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- PDB-2gr8: Hia 1022-1098 -

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Basic information

Entry
Database: PDB / ID: 2gr8
TitleHia 1022-1098
ComponentsAdhesin
KeywordsMEMBRANE PROTEIN / Trimeric autotransporter / adhesion / protein secretion / microbial pathogenesis
Function / homology
Function and homology information


outer membrane / cell surface
Similarity search - Function
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 / GSPII I/J protein-like / Trimeric autotransporter adhesin YadA-like, stalk domain / Coiled stalk of trimeric autotransporter 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 / GSPII I/J protein-like / 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 / Pantoate--beta-alanine Ligase; Chain: A,domain 2 / Pilin-like / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsMeng, G. / Waksman, G.
CitationJournal: Embo J. / Year: 2006
Title: Structure of the outer membrane translocator domain of the Haemophilus influenzae Hia trimeric autotransporter.
Authors: Meng, G. / Surana, N.K. / St Geme III, J.W. / Waksman, G.
History
DepositionApr 23, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adhesin
B: Adhesin
C: Adhesin
D: Adhesin
E: Adhesin
F: Adhesin


Theoretical massNumber of molelcules
Total (without water)59,0466
Polymers59,0466
Non-polymers00
Water3,981221
1
A: Adhesin
C: Adhesin
D: Adhesin


Theoretical massNumber of molelcules
Total (without water)29,5233
Polymers29,5233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6360 Å2
ΔGint-35 kcal/mol
Surface area8990 Å2
MethodPISA
2
B: Adhesin
E: Adhesin
F: Adhesin


Theoretical massNumber of molelcules
Total (without water)29,5233
Polymers29,5233
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6280 Å2
ΔGint-30 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.263, 82.261, 82.502
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Adhesin


Mass: 9840.964 Da / Num. of mol.: 6 / Fragment: residues 1128-1204
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: strain 11 / Plasmid: pASK-iba12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(B834) / References: UniProt: Q48152
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 3 Å3/Da / Density % sol: 59.04 %
Crystal growTemperature: 298 K / pH: 7.5
Details: 34% (w/v) MPD, 0.2 M NaNO3, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 26, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 38510 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / Net I/σ(I): 12
Reflection shellResolution: 2→2.05 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.48 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
DENZOdata reduction
SCALEPACKdata scaling
ProDCdata collection
RefinementMethod to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.925 / SU B: 6.498 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1950 5.1 %RANDOM
Rwork0.193 ---
obs0.193 38452 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.35 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2--0.57 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3211 0 0 221 3432
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223239
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8471.954369
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5895462
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.21125.52196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.31115522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7791513
X-RAY DIFFRACTIONr_chiral_restr0.0490.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022371
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1560.21443
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2750.22300
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0780.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.2212
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0640.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1481.52343
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.22923562
X-RAY DIFFRACTIONr_scbond_it0.39231036
X-RAY DIFFRACTIONr_scangle_it0.6894.5807
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 140 -
Rwork0.211 2641 -
obs--100 %
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)
12.3571-0.75830.19483.1438-0.57332.37130.0136-0.07720.03740.29970.12980.2965-0.2636-0.1289-0.1434-0.07550.03090.0449-0.1286-0.033-0.14467.228641.160212.8344
24.4271-0.6979-0.31981.43170.01061.0104-0.02720.24630.053-0.0377-0.0414-0.0968-0.0088-0.0550.0686-0.1612-0.02540.003-0.13760.0164-0.1535-3.222216.83782.8842
32.9411-0.91640.13712.155-0.27632.26140.13740.1801-0.1789-0.0185-0.04280.2473-0.01450.0233-0.0946-0.1425-0.0023-0.0054-0.1288-0.016-0.13667.906733.17965.7051
41.667-0.59780.58432.1637-0.88533.75380.02460.08860.1030.18310.0251-0.0638-0.32240.1603-0.0498-0.112-0.00380.026-0.1136-0.0298-0.143716.075939.96916.9541
52.81710.29-0.17113.16080.15541.4564-0.04390.0855-0.0823-0.2267-0.01590.14880.0646-0.01930.0598-0.13860.02350.0049-0.1358-0.0328-0.15522.823152.660828.9004
62.90530.28340.28292.28470.09531.7865-0.0581-0.13520.3256-0.0020.0090.1275-0.1496-0.07790.0491-0.16310.02850.0006-0.1363-0.0158-0.126731.527333.1262-4.8296
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1021 - 109822 - 99
2X-RAY DIFFRACTION2BB1021 - 109822 - 99
3X-RAY DIFFRACTION3CC1021 - 109822 - 99
4X-RAY DIFFRACTION4DD1021 - 109822 - 99
5X-RAY DIFFRACTION5EE1021 - 109822 - 99
6X-RAY DIFFRACTION6FF1021 - 109822 - 99

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