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- PDB-3ntn: Crystal Structure of UspA1 head and neck domain from Moraxella ca... -

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Basic information

Entry
Database: PDB / ID: 3ntn
TitleCrystal Structure of UspA1 head and neck domain from Moraxella catarrhalis
ComponentsUspA1
KeywordsMEMBRANE PROTEIN / Beta roll / Trimeric autotransporter proteins / Outer membrane
Function / homology
Function and homology information


cell outer membrane / protein transport / cell surface
Similarity search - Function
Ubiquitous surface protein / Repeat of unknown function DUF1079 / Ubiquitous surface protein adhesin repeat / Repeat of unknown function (DUF1079) / Ubiquitous surface protein adhesin repeat / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 ...Ubiquitous surface protein / Repeat of unknown function DUF1079 / Ubiquitous surface protein adhesin repeat / Repeat of unknown function (DUF1079) / Ubiquitous surface protein adhesin repeat / Trimeric autotransporter adhesin YadA-like, head domain / YadA head domain repeat (2 copies) / Serralysin-like metalloprotease, C-terminal / 2 Solenoid / Alkaline Protease, subunit P, domain 1 / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Serralysin-like metalloprotease, C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #170 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
NICKEL (II) ION / UspA1
Similarity search - Component
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsConners, R. / Zaccai, N. / Agnew, C. / Burton, N. / Brady, R.L.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Correlation of in situ mechanosensitive responses of the Moraxella catarrhalis adhesin UspA1 with fibronectin and receptor CEACAM1 binding.
Authors: Agnew, C. / Borodina, E. / Zaccai, N.R. / Conners, R. / Burton, N.M. / Vicary, J.A. / Cole, D.K. / Antognozzi, M. / Virji, M. / Brady, R.L.
History
DepositionJul 5, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 7, 2011Group: Database references
Revision 1.3Sep 14, 2011Group: Database references
Revision 1.4Sep 28, 2011Group: Database references
Revision 1.5Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: UspA1
B: UspA1
C: UspA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,9918
Polymers66,6093
Non-polymers3825
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19350 Å2
ΔGint-182 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.295, 142.847, 50.268
Angle α, β, γ (deg.)90.000, 119.960, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Ens-ID: 1 / Refine code: 3

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNASNASNAA169 - 21617 - 64
21ASNASNASNASNBB169 - 21617 - 64
31ASNASNASNASNCC169 - 21617 - 64
12ASPASPILEILEAA218 - 22966 - 77
22ASPASPILEILEBB218 - 22966 - 77
32ASPASPILEILECC218 - 22966 - 77
13PHEPHETHRTHRAA251 - 26099 - 108
23PHEPHETHRTHRBB251 - 26099 - 108
33PHEPHETHRTHRCC251 - 26099 - 108
14VALVALALAALAAA267 - 284115 - 132
24VALVALALAALABB267 - 284115 - 132
34VALVALALAALACC267 - 284115 - 132
15GLUGLUGLYGLYAA313 - 322161 - 170
25GLUGLUGLYGLYBB313 - 322161 - 170
35GLUGLUGLYGLYCC313 - 322161 - 170
16ASNASNLEULEUAA333 - 361181 - 209
26ASNASNLEULEUBB333 - 361181 - 209
36ASNASNLEULEUCC333 - 361181 - 209

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Components

#1: Protein UspA1


Mass: 22202.984 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella catarrhalis (bacteria) / Strain: ATCC25238 / Gene: uspA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XD56
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O

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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: 2.35 Å3/Da / Density % sol: 47.63 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG, Tris, Ammonium Sulphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9763 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 27, 2009
RadiationMonochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.2→100 Å / Num. all: 31185 / Num. obs: 30697 / % possible obs: 98.5 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5 / Redundancy: 3.4 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.086 / Χ2: 1.004 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.2-2.282.60.55229030.809193.9
2.28-2.373.10.4630350.785198.1
2.37-2.483.40.3830890.835199.6
2.48-2.613.50.33630950.744199.3
2.61-2.773.40.24130810.785198.8
2.77-2.993.50.15530520.804198.5
2.99-3.293.50.10130590.949198.7
3.29-3.763.50.06830991.223199.3
3.76-4.743.40.04131231.455199.7
4.74-1003.70.03131611.472199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 55.68 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.68 Å
Translation2.5 Å41.68 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3LAA, 3EMO, 1P9H

3laa

3emo

1p9h


Resolution: 2.2→71.42 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / WRfactor Rfree: 0.2437 / WRfactor Rwork: 0.1851 / Occupancy max: 1 / Occupancy min: 0.01 / FOM work R set: 0.8136 / SU B: 15.026 / SU ML: 0.17 / SU R Cruickshank DPI: 0.2817 / SU Rfree: 0.2218 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.222 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2437 1543 5 %RANDOM
Rwork0.182 ---
obs0.1852 30625 98.23 %-
all-31185 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 168.24 Å2 / Biso mean: 52.5494 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å21.07 Å2
2---2.71 Å20 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 2.2→71.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4519 0 17 170 4706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214632
X-RAY DIFFRACTIONr_angle_refined_deg1.681.9146262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6175651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.40727.15214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0815736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.794159
X-RAY DIFFRACTIONr_chiral_restr0.1120.2721
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023542
X-RAY DIFFRACTIONr_mcbond_it0.751.53117
X-RAY DIFFRACTIONr_mcangle_it1.30224914
X-RAY DIFFRACTIONr_scbond_it2.63331515
X-RAY DIFFRACTIONr_scangle_it3.7724.51339
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A509TIGHT POSITIONAL0.030.05
2B509TIGHT POSITIONAL0.040.05
3C509TIGHT POSITIONAL0.040.05
1A398LOOSE POSITIONAL0.045
2B398LOOSE POSITIONAL0.045
3C398LOOSE POSITIONAL0.055
1A509TIGHT THERMAL0.150.5
2B509TIGHT THERMAL0.170.5
3C509TIGHT THERMAL0.160.5
1A398LOOSE THERMAL0.1610
2B398LOOSE THERMAL0.1610
3C398LOOSE THERMAL0.1610
LS refinement shellResolution: 2.2→2.255 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 109 -
Rwork0.281 1921 -
all-2030 -
obs--89.86 %
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)
18.898-0.35581.61226.989-2.21717.3123-0.37920.1461.0077-0.7527-0.08930.0154-0.0838-0.30570.46850.394-0.00780.00660.25780.03980.339214.461217.4232-2.4138
22.19911.91850.52143.44790.10140.9746-0.08710.29620.2963-0.59010.0102-0.0781-0.16580.03110.0770.32980.01870.03030.26830.04140.246214.802210.3298-3.1447
33.2744-0.11040.15333.6765-0.64291.8148-0.04170.22480.2842-0.58-0.07260.017-0.0483-0.10580.11440.27570.00330.01620.21390.01590.180113.42751.8974-3.7049
43.6351-0.1602-1.45456.4293-0.84843.52620.10230.05520.2082-0.6829-0.066-0.3265-0.15440.0344-0.03640.2752-0.00660.05260.21060.02050.150917.0083-4.4232-2.3972
52.1609-0.5468-0.26565.3240.63242.82540.01420.3231-0.2077-0.97060.04370.11340.1347-0.1065-0.05790.3233-0.02190.02090.25510.02290.170115.9724-11.96-6.0395
60.99021.76690.1685.67530.21450.7226-0.05470.2122-0.104-0.61620.1664-0.09510.1283-0.0269-0.11170.29550.0053-0.03290.2603-0.01120.158813.0239-29.4146-3.3588
71.441-0.0297-0.72894.4505-0.57891.9360.04490.22170.0684-0.2665-0.0272-0.1461-0.0022-0.1283-0.01760.18820.0094-0.01180.245-0.00630.211515.9435-24.96954.6646
80.1881-0.2085-0.24083.8767-0.58890.89770.04060.0192-0.10020.0914-0.1217-0.03230.10650.03870.08120.2212-0.0049-0.00190.2407-0.01260.213811.259-44.444511.0939
91.7554-5.5596-2.415352.906110.63717.5049-0.0862-0.2173-0.27470.69920.1867-0.14920.3391-0.1699-0.10050.23070.0039-0.04830.36290.03260.244217.9468-72.151210.5152
105.6765.11681.20064.6151.08080.26860.00150.2707-0.78750.02020.2219-0.6749-0.02240.1559-0.22340.39510.01740.10090.8684-0.05550.692219.6054-86.80737.3358
114.2082-2.2889-0.86891.26370.47440.17970.45280.48330.3243-0.2568-0.3626-0.0638-0.1022-0.1149-0.09020.90970.1087-0.20240.7649-0.14490.9458-0.278420.527911.6131
126.7066-0.9325-2.60835.80640.99413.5051-0.3233-0.43710.07630.21990.00110.4161-0.7590.08410.32220.38770.07110.01420.1856-0.01560.41123.429917.314810.616
131.0348-1.47990.4583.4639-1.92411.8721-0.0071-0.0420.07250.2090.05450.34-0.1824-0.2397-0.04740.2449-0.00610.03170.2915-0.10450.4172.452210.339210.5202
142.9566-0.9307-0.11213.50060.00274.261-0.0170.00550.03220.2154-0.02090.5347-0.0678-0.18910.03780.196-0.00250.00950.1860.00680.24312.39910.88049.877
154.37260.5571-0.62086.31521.63022.8789-0.0229-0.21450.15540.4808-0.03440.79450.1257-0.17770.05730.16620.02940.02250.23930.01150.27840.2909-9.763310.9161
160.8553-0.25040.18345.5728-1.42991.123-0.1033-0.1362-0.14750.21830.12840.48110.136-0.2352-0.02510.2086-0.00620.06270.2304-0.00660.22123.1519-29.394812.213
173.4452-1.16460.37725.0559-0.24220.96480.0378-0.13890.10740.0342-0.04980.23760.034-0.16210.0120.1963-0.0197-0.01070.2312-0.01590.1788.5174-25.04615.9384
180.8082-0.1875-0.0824.29740.0420.00850.04340.026-0.1015-0.1302-0.0562-0.0735-0.0036-0.00080.01270.2183-0.0027-0.01330.24440.01520.217216.5761-44.71826.2864
195.66426.71431.043449.1299-5.78162.80090.19-0.3348-0.2714-1.02590.0303-0.29150.45570.1589-0.22040.33520.0107-0.03350.37670.0190.165211.6294-74.78570.936
2031.1181-6.837834.628930.3604-35.990366.55510.48540.5318-1.0625-1.40490.5213-0.16621.7585-0.2404-1.00670.6292-0.0309-0.03210.63170.07960.60099.509-88.8372.0277
218.454.295-0.31258.69563.81444.22280.30860.04920.1150.41520.0284-0.5203-0.68680.2407-0.3370.4279-0.0455-0.04890.258-0.00540.411320.120617.45813.8521
227.195-3.3548-4.01562.53482.36644.51550.1303-0.33050.35330.24280.0246-0.5021-0.36830.4429-0.15490.2874-0.0792-0.04980.2474-0.0080.350721.97712.254213.7056
231.2262-0.09390.20665.36150.50371.62890.0544-0.09010.09930.2961-0.043-0.3605-0.20810.1178-0.01140.2213-0.0123-0.0550.2331-0.00780.21119.60373.495714.4504
242.9870.8750.25446.2216-0.80632.5293-0.0773-0.0653-0.0380.49260.0569-0.75920.00710.2320.02050.2064-0.007-0.06360.25-0.01720.217321.7-9.719115.9885
250.8476-1.8499-0.23587.84071.61191.398-0.0256-0.0945-0.17940.40880.1125-0.44160.15840.2376-0.08690.16890.0063-0.04240.23740.01410.272821.2598-31.112713.201
2610.551711.472418.084712.743919.833431.1404-1.04331.4347-0.4273-0.52491.8253-0.6859-1.27462.7985-0.7821.37420.56130.06351.11310.07591.236425.2432-23.9688.7625
270.5886-0.0171-0.11643.56610.04510.91310.02890.0055-0.0105-0.0119-0.05290.08540.0397-0.00320.02410.1820.0068-0.00230.2357-0.00210.195810.1315-34.87527.1893
281.7105-4.06220.176837.2968-11.95934.8367-0.00210.0587-0.2169-0.1282-0.03990.33750.0387-0.05510.0420.2207-0.03320.00830.3455-0.02960.21566.6182-65.83739.4514
290.84572.2834-4.175443.0303-2.949622.5054-0.1384-0.1070.0678-0.22240.26261.31580.69680.597-0.12420.27190.06450.05360.48480.05150.3287.9269-79.690911.8101
3016.0459-6.9034-23.258330.796942.154970.8695-0.9529-0.53670.36490.24560.2290.90021.21780.59660.72390.55050.22390.06370.92030.17340.36149.699-88.741512.5991
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A159 - 170
2X-RAY DIFFRACTION2A171 - 201
3X-RAY DIFFRACTION3A202 - 221
4X-RAY DIFFRACTION4A222 - 241
5X-RAY DIFFRACTION5A242 - 263
6X-RAY DIFFRACTION6A264 - 295
7X-RAY DIFFRACTION7A296 - 323
8X-RAY DIFFRACTION8A324 - 353
9X-RAY DIFFRACTION9A354 - 364
10X-RAY DIFFRACTION10A365 - 372
11X-RAY DIFFRACTION11B153 - 158
12X-RAY DIFFRACTION12B159 - 170
13X-RAY DIFFRACTION13B171 - 201
14X-RAY DIFFRACTION14B202 - 228
15X-RAY DIFFRACTION15B229 - 263
16X-RAY DIFFRACTION16B264 - 295
17X-RAY DIFFRACTION17B296 - 323
18X-RAY DIFFRACTION18B324 - 353
19X-RAY DIFFRACTION19B354 - 367
20X-RAY DIFFRACTION20B368 - 372
21X-RAY DIFFRACTION21C159 - 170
22X-RAY DIFFRACTION22C171 - 189
23X-RAY DIFFRACTION23C190 - 225
24X-RAY DIFFRACTION24C226 - 267
25X-RAY DIFFRACTION25C268 - 295
26X-RAY DIFFRACTION26C296 - 305
27X-RAY DIFFRACTION27C306 - 349
28X-RAY DIFFRACTION28C350 - 360
29X-RAY DIFFRACTION29C361 - 367
30X-RAY DIFFRACTION30C368 - 372

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