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- PDB-1t7v: Zn-alpha-2-glycoprotein; baculo-ZAG PEG 200 -

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Basic information

Entry
Database: PDB / ID: 1t7v
TitleZn-alpha-2-glycoprotein; baculo-ZAG PEG 200
ComponentsZinc-alpha-2-glycoprotein
KeywordsLIPID BINDING PROTEIN / MHC class I homolog / PEG
Function / homology
Function and homology information


Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / protein transmembrane transporter activity / RNA nuclease activity / positive regulation of T cell mediated cytotoxicity / : / cell adhesion / immune response ...Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent / antigen processing and presentation of endogenous peptide antigen via MHC class Ib / protein transmembrane transporter activity / RNA nuclease activity / positive regulation of T cell mediated cytotoxicity / : / cell adhesion / immune response / negative regulation of cell population proliferation / external side of plasma membrane / extracellular space / extracellular exosome / extracellular region / nucleus
Similarity search - Function
MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...MHC class I-like antigen recognition-like / Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 / MHC class I alpha chain, alpha1 alpha2 domains / Class I Histocompatibility antigen, domains alpha 1 and 2 / : / MHC class I-like antigen recognition-like / MHC class I-like antigen recognition-like superfamily / MHC classes I/II-like antigen recognition protein / 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 / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Zinc-alpha-2-glycoprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsDelker, S.L. / West Jr., A.P. / McDermott, L. / Kennedy, M.W. / Bjorkman, P.J.
Citation
Journal: J.Struct.Biol. / Year: 2004
Title: Crystallographic studies of ligand binding by Zn-alpha2-glycoprotein.
Authors: Delker, S.L. / West Jr., A.P. / McDermott, L. / Kennedy, M.W. / Bjorkman, P.J.
#1: Journal: Science / Year: 1999
Title: Crystal structure of human ZAG, a fat-depleting factor related to MHC molecules
Authors: Sanchez, L.M. / Chirino, A.J. / Bjorkman, P.
History
DepositionMay 11, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
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 / pdbx_struct_special_symmetry / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 27, 2021Group: Database references / Structure summary / Category: chem_comp / database_2 / struct_ref_seq_dif
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 2.2Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 3.0Dec 25, 2024Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_conn
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_seq_id / _atom_site.occupancy / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_special_symmetry.auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc-alpha-2-glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,1144
Polymers32,1861
Non-polymers9283
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)122.878, 122.878, 65.227
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-567-

HOH

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Components

#1: Protein Zinc-alpha-2-glycoprotein / Zn-alpha-2-glycoprotein / Zn-alpha-2-GP


Mass: 32185.953 Da / Num. of mol.: 1 / Mutation: N89K, N92T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AZGP1, ZAG, ZNGP1 / Plasmid: pVL1393 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P25311
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: 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.: 1
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
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 3.82 Å3/Da / Density % sol: 67.84 %
Crystal growTemperature: 298 K / Method: microbatch / pH: 7.5
Details: Ammonium sulfate, PEG 200, HEPES, pH 7.5, Microbatch, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1271 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2003
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.95→20 Å / Num. obs: 36424 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.8
Reflection shellResolution: 1.95→2.02 Å / % possible obs: 98.9 % / Rmerge(I) obs: 0.487 / Mean I/σ(I) obs: 2.8 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZAG

1zag


Resolution: 1.95→20 Å / Rfactor Rfree error: 0.006 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1650 4.5 %RANDOM
Rwork0.214 ---
all-36906 --
obs-36617 99.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 63.5282 Å2 / ksol: 0.378422 e/Å3
Displacement parametersBiso max: 114.61 Å2 / Biso mean: 46.52 Å2 / Biso min: 15.48 Å2
Baniso -1Baniso -2Baniso -3
1-2.59 Å20 Å20 Å2
2--2.59 Å20 Å2
3----5.17 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.95→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 61 185 2478
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_torsion_deg24.8
X-RAY DIFFRACTIONc_torsion_impr_deg0.96
X-RAY DIFFRACTIONc_mcbond_it4.231.5
X-RAY DIFFRACTIONc_mcangle_it5.422
X-RAY DIFFRACTIONc_scbond_it6.412
X-RAY DIFFRACTIONc_scangle_it8.872.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.95-2.020.3241464.10.28634250.0273645357197.9
2.02-2.10.2811664.70.24933990.0223628356598.2
2.1-2.20.2851855.10.23434110.0213637359698.9
2.2-2.310.29614640.22234800.0253649362699.3
2.31-2.460.2751183.30.22335090.0253654362799.3
2.46-2.650.2241754.80.20934730.0173666364899.5
2.65-2.910.2671935.30.22834720.0193675366599.7
2.91-3.330.2711664.50.22235350.0213708370199.8
3.33-4.190.2211664.40.19835670.0173748373399.6
4.19-19.630.2341894.90.20436960.0173928388598.9

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