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- PDB-6fpz: Inter-alpha-inhibitor heavy chain 1, D298A -

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Basic information

Entry
Database: PDB / ID: 6fpz
TitleInter-alpha-inhibitor heavy chain 1, D298A
ComponentsInter-alpha-trypsin inhibitor heavy chain H1
KeywordsSTRUCTURAL PROTEIN / Extracellular Matrix / Sugar-binding / Adhesion.
Function / homology
Function and homology information


hyaluronan metabolic process / hyaluronic acid binding / serine-type endopeptidase inhibitor activity / carbohydrate binding / : / blood microparticle / calcium ion binding / extracellular exosome / extracellular region
Similarity search - Function
Inter-alpha-trypsin inhibitor heavy chain, C-terminal / : / Inter-alpha-trypsin inhibitor heavy chain C-terminus / VIT domain / Vault protein inter-alpha-trypsin domain / VIT domain profile. / Vault protein Inter-alpha-Trypsin domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. ...Inter-alpha-trypsin inhibitor heavy chain, C-terminal / : / Inter-alpha-trypsin inhibitor heavy chain C-terminus / VIT domain / Vault protein inter-alpha-trypsin domain / VIT domain profile. / Vault protein Inter-alpha-Trypsin domain / von Willebrand factor type A domain / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
ACETATE ION / Inter-alpha-trypsin inhibitor heavy chain H1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsBriggs, D.C. / Day, A.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Arthritis Research UK19489 United Kingdom
Citation
Journal: J.Biol.Chem. / Year: 2020
Title: Inter-alpha-inhibitor heavy chain-1 has an integrin-like 3D structure mediating immune regulatory activities and matrix stabilization during ovulation
Authors: Briggs, D.C. / Langford-Smith, A.W.W. / Birchenough, H.L. / Jowitt, T.A. / Kielty, C.M. / Enghild, J.J. / Baldock, C. / Milner, C.M. / Day, A.J.
#1: Journal: Biorxiv / Year: 2019
Title: Heavy chain-1 of inter-alpha-inhibitor has an integrin-like structure with immune regulatory activities
Authors: Briggs, D.C. / Langford-Smith, A.W.W. / Jowitt, T.A. / Kielty, C.M. / Enghild, J.J. / Baldock, C. / Milner, C.M. / Day, A.J.
History
DepositionFeb 12, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 27, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / citation_author
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Inter-alpha-trypsin inhibitor heavy chain H1
B: Inter-alpha-trypsin inhibitor heavy chain H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,67912
Polymers147,7912
Non-polymers88810
Water12,845713
1
A: Inter-alpha-trypsin inhibitor heavy chain H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3566
Polymers73,8951
Non-polymers4605
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Inter-alpha-trypsin inhibitor heavy chain H1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3236
Polymers73,8951
Non-polymers4275
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)159.700, 159.700, 65.745
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 45 through 168 or (resid 169...
21(chain B and (resid 45 through 123 or (resid 124...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPLEULEU(chain A and (resid 45 through 168 or (resid 169...AA45 - 16833 - 156
12LYSLYSLYSLYS(chain A and (resid 45 through 168 or (resid 169...AA169157
13ASPASPPROPRO(chain A and (resid 45 through 168 or (resid 169...AA45 - 65233 - 640
14ASPASPPROPRO(chain A and (resid 45 through 168 or (resid 169...AA45 - 65233 - 640
15ASPASPPROPRO(chain A and (resid 45 through 168 or (resid 169...AA45 - 65233 - 640
16ASPASPPROPRO(chain A and (resid 45 through 168 or (resid 169...AA45 - 65233 - 640
21ASPASPTYRTYR(chain B and (resid 45 through 123 or (resid 124...BB45 - 12333 - 111
22ARGARGARGARG(chain B and (resid 45 through 123 or (resid 124...BB124112
23ASPASPPROPRO(chain B and (resid 45 through 123 or (resid 124...BB45 - 65233 - 640
24ASPASPPROPRO(chain B and (resid 45 through 123 or (resid 124...BB45 - 65233 - 640
25ASPASPPROPRO(chain B and (resid 45 through 123 or (resid 124...BB45 - 65233 - 640
26ASPASPPROPRO(chain B and (resid 45 through 123 or (resid 124...BB45 - 65233 - 640

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Components

#1: Protein Inter-alpha-trypsin inhibitor heavy chain H1 / Inter-alpha-inhibitor heavy chain 1 / Inter-alpha-trypsin inhibitor complex component III / Serum- ...Inter-alpha-inhibitor heavy chain 1 / Inter-alpha-trypsin inhibitor complex component III / Serum-derived hyaluronan-associated protein / SHAP


Mass: 73895.336 Da / Num. of mol.: 2 / Mutation: D298A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITIH1, IGHEP1 / Plasmid: pET-45b+ / Production host: Escherichia coli K-12 (bacteria) / Variant (production host): SHuffle / References: UniProt: P19827
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 713 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.93 Å3/Da / Density % sol: 58.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM HEPES, pH 7.5, 100mM Sodium acetate, 10% PEG8K, 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9282 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 27, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9282 Å / Relative weight: 1
ReflectionResolution: 2.2→71.41 Å / Num. obs: 83846 / % possible obs: 99.2 % / Redundancy: 3.7 % / Biso Wilson estimate: 34.7 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.039 / Rrim(I) all: 0.077 / Net I/σ(I): 10.9 / Num. measured all: 312057 / Scaling rejects: 154
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
2.2-2.263.10.49860400.3920.310.59197.6
9.84-71.413.90.02510190.9880.0150.0399.5

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.32data scaling
PHENIXrefinement
PDB_EXTRACT3.24data extraction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→71.41 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.82
RfactorNum. reflection% reflection
Rfree0.2476 3983 5 %
Rwork0.2169 --
obs0.2184 79666 94.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.44 Å2 / Biso mean: 50.048 Å2 / Biso min: 20.24 Å2
Refinement stepCycle: final / Resolution: 2.2→71.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9309 0 128 713 10150
Biso mean--79.6 43.54 -
Num. residues----1196
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5501X-RAY DIFFRACTION9.59TORSIONAL
12B5501X-RAY DIFFRACTION9.59TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.22680.3786910.37522459255086
2.2268-2.2550.38831410.37462541268289
2.255-2.28470.33711420.35952542268490
2.2847-2.3160.39031400.33852610275092
2.316-2.34910.38851340.33192699283393
2.3491-2.38420.37461340.32032593272793
2.3842-2.42140.33491500.32322667281793
2.4214-2.46110.35581360.30732669280594
2.4611-2.50360.34021510.3162675282694
2.5036-2.54910.31161400.28582652279294
2.5491-2.59810.33041540.29292626278094
2.5981-2.65110.31961390.27992728286794
2.6511-2.70880.3241480.26982677282595
2.7088-2.77180.3181340.2682707284195
2.7718-2.84110.33771540.26312710286494
2.8411-2.91790.31271330.25812688282195
2.9179-3.00380.33641370.2542720285794
3.0038-3.10080.23681330.24272689282294
3.1008-3.21160.3051420.23082656279893
3.2116-3.34020.26441480.21332684283294
3.3402-3.49220.21611570.19162805296298
3.4922-3.67630.20881530.17992811296498
3.6763-3.90660.22711580.17022811296998
3.9066-4.20820.16761560.14972822297898
4.2082-4.63160.14331390.13222843298298
4.6316-5.30170.16421320.13822850298298
5.3017-6.67880.21841600.20122779293995
6.6788-71.45760.20491470.20812970311799
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)
10.8098-0.31010.39062.1848-0.85391.1852-0.0418-0.1861-0.05340.53370.24120.1354-0.1458-0.066-0.1660.39480.09770.07320.37510.070.380246.999282.60012.8506
22.3183-0.64220.00051.56720.00961.2918-0.08630.0225-0.3079-0.13510.09020.39160.0595-0.1829-0.00290.29460.00850.04150.28270.10730.454926.176194.5957-22.4452
30.85360.10280.03112.5578-1.18461.75380.03920.0347-0.1238-0.19610.0597-0.17570.20740.181-0.09120.27240.05890.05280.32220.03050.410751.099478.3312-14.8756
41.48170.0537-0.52550.90730.24612.18380.1568-0.52310.1740.25710.01030.046-0.08290.1201-0.09840.3394-0.07210.02850.3355-0.06760.27043.659633.32683.0134
51.32720.849-0.20863.0709-0.2431.0903-0.01130.15190.1577-0.142-0.00230.0626-0.08980.17840.01190.2768-0.0491-0.00060.3377-0.0390.376119.620643.2875-24.6005
62.8927-0.4261-1.59261.5507-0.27622.84620.17330.12840.16750.010.0450.2267-0.1229-0.2509-0.21390.262-0.0455-0.02240.2884-0.03220.4025-6.58934.5206-13.7398
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 45 through 290 )A45 - 290
2X-RAY DIFFRACTION2chain 'A' and (resid 291 through 508 )A291 - 508
3X-RAY DIFFRACTION3chain 'A' and (resid 509 through 652 )A509 - 652
4X-RAY DIFFRACTION4chain 'B' and (resid 45 through 253 )B45 - 253
5X-RAY DIFFRACTION5chain 'B' and (resid 254 through 556 )B254 - 556
6X-RAY DIFFRACTION6chain 'B' and (resid 557 through 652 )B557 - 652

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