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- PDB-2qih: Crystal structure of 527-665 fragment of UspA1 protein from Morax... -

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Basic information

Entry
Database: PDB / ID: 2qih
TitleCrystal structure of 527-665 fragment of UspA1 protein from Moraxella catarrhalis
Componentsprotein UspA1
KeywordsCELL ADHESION / Trimeric / parallel alpha-helical coiled-coil
Function / homology
Function and homology information


cell outer membrane / protein transport / cell surface
Similarity search - Function
Ubiquitous surface protein / Repeat of unknown function DUF1079 / Repeat of unknown function (DUF1079) / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / 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 ...Ubiquitous surface protein / Repeat of unknown function DUF1079 / Repeat of unknown function (DUF1079) / : / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #340 / 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / UspA1 / UspA1
Similarity search - Component
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å
AuthorsConners, R. / Brady, R.L.
CitationJournal: Embo J. / Year: 2008
Title: The Moraxella adhesin UspA1 binds to its human CEACAM1 receptor by a deformable trimeric coiled-coil.
Authors: Conners, R. / Hill, D.J. / Borodina, E. / Agnew, C. / Daniell, S.J. / Burton, N.M. / Sessions, R.B. / Clarke, A.R. / Catto, L.E. / Lammie, D. / Wess, T. / Brady, R.L. / Virji, M.
History
DepositionJul 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,79322
Polymers33,8462
Non-polymers94720
Water6,954386
1
A: protein UspA1
hetero molecules

A: protein UspA1
hetero molecules

A: protein UspA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,18933
Polymers50,7683
Non-polymers1,42130
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area15060 Å2
ΔGint-152.5 kcal/mol
Surface area24370 Å2
MethodPISA
2
B: protein UspA1
hetero molecules

B: protein UspA1
hetero molecules

B: protein UspA1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,18933
Polymers50,7683
Non-polymers1,42130
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area15040 Å2
ΔGint-151.9 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.234, 37.234, 224.475
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number143
Space group name H-MP3
Components on special symmetry positions
IDModelComponents
11A-1003-

PO4

21A-1004-

PO4

31A-1004-

PO4

41A-1005-

CL

51A-1006-

CL

61A-1007-

CL

71A-1009-

CL

81A-1010-

CL

91A-1011-

CL

101A-1012-

CL

111A-1013-

CL

121B-1001-

PO4

131B-1001-

PO4

141B-1002-

PO4

151B-1002-

PO4

161B-1008-

CL

171B-1014-

CL

181B-1015-

CL

191B-1016-

CL

201B-1017-

CL

211B-1018-

CL

221B-1019-

CL

231B-1020-

CL

241A-326-

HOH

251A-327-

HOH

261A-333-

HOH

271A-351-

HOH

281B-359-

HOH

291B-361-

HOH

301B-362-

HOH

311B-386-

HOH

DetailsThere are two monomers in the asymmetric unit (chains A and B). The biological assembly is a trimer generated from chain A by the operations: -x+y, -x+1, z and -y+1, x-y+1, z A second biological trimer can be generated from chain B by the operations: -x+y, -x, z and -y, x-y, z

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Components

#1: Protein protein UspA1


Mass: 16922.752 Da / Num. of mol.: 2 / Fragment: residues 527-665 / Mutation: S528T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella catarrhalis (bacteria) / Strain: ATCC25238 / Gene: UspA1 / Plasmid: PQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q9XD56, UniProt: Q9XD54*PLUS
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.65 Å3/Da / Density % sol: 53.66 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 12% PEG 3350, 0.2M Ammonium Phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9535 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 24, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9535 Å / Relative weight: 1
ReflectionResolution: 1.897→223.61 Å / Num. all: 27647 / Num. obs: 25857 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Rmerge(I) obs: 0.086 / Χ2: 1.008 / Net I/σ(I): 11
Reflection shellResolution: 1.897→1.97 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / Num. unique all: 1963 / Χ2: 0.708 / % possible all: 69.9

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.61 Å
Translation2.5 Å29.61 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Chain A of 1D7M

1d7m


Resolution: 1.897→223.61 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.894 / SU B: 2.138 / SU ML: 0.067 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.159 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.253 1300 5 %RANDOM
Rwork0.194 ---
all0.207 27647 --
obs0.197 25855 93.52 %-
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 mean: 22.946 Å2
Baniso -1Baniso -2Baniso -3
1-0.91 Å20.45 Å20 Å2
2--0.91 Å20 Å2
3----1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.897→223.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2088 0 36 386 2510
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222117
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9382860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.945281
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.26127.944107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.47815408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.475156
X-RAY DIFFRACTIONr_chiral_restr0.0870.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021564
X-RAY DIFFRACTIONr_nbd_refined0.2120.2950
X-RAY DIFFRACTIONr_nbtor_refined0.290.21502
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2233
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2130.2271
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1790.280
X-RAY DIFFRACTIONr_mcbond_it0.9731.51422
X-RAY DIFFRACTIONr_mcangle_it1.40222184
X-RAY DIFFRACTIONr_scbond_it2.5293763
X-RAY DIFFRACTIONr_scangle_it3.7594.5671
LS refinement shellResolution: 1.897→1.946 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 76 -
Rwork0.206 1332 -
obs-1408 68.02 %

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