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- PDB-1t7y: Zn-alpha-2-glycoprotein; baculo-ZAG PEG 200, no glycerol -

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Basic information

Entry
Database: PDB / ID: 1t7y
TitleZn-alpha-2-glycoprotein; baculo-ZAG PEG 200, no glycerol
ComponentsZinc-alpha-2-glycoprotein
KeywordsLIPID BINDING PROTEIN / MHC class I homolog
Function / homology
Function and homology information


Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / protein transmembrane transporter activity / RNA nuclease activity / collagen-containing extracellular matrix / cell adhesion / immune response / negative regulation of cell population proliferation / external side of plasma membrane / extracellular space ...Miscellaneous transport and binding events / detection of chemical stimulus involved in sensory perception of bitter taste / protein transmembrane transporter activity / RNA nuclease activity / collagen-containing extracellular matrix / 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 / Immunoglobulins / Immunoglobulin-like fold / 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: 2.8 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.J.
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 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_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 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 2.3Oct 9, 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: Zinc-alpha-2-glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8323
Polymers32,1861
Non-polymers6462
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.937, 121.937, 64.904
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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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
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: 3.75 Å3/Da / Density % sol: 67.18 %
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 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 28, 2003
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 12197 / % possible obs: 97.4 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.3
Reflection shellResolution: 2.8→2.9 Å / % possible obs: 95.5 % / Rmerge(I) obs: 0.441 / Mean I/σ(I) obs: 2.4 / % possible all: 94.2

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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 1T7V

1t7v


Resolution: 2.8→20 Å / Rfactor Rfree error: 0.011 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 624 5.1 %Random
Rwork0.231 ---
all-12500 --
obs-12184 97.5 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 20.6969 Å2 / ksol: 0.313838 e/Å3
Displacement parametersBiso max: 199.52 Å2 / Biso mean: 51.35 Å2 / Biso min: 3.7 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20 Å20 Å2
2--1.79 Å20 Å2
3----3.59 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.51 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2232 0 42 0 2274
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_torsion_deg24.1
X-RAY DIFFRACTIONx_torsion_impr_deg0.81
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.8-2.90.481685.90.39210790.0581222114793.8
2.9-3.020.424494.20.33611150.0611222116495.3
3.02-3.150.347544.60.29211260.0471225118096.3
3.15-3.320.26615.10.28411380.0331235119997.1
3.32-3.520.297695.80.26411300.0361222119998.1
3.52-3.790.2756150.21511690.0351244123098.9
3.79-4.170.268594.80.21811760.0351244123599.2
4.17-4.770.187614.90.15711930.0241265125499.1
4.77-5.980.21735.70.18212070.0251282128099.8
5.98-19.90.247695.30.22712270.031350129696

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