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- PDB-2gr7: Hia 992-1098 -

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Basic information

Entry
Database: PDB / ID: 2gr7
TitleHia 992-1098
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Advisory / Version format compliance
Revision 1.3Feb 14, 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 / 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 / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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: Adhesin
B: Adhesin
C: Adhesin
D: Adhesin
E: Adhesin
F: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,74811
Polymers77,2166
Non-polymers1,5325
Water5,981332
1
A: Adhesin
B: Adhesin
C: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2215
Polymers38,6083
Non-polymers6132
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9150 Å2
ΔGint-52 kcal/mol
Surface area12730 Å2
MethodPISA
2
D: Adhesin
E: Adhesin
F: Adhesin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5276
Polymers38,6083
Non-polymers9193
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint-51 kcal/mol
Surface area13170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.340, 56.296, 158.706
Angle α, β, γ (deg.)90.00, 90.04, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: TRP / End label comp-ID: TRP / Refine code: 1 / Auth seq-ID: 998 - 1098 / Label seq-ID: 29 - 129

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF

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Components

#1: Protein
Adhesin


Mass: 12869.364 Da / Num. of mol.: 6 / Fragment: residues 1104-1204
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: Chemical
ChemComp-C8E / (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE


Mass: 306.438 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C16H34O5 / Comment: C8E, detergent*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 100 mM CHES, 12% PEG 4000 and 200 mM ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 38510 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
ADSCdata collection
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.898 / SU B: 11.022 / SU ML: 0.147 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.212 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1902 5 %RANDOM
Rwork0.226 ---
all0.227 ---
obs0.226 37886 98.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.614 Å2
Baniso -1Baniso -2Baniso -3
1-1.16 Å20 Å2-0.18 Å2
2--1.24 Å20 Å2
3----2.4 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4177 0 104 332 4613
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0224306
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9655774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.4315600
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.61226.296135
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14715687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2011516
X-RAY DIFFRACTIONr_chiral_restr0.0750.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023088
X-RAY DIFFRACTIONr_nbd_refined0.1940.21962
X-RAY DIFFRACTIONr_nbtor_refined0.280.22979
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1570.218
X-RAY DIFFRACTIONr_mcbond_it0.2741.53007
X-RAY DIFFRACTIONr_mcangle_it0.35124608
X-RAY DIFFRACTIONr_scbond_it0.90931453
X-RAY DIFFRACTIONr_scangle_it1.4084.51166
Refine LS restraints NCS

Ens-ID: 1 / Number: 691 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ATIGHT POSITIONAL0.090.05
2BTIGHT POSITIONAL0.080.05
3CTIGHT POSITIONAL0.060.05
4DTIGHT POSITIONAL0.060.05
5ETIGHT POSITIONAL0.060.05
6FTIGHT POSITIONAL0.060.05
1ATIGHT THERMAL0.080.5
2BTIGHT THERMAL0.080.5
3CTIGHT THERMAL0.080.5
4DTIGHT THERMAL0.070.5
5ETIGHT THERMAL0.080.5
6FTIGHT THERMAL0.080.5
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 119 -
Rwork0.281 2356 -
obs-2475 86.81 %
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)
11.01320.1275-0.25160.9357-0.16033.11410.00220.3054-0.0478-0.28530.04080.08010.315-0.3461-0.043-0.119-0.01030.0016-0.1296-0.0274-0.065711.72314.76547.874
20.9048-0.05770.20050.724-0.19722.50080.03780.2988-0.0435-0.25480.0086-0.07050.12250.403-0.0464-0.14520.0130.0326-0.10430.0092-0.07322.08717.27648.115
30.9365-0.0603-0.22450.91250.222.92970.04020.26840.1321-0.28090.04650.0187-0.4026-0.0747-0.0867-0.11670.0071-0.0145-0.13570.0219-0.07214.73625.06648.326
40.86250.0959-0.51561.10230.37934.04190.04830.30680.056-0.32240.0398-0.0626-0.42050.0198-0.0881-0.10230.0088-0.0086-0.080.0205-0.061433.617-3.07448.032
51.1420.0526-0.31290.9116-0.61453.38520.00530.33180.0275-0.30530.03780.08110.1697-0.3769-0.0431-0.0931-0.0041-0.0171-0.0935-0.0158-0.071326.591-11.0948.031
60.9037-0.05250.56531.07180.23943.6146-0.00350.3292-0.0328-0.32390.0542-0.010.22970.2822-0.0507-0.0861-0.01760.0152-0.08940.0089-0.067337.022-13.16148.182
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth seq-ID: 998 - 1098 / Label seq-ID: 29 - 129

IDRefine TLS-IDAuth asym-IDLabel asym-ID
11AA
22BB
33CC
44DD
55EE
66FF

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