calcium in extending RTX adhesins to their target.
Authors: Vance, T.D.R. / Ye, Q. / Conroy, B. / Davies, P.L.
History
DepositionJun 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2022Group: Database references / Category: database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: Large adhesion protein (Lap) involved in biofilm formation
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,32612
Polymers40,5501
Non-polymers77711
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-60 kcal/mol
Surface area19280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)202.833, 45.631, 58.600
Angle α, β, γ (deg.)90.000, 99.994, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11AAA-926-

HOH

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Components

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Protein , 1 types, 1 molecules AAA

#1: Protein Large adhesion protein (Lap) involved in biofilm formation


Mass: 40549.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinobacter hydrocarbonoclasticus (strain ATCC 49840 / DSM 8798 / SP17) (bacteria)
Strain: ATCC 49840 / DSM 8798 / SP17 / Gene: MARHY3363 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H8W6K8

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Non-polymers , 7 types, 509 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N2O8
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.3 Å3/Da / Density % sol: 62.77 %
Crystal growTemperature: 296 K / Method: microbatch / pH: 5 / Details: PEG 6000, sodium acetate, sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.7712 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 18, 2015 / Details: Ultra-low expansion titanium siliicate flat mirror
RadiationMonochromator: DCM, Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 35779 / % possible obs: 99 % / Redundancy: 14.1 % / Biso Wilson estimate: 17.218 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.028 / Rrim(I) all: 0.107 / Χ2: 0.93 / Net I/σ(I): 19.6
Reflection shellResolution: 2→2.05 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.471 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 2310 / CC1/2: 0.99 / Rpim(I) all: 0.144 / Rrim(I) all: 0.493 / Χ2: 0.69 / % possible all: 87.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
AutoSolphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2→46.63 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.059 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.141 / ESU R Free: 0.144
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2308 1769 4.944 %
Rwork0.1791 34009 -
all0.182 --
obs-35778 99.05 %
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: 28.192 Å2
Baniso -1Baniso -2Baniso -3
1--0.931 Å2-0 Å23.106 Å2
2--1.84 Å20 Å2
3----1.887 Å2
Refinement stepCycle: LAST / Resolution: 2→46.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2638 0 42 498 3178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0132676
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172347
X-RAY DIFFRACTIONr_angle_refined_deg1.6421.6373676
X-RAY DIFFRACTIONr_angle_other_deg1.561.585453
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1165387
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.76527.981104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.93215360
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.501154
X-RAY DIFFRACTIONr_chiral_restr0.0650.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023155
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02425
X-RAY DIFFRACTIONr_nbd_refined0.2170.2459
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.22117
X-RAY DIFFRACTIONr_nbtor_refined0.1440.21376
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0890.21226
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2377
X-RAY DIFFRACTIONr_metal_ion_refined0.1570.220
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1480.212
X-RAY DIFFRACTIONr_nbd_other0.2050.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.223
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.0720.23
X-RAY DIFFRACTIONr_mcbond_it2.1042.7991551
X-RAY DIFFRACTIONr_mcbond_other2.0922.7981550
X-RAY DIFFRACTIONr_mcangle_it2.764.1851937
X-RAY DIFFRACTIONr_mcangle_other2.764.1871938
X-RAY DIFFRACTIONr_scbond_it3.4743.1711125
X-RAY DIFFRACTIONr_scbond_other3.4733.1741126
X-RAY DIFFRACTIONr_scangle_it5.0194.6061739
X-RAY DIFFRACTIONr_scangle_other5.0184.6091740
X-RAY DIFFRACTIONr_lrange_it7.10538.5322964
X-RAY DIFFRACTIONr_lrange_other6.80637.2122817
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.2731360.2422173X-RAY DIFFRACTION87.5948
2.052-2.1080.2771430.2152427X-RAY DIFFRACTION99.6897
2.108-2.1690.2591250.2062443X-RAY DIFFRACTION99.9611
2.169-2.2360.2541310.1942250X-RAY DIFFRACTION99.958
2.236-2.3090.2491120.1812263X-RAY DIFFRACTION99.9159
2.309-2.390.2391240.1782173X-RAY DIFFRACTION100
2.39-2.480.2861150.1682089X-RAY DIFFRACTION100
2.48-2.5820.254990.1712020X-RAY DIFFRACTION100
2.582-2.6960.217930.1721972X-RAY DIFFRACTION100
2.696-2.8280.225970.1711855X-RAY DIFFRACTION100
2.828-2.9810.197820.1691788X-RAY DIFFRACTION100
2.981-3.1610.21770.1751659X-RAY DIFFRACTION100
3.161-3.3790.228770.1941611X-RAY DIFFRACTION100
3.379-3.650.235750.2021469X-RAY DIFFRACTION100
3.65-3.9980.209630.1791368X-RAY DIFFRACTION100
3.998-4.4690.246550.1561245X-RAY DIFFRACTION100
4.469-5.1580.172560.1421101X-RAY DIFFRACTION100
5.158-6.3130.226500.181933X-RAY DIFFRACTION100
6.313-8.9110.206380.158740X-RAY DIFFRACTION100
8.911-9.560.215210.153430X-RAY DIFFRACTION99.3392

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