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- PDB-6qp4: Structure of 299-452 fragment of the UspA1 protein from Moraxella... -

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Basic information

Entry
Database: PDB / ID: 6qp4
TitleStructure of 299-452 fragment of the UspA1 protein from Moraxella catarrhalis
ComponentsUspA1
KeywordsCELL ADHESION / Moraxella catarrhalis / UspA1 / trimeric autotransporter / C3d protein binding
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) / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain ...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) / 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
Similarity search - Domain/homology
HEXANE-1,6-DIOL / UspA1
Similarity search - Component
Biological speciesMoraxella catarrhalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMikula, K.M. / Kolodziejczyk, R. / Goldman, A.
Funding support Finland, United Kingdom, 2items
OrganizationGrant numberCountry
Academy of Finland1286429 and 1252206 Finland
Wellcome Trust478571 United Kingdom
CitationJournal: J.Struct.Biol. / Year: 2019
Title: Structure of the UspA1 protein fragment from Moraxella catarrhalis responsible for C3d binding.
Authors: Mikula, K.M. / Kolodziejczyk, R. / Goldman, A.
History
DepositionFeb 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 21, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry

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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)52,82821
Polymers51,1373
Non-polymers1,69118
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22040 Å2
ΔGint-194 kcal/mol
Surface area26120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.639, 44.565, 128.436
Angle α, β, γ (deg.)90.00, 92.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein UspA1


Mass: 17045.699 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Moraxella catarrhalis (bacteria) / Gene: uspA1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9XD56
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C6H14O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.56 Å3/Da / Density % sol: 65.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 2.9 M 1,6-Hexanediol, 0.1M Tris-HCl pH 8.5, 20mM magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 2.5→46.01 Å / Num. obs: 25116 / % possible obs: 98.4 % / Redundancy: 3.7 % / Rrim(I) all: 0.076 / Net I/σ(I): 16.66
Reflection shellResolution: 2.5→2.65 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 4.74 / Num. unique obs: 3950 / Rrim(I) all: 0.362 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PR7
Resolution: 2.5→46 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.79
RfactorNum. reflection% reflection
Rfree0.272 1283 5.12 %
Rwork0.2122 --
obs0.2152 25066 98.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3526 0 102 199 3827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143623
X-RAY DIFFRACTIONf_angle_d1.4924846
X-RAY DIFFRACTIONf_dihedral_angle_d8.9682243
X-RAY DIFFRACTIONf_chiral_restr0.063570
X-RAY DIFFRACTIONf_plane_restr0.008649
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4966-2.59660.26831310.23182551X-RAY DIFFRACTION96
2.5966-2.71480.29351530.23272585X-RAY DIFFRACTION99
2.7148-2.85790.30751530.2252625X-RAY DIFFRACTION99
2.8579-3.03690.26551680.2142624X-RAY DIFFRACTION99
3.0369-3.27130.27831310.22062648X-RAY DIFFRACTION99
3.2713-3.60040.25811320.20082677X-RAY DIFFRACTION99
3.6004-4.12110.27381520.18492683X-RAY DIFFRACTION99
4.1211-5.1910.24851350.18232662X-RAY DIFFRACTION98
5.191-46.0190.28431280.26222728X-RAY DIFFRACTION96

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