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- PDB-6p3s: Crystal structure of human Fab H5.28 in complex with influenza A ... -

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Basic information

Entry
Database: PDB / ID: 6p3s
TitleCrystal structure of human Fab H5.28 in complex with influenza A H5N1 Vietnam hemagglutinin head domain
Components
  • (Human Fab H5.28 ...) x 2
  • Hemagglutinin
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / human monoclonal antibody / antigen-antibody complex / influenza A virus / H5N1 vietnam / hemagglutinin / head domain / VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like ...Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Influenza A virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4 Å
AuthorsDong, J. / Crowe, J.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)5U19AI117905-05 United States
CitationJournal: To Be Published
Title: crystal structure of human Fab H5.28 in complex with influenza A H5N1 Vietnam hemagglutinin head domain
Authors: Dong, J. / Crowe, J.E.
History
DepositionMay 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Human Fab H5.28 heavy chain
B: Human Fab H5.28 light chain
C: Human Fab H5.28 heavy chain
D: Human Fab H5.28 light chain
E: Hemagglutinin
F: Human Fab H5.28 heavy chain
G: Human Fab H5.28 light chain
H: Hemagglutinin
I: Human Fab H5.28 heavy chain
J: Human Fab H5.28 light chain
K: Hemagglutinin
L: Hemagglutinin
M: Human Fab H5.28 heavy chain
N: Human Fab H5.28 light chain
O: Hemagglutinin
P: Human Fab H5.28 heavy chain
Q: Human Fab H5.28 light chain
R: Hemagglutinin
S: Human Fab H5.28 heavy chain
T: Human Fab H5.28 light chain
U: Hemagglutinin
V: Human Fab H5.28 heavy chain
W: Human Fab H5.28 light chain
X: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)596,22837
Polymers584,89624
Non-polymers11,33213
Water00
1
A: Human Fab H5.28 heavy chain
B: Human Fab H5.28 light chain
L: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3325
Polymers73,1123
Non-polymers1,2202
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Human Fab H5.28 heavy chain
D: Human Fab H5.28 light chain
E: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5174
Polymers73,1123
Non-polymers1,4051
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
F: Human Fab H5.28 heavy chain
G: Human Fab H5.28 light chain
H: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7195
Polymers73,1123
Non-polymers2,6072
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
I: Human Fab H5.28 heavy chain
J: Human Fab H5.28 light chain
K: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,5174
Polymers73,1123
Non-polymers1,4051
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
M: Human Fab H5.28 heavy chain
N: Human Fab H5.28 light chain
O: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7385
Polymers73,1123
Non-polymers1,6262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
P: Human Fab H5.28 heavy chain
Q: Human Fab H5.28 light chain
R: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,3325
Polymers73,1123
Non-polymers1,2202
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
S: Human Fab H5.28 heavy chain
T: Human Fab H5.28 light chain
U: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,3334
Polymers73,1123
Non-polymers2211
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
8
V: Human Fab H5.28 heavy chain
W: Human Fab H5.28 light chain
X: Hemagglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7385
Polymers73,1123
Non-polymers1,6262
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.480, 187.225, 342.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121

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Components

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Protein , 1 types, 8 molecules EHKLORUX

#3: Protein
Hemagglutinin


Mass: 25162.408 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus (A/chicken/Vietnam/32/2004(H5N1))
Strain: A/chicken/Vietnam/32/2004(H5N1) / Gene: HA / Variant: A/chicken/Vietnam/32/2004(H5N1) / Production host: Homo sapiens (human) / References: UniProt: Q1KHK2

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Antibody , 2 types, 16 molecules ACFIMPSVBDGJNQTW

#1: Antibody
Human Fab H5.28 heavy chain


Mass: 24616.691 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
Human Fab H5.28 light chain


Mass: 23332.842 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 9 types, 13 molecules

#4: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1405.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAca1-2DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-2-3-4-5/a4-b1_b4-c1_c6-d1_d2-e1_e4-f1_f6-g2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}}}LINUCSPDB-CARE
#5: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1405.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpb1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-2-1-3-4/a4-b1_b4-c1_c6-d1_d2-e1_e4-f1_f6-g2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][b-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}}}LINUCSPDB-CARE
#6: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1202.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpa1-4DGlcpNAca1-2DManpa1-6DManpa1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a2122h-1a_1-5_2*NCC/3=O][a2112h-1a_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-2-3-4-5/a4-b1_b6-c1_c2-d1_d4-e1_e6-f2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][a-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}LINUCSPDB-CARE
#7: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-alpha-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1405.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpa1-4DGlcpNAcb1-2DManpa1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a2112h-1a_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-2-1-3-4/a4-b1_b4-c1_c6-d1_d2-e1_e4-f1_f6-g2WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][a-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}}}LINUCSPDB-CARE
#8: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-beta-D-mannopyranose


Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAca1-2DManpb1-6DManpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a1122h-1b_1-5][a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-3-4/a6-b1_b2-c1_c4-d1_d6-e2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(6+1)][b-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#9: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1405.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAca1-2DManpb1-6DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/6,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5][a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-3-4-5-6/a4-b1_b4-c1_c6-d1_d2-e1_e4-f1_f6-g2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(6+1)][b-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}}LINUCSPDB-CARE
#10: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-6)-alpha-D-mannopyranose


Type: oligosaccharide / Mass: 998.885 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAca1-2DManpb1-6DManpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,5,4/[a1122h-1a_1-5][a1122h-1b_1-5][a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4-5/a6-b1_b2-c1_c4-d1_d6-e2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Manp]{[(6+1)][b-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE
#11: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1405.271 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAca1-2DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/6,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-3-4-5-6/a4-b1_b4-c1_c6-d1_d2-e1_e4-f1_f6-g2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}}}}LINUCSPDB-CARE
#12: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

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: 3.71 Å3/Da / Density % sol: 66.86 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 8% PEG 8000, 0.5 M Ca(OAC)2, 0.1 M imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 4→49.46 Å / Num. obs: 74362 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.21 / Net I/σ(I): 8.2
Reflection shellResolution: 4→4.22 Å / Rmerge(I) obs: 0.625 / Num. unique obs: 10717

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Processing

Software
NameVersionClassification
PHENIX(1.15.2_3472: ???)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XNQ, 4GSD

4xnq

4gsd


Resolution: 4→49.46 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 32.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.326 3660 4.93 %
Rwork0.281 --
obs0.283 74234 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31337 0 760 0 32097
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232939
X-RAY DIFFRACTIONf_angle_d0.54345423
X-RAY DIFFRACTIONf_dihedral_angle_d5.50718840
X-RAY DIFFRACTIONf_chiral_restr0.0475190
X-RAY DIFFRACTIONf_plane_restr0.0036133
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4-4.05260.33511090.3022703X-RAY DIFFRACTION100
4.0526-4.10810.30971380.30982695X-RAY DIFFRACTION100
4.1081-4.16680.37881230.30792678X-RAY DIFFRACTION100
4.1668-4.22890.33811430.30512704X-RAY DIFFRACTION100
4.2289-4.2950.34421260.27822656X-RAY DIFFRACTION100
4.295-4.36540.36031570.28822700X-RAY DIFFRACTION100
4.3654-4.44060.29881330.26952689X-RAY DIFFRACTION100
4.4406-4.52130.28411400.24352694X-RAY DIFFRACTION100
4.5213-4.60820.2841240.25662685X-RAY DIFFRACTION100
4.6082-4.70220.32681510.26042698X-RAY DIFFRACTION100
4.7022-4.80430.28961450.25182684X-RAY DIFFRACTION100
4.8043-4.9160.3041550.25942691X-RAY DIFFRACTION100
4.916-5.03880.3381360.26392685X-RAY DIFFRACTION100
5.0388-5.17490.27971590.26782661X-RAY DIFFRACTION100
5.1749-5.3270.33181270.26552718X-RAY DIFFRACTION100
5.327-5.49880.32861280.27752727X-RAY DIFFRACTION100
5.4988-5.6950.34441420.29282692X-RAY DIFFRACTION100
5.695-5.92270.38021390.30182734X-RAY DIFFRACTION100
5.9227-6.19180.33411330.2942721X-RAY DIFFRACTION100
6.1918-6.51750.40351660.29482700X-RAY DIFFRACTION100
6.5175-6.92480.31221400.30492722X-RAY DIFFRACTION100
6.9248-7.45780.40511550.3122740X-RAY DIFFRACTION100
7.4578-8.20530.31641450.29052743X-RAY DIFFRACTION100
8.2053-9.38560.2931350.25052789X-RAY DIFFRACTION100
9.3856-11.79830.22451570.22332775X-RAY DIFFRACTION99
11.7983-49.46140.39441540.34812890X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -33.0179 Å / Origin y: 18.4371 Å / Origin z: -48.9677 Å
111213212223313233
T0.4521 Å20.0335 Å2-0.0622 Å2-0.5952 Å20.0284 Å2--0.4416 Å2
L0.0387 °20.0081 °2-0.1407 °2-0.1735 °20.0786 °2--0.3272 °2
S0.0945 Å °0.032 Å °-0.0086 Å °0.0071 Å °-0.0717 Å °0.0649 Å °-0.0743 Å °-0.2764 Å °-0.0193 Å °
Refinement TLS groupSelection details: ALL

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