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- PDB-5u52: 2 helix minimized version of the B-domain from Protein A (Z34C0 b... -

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Basic information

Entry
Database: PDB / ID: 5u52
Title2 helix minimized version of the B-domain from Protein A (Z34C0 bound to IgG1 Fc (monoclinic form)
Components
  • IGG1 FC
  • Mini Z domain
KeywordsIMMUNE SYSTEM / 2 helix bundle / Protein A / B-domain / IgG1 fc
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex / FCGR activation ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / immunoglobulin complex / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 1 / Uncharacterized protein DKFZp686C11235
Similarity search - Component
Biological speciesHomo sapiens (human)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.942 Å
AuthorsUltsch, M.H. / Eigenbrot, C.
Citation
Journal: Protein Eng. Des. Sel. / Year: 2017
Title: 3-2-1: Structural insights from stepwise shrinkage of a three-helix Fc-binding domain to a single helix.
Authors: Ultsch, M. / Braisted, A. / Maun, H.R. / Eigenbrot, C.
#1: Journal: J. Immunol. / Year: 2000
Title: Mapping of the C1q binding site on rituxan, a chimeric antibody with a human IgG1 Fc.
Authors: Idusogie, E.E. / Presta, L.G. / Gazzano-Santoro, H. / Totpal, K. / Wong, P.Y. / Ultsch, M. / Meng, Y.G. / Mulkerrin, M.G.
History
DepositionDec 6, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IGG1 FC
B: IGG1 FC
E: Mini Z domain
Z: Mini Z domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6136
Polymers55,7694
Non-polymers2,8452
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10500 Å2
ΔGint39 kcal/mol
Surface area25190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.392, 76.390, 66.202
Angle α, β, γ (deg.)90.00, 112.99, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein IGG1 FC


Mass: 23693.762 Da / Num. of mol.: 2 / Fragment: unp residues 262-469
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DKFZp686C11235 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q6MZV7, UniProt: P01857*PLUS
#2: Protein/peptide Mini Z domain


Mass: 4190.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Production host: synthetic construct (others)
#3: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1422.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-2-2-1-3-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.44 Å3/Da / Density % sol: 49.64 % / Description: Thin parallelepipeds.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG monomethyl ether 550, 0.1M bis-tris propane pH 6.5, 0.1M NaCl, 5mg/mL protein concentration.
PH range: 6.0-7.0

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Data collection

DiffractionMean temperature: 170 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.95 Å
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 24, 1996 / Details: Monochromatic
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.942→30 Å / Num. obs: 65918 / % possible obs: 94.8 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 23.6 Å2 / Rsym value: 0.055 / Net I/σ(I): 15
Reflection shellResolution: 1.942→2.02 Å / Redundancy: 1.4 % / Rmerge(I) obs: 0.224 / Mean I/σ(I) obs: 4.3 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACK1.5.10data scaling
X-PLOR3.1fmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FC1

1fc1


Resolution: 1.942→19.358 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2275 1890 5.17 %
Rwork0.19 --
obs0.1919 36533 92.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.942→19.358 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3908 0 192 380 4480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064222
X-RAY DIFFRACTIONf_angle_d1.0645750
X-RAY DIFFRACTIONf_dihedral_angle_d14.5281640
X-RAY DIFFRACTIONf_chiral_restr0.039666
X-RAY DIFFRACTIONf_plane_restr0.004718
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9423-1.99080.30931210.23492130X-RAY DIFFRACTION81
1.9908-2.04460.25481500.23222538X-RAY DIFFRACTION95
2.0446-2.10470.27461450.2272549X-RAY DIFFRACTION95
2.1047-2.17250.23961300.21912511X-RAY DIFFRACTION94
2.1725-2.25010.23971350.20942462X-RAY DIFFRACTION92
2.2501-2.340.2621350.21762466X-RAY DIFFRACTION92
2.34-2.44630.22761180.20272477X-RAY DIFFRACTION92
2.4463-2.5750.27531310.20492552X-RAY DIFFRACTION96
2.575-2.73590.23881530.20742579X-RAY DIFFRACTION97
2.7359-2.94650.23241430.19962609X-RAY DIFFRACTION98
2.9465-3.24180.22631560.18642622X-RAY DIFFRACTION98
3.2418-3.7080.21081260.16882541X-RAY DIFFRACTION94
3.708-4.66090.19981170.15772387X-RAY DIFFRACTION88
4.6609-19.35890.18861300.17222220X-RAY DIFFRACTION81
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)
12.9221-0.2317-0.22021.9357-0.12643.1521-0.05940.2877-0.1795-0.16940.01180.16150.2588-0.24140.13340.23060.01580.02660.1575-0.00660.189943.5384-6.291713.5577
21.40640.5733-0.41791.31060.32334.24240.0981-0.0280.06930.0627-0.07770.0637-0.11810.00090.09360.05940.0935-0.01580.0410.04440.155840.64961.544337.0314
32.7738-0.2844-0.68511.1506-0.12783.4116-0.1896-0.1615-0.3796-0.0023-0.0879-0.03410.63240.09490.12910.24570.00580.05640.12130.02310.126441.6467-4.915244.4071
43.80410.18730.02062.080.26123.84210.1850.34840.2199-0.4230.02210.1561-0.2050.36150.0020.22120.004-0.05830.19860.01920.283319.216518.929318.4727
52.1166-0.31381.57931.6815-0.85232.95340.14910.0328-0.0745-0.1980.0450.28270.3856-0.0383-0.19430.16080.0181-0.0070.0994-0.03450.208519.905110.468431.9854
62.8884-0.18170.22282.9434-0.33644.0088-0.1139-0.00850.10970.04640.13940.044-0.1775-0.21840.00140.09530.0195-0.01540.1177-0.01450.109131.470610.360445.9831
73.47952.93964.85214.8792.29968.14230.0162-0.24010.14380.2380.11090.095-0.3224-0.30550.12120.17930.05270.05190.2708-0.04140.186826.007114.055450.7681
88.1238-0.98243.87461.8497-1.04552.9377-0.2017-0.73930.14710.40180.28060.3405-0.2323-0.6365-0.00040.21180.05020.04850.36660.06060.188122.562713.104853.0848
92.7620.3362-0.65072.01180.33952.47570.0948-0.5386-0.4020.6355-0.0645-0.36930.3520.62640.04450.41580.24340.03740.41010.07130.377261.828-10.799234.5855
103.2029-0.1261-0.54823.2886-0.27840.97010.01710.098-0.1868-0.13220.2676-0.03160.70880.460.37250.56830.65340.26130.395-0.04050.354862.8832-14.253825.9872
113.039-0.0352-0.06452.6316-0.27331.97880.3559-0.9469-0.55461.24030.31770.8261-0.5061-0.59210.05690.32030.05880.17320.46150.15660.55466.540818.272346.6746
124.9992.31550.71234.6374-0.02312.6491-0.23450.2067-0.4304-0.14650.24840.3072-0.2002-0.1693-0.1470.210.03230.08890.26930.04470.532.896723.433939.3787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 237 through 325 )
2X-RAY DIFFRACTION2chain 'A' and (resid 326 through 372 )
3X-RAY DIFFRACTION3chain 'A' and (resid 373 through 443 )
4X-RAY DIFFRACTION4chain 'B' and (resid 235 through 301 )
5X-RAY DIFFRACTION5chain 'B' and (resid 302 through 361 )
6X-RAY DIFFRACTION6chain 'B' and (resid 362 through 418 )
7X-RAY DIFFRACTION7chain 'B' and (resid 419 through 432 )
8X-RAY DIFFRACTION8chain 'B' and (resid 433 through 443 )
9X-RAY DIFFRACTION9chain 'E' and (resid 6 through 24 )
10X-RAY DIFFRACTION10chain 'E' and (resid 25 through 39 )
11X-RAY DIFFRACTION11chain 'Z' and (resid 6 through 24 )
12X-RAY DIFFRACTION12chain 'Z' and (resid 25 through 39 )

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