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- PDB-3emf: Crystal structure of Haemophilus influenzae HiaBD2 -

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Basic information

Entry
Database: PDB / ID: 3emf
TitleCrystal structure of Haemophilus influenzae HiaBD2
ComponentsHia (Adhesin)
KeywordsCELL ADHESION / Hia / adhesin / binding domain / autotransporter / trimeric
Function / homology
Function and homology information


outer membrane / cell surface
Similarity search - Function
Trimeric adhesin / Trimeric adhesin / Trimeric autotransporter adhesin, tryptophan-ring motif / Trimeric autotransporter adhesin, putative GIN domain / Trimeric adhesin / Trimeric autotransporter adhesin, Trp ring domain / Tryptophan-ring motif of head of Trimeric autotransporter adhesin / HiaBD2_N domain of Trimeric autotransporter adhesin (GIN) / Trimeric autotransporter adhesin Trp ring domain / Trimeric autotransporter adhesin YadA-like, stalk domain ...Trimeric adhesin / Trimeric adhesin / Trimeric autotransporter adhesin, tryptophan-ring motif / Trimeric autotransporter adhesin, putative GIN domain / Trimeric adhesin / Trimeric autotransporter adhesin, Trp ring domain / Tryptophan-ring motif of head of Trimeric autotransporter adhesin / HiaBD2_N domain of Trimeric autotransporter adhesin (GIN) / Trimeric autotransporter adhesin Trp ring domain / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter adhesin / ESPR domain / Extended Signal Peptide of Type V secretion system / Trimeric autotransporter adhesin YadA-like, C-terminal membrane anchor domain / YadA-like membrane anchor domain / Pilin-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMeng, G. / Waksman, G.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Repetitive Architecture of the Haemophilus influenzae Hia Trimeric Autotransporter
Authors: Meng, G. / St Geme, J.W. / Waksman, G.
History
DepositionSep 24, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hia (Adhesin)
B: Hia (Adhesin)
C: Hia (Adhesin)


Theoretical massNumber of molelcules
Total (without water)37,7913
Polymers37,7913
Non-polymers00
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-43 kcal/mol
Surface area15810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.292, 91.035, 94.669
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Hia (Adhesin)


Mass: 12596.892 Da / Num. of mol.: 3 / Fragment: Hia BD2, UNP residues 51-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: hia / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q48152
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 47.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9729 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 27, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9729 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 24079 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 30.824 Å2 / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 19
Reflection shellResolution: 2→2.11 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.31 / % possible all: 95.6

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Processing

Software
NameClassification
DNAdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1S7M

1s7m


Resolution: 2→28.471 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.819 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 1220 5.09 %random
Rwork0.194 22745 --
obs-23965 98.27 %-
Solvent computationBsol: 61.005 Å2 / ksol: 0.397 e/Å3
Displacement parametersBiso max: 120.45 Å2 / Biso mean: 44.355 Å2 / Biso min: 13.2 Å2
Baniso -1Baniso -2Baniso -3
1--5.537 Å20 Å20 Å2
2--4.267 Å20 Å2
3---1.27 Å2
Refinement stepCycle: LAST / Resolution: 2→28.471 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2528 0 0 192 2720
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.0791
X-RAY DIFFRACTIONf_bond_d0.0081
X-RAY DIFFRACTIONf_chiral_restr0.0691
X-RAY DIFFRACTIONf_dihedral_angle_d15.6661
X-RAY DIFFRACTIONf_plane_restr0.0041
X-RAY DIFFRACTIONf_nbd_refined4.1151
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2-2.0150.239476X-RAY DIFFRACTION4589
2.015-2.030.209483X-RAY DIFFRACTION4591
2.03-2.0460.209484X-RAY DIFFRACTION4592
2.046-2.0630.195504X-RAY DIFFRACTION4592
2.063-2.080.217480X-RAY DIFFRACTION4592
2.08-2.0980.222501X-RAY DIFFRACTION4592
2.098-2.1160.224490X-RAY DIFFRACTION4591
2.116-2.1350.212464X-RAY DIFFRACTION4591
2.135-2.1540.206523X-RAY DIFFRACTION4592
2.154-2.1750.204492X-RAY DIFFRACTION4596
2.175-2.1960.222484X-RAY DIFFRACTION4592
2.196-2.2180.21509X-RAY DIFFRACTION4593
2.218-2.2410.199478X-RAY DIFFRACTION4591
2.241-2.2640.202503X-RAY DIFFRACTION4592
2.264-2.2890.2501X-RAY DIFFRACTION4594
2.289-2.3150.213501X-RAY DIFFRACTION4595
2.315-2.3420.197510X-RAY DIFFRACTION4593
2.342-2.3710.217488X-RAY DIFFRACTION4593
2.371-2.4010.195490X-RAY DIFFRACTION4591
2.401-2.4330.211505X-RAY DIFFRACTION4594
2.433-2.4660.225487X-RAY DIFFRACTION4592
2.466-2.5010.201535X-RAY DIFFRACTION4594
2.501-2.5390.211471X-RAY DIFFRACTION4590
2.539-2.5780.207511X-RAY DIFFRACTION4593
2.578-2.620.195490X-RAY DIFFRACTION4594
2.62-2.6650.214515X-RAY DIFFRACTION4593
2.665-2.7140.195485X-RAY DIFFRACTION4593
2.714-2.7660.211532X-RAY DIFFRACTION4596
2.766-2.8220.176484X-RAY DIFFRACTION4594
2.822-2.8840.177518X-RAY DIFFRACTION4594
2.884-2.9510.211501X-RAY DIFFRACTION4592
2.951-3.0250.196506X-RAY DIFFRACTION4595
3.025-3.1060.18526X-RAY DIFFRACTION4595
3.106-3.1970.18498X-RAY DIFFRACTION4595
3.197-3.3010.177530X-RAY DIFFRACTION4596
3.301-3.4180.205525X-RAY DIFFRACTION4596
3.418-3.5550.173516X-RAY DIFFRACTION4595
3.555-3.7170.166514X-RAY DIFFRACTION4593
3.717-3.9120.148528X-RAY DIFFRACTION4596
3.912-4.1560.135523X-RAY DIFFRACTION4595
4.156-4.4760.166524X-RAY DIFFRACTION4595
4.476-4.9240.172530X-RAY DIFFRACTION4594
4.924-5.6320.199528X-RAY DIFFRACTION4594
5.632-7.0780.231559X-RAY DIFFRACTION4597
7.078-28.4740.247543X-RAY DIFFRACTION4590

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