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- PDB-2bgn: HIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bo... -

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Basic information

Entry
Database: PDB / ID: 2bgn
TitleHIV-1 Tat protein derived N-terminal nonapeptide Trp2-Tat(1-9) bound to the active site of Dipeptidyl peptidase IV (CD26)
Components
  • ADENOSINE DEAMINASE
  • DIPEPTIDYL PEPTIDASE IV
  • TAT PROTEIN
KeywordsHYDROLASE / HYDROLASE-COMPLEX / DIPETIDYL PEPTIDASE IV / DPPIV / CD26 / ALPHA/BETA-HYDROLASE FOLD / BETA-PROPELLER FOLD / PROTEIN-PROTEIN COMPLEX / ADENOSINE DEAMINASE / ADA / SERINE PROTEASE / AMINOPEPTIDASE / HIV-1 TAT PROTEIN
Function / homology
Function and homology information


viral gene expression / trans-activation response element binding / 2'-deoxyadenosine deaminase activity / negative regulation of adenosine receptor signaling pathway / regulatory region RNA binding / cytoplasmic vesicle lumen / protein serine/threonine phosphatase inhibitor activity / positive regulation of viral transcription / purine ribonucleoside monophosphate biosynthetic process / inosine biosynthetic process ...viral gene expression / trans-activation response element binding / 2'-deoxyadenosine deaminase activity / negative regulation of adenosine receptor signaling pathway / regulatory region RNA binding / cytoplasmic vesicle lumen / protein serine/threonine phosphatase inhibitor activity / positive regulation of viral transcription / purine ribonucleoside monophosphate biosynthetic process / inosine biosynthetic process / adenosine deaminase / adenosine catabolic process / hypoxanthine salvage / adenosine deaminase activity / glucagon processing / symbiont-mediated perturbation of host chromatin organization / negative regulation of neutrophil chemotaxis / symbiont-mediated suppression of host translation initiation / regulation of circadian sleep/wake cycle, sleep / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / dipeptidyl-peptidase IV / negative regulation of extracellular matrix disassembly / host cell nucleolus / psychomotor behavior / chemorepellent activity / intercellular canaliculus / nucleotide metabolic process / dipeptidyl-peptidase activity / anchoring junction / peptide hormone processing / actinin binding / lamellipodium membrane / locomotory exploration behavior / endocytic vesicle / aminopeptidase activity / endothelial cell migration / behavioral fear response / RNA-binding transcription regulator activity / T cell costimulation / receptor-mediated endocytosis of virus by host cell / serine-type peptidase activity / cyclin binding / T cell activation / positive regulation of transcription elongation by RNA polymerase II / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / host cell cytoplasm / membrane fusion / response to hypoxia / receptor-mediated virion attachment to host cell / lysosome / cell adhesion / apical plasma membrane / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / membrane raft / signaling receptor binding / serine-type endopeptidase activity / protein domain specific binding / external side of plasma membrane / lysosomal membrane / focal adhesion / positive regulation of cell population proliferation / symbiont entry into host cell / DNA-templated transcription / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / zinc ion binding / membrane / metal ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat) / Adenosine deaminase / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Dipeptidylpeptidase IV, N-terminal domain ...Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat) / Adenosine deaminase / Adenosine/AMP deaminase active site / Adenosine and AMP deaminase signature. / Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Dipeptidylpeptidase IV, N-terminal domain / 8 Propeller / Methanol Dehydrogenase; Chain A / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Metal-dependent hydrolases / Metal-dependent hydrolase / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein Tat / Dipeptidyl peptidase 4 / Adenosine deaminase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
BOS TAURUS (domestic cattle)
HUMAN IMMUNODEFICIENCY VIRUS TYPE 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsWeihofen, W.A. / Liu, J. / Reutter, W. / Saenger, W. / Fan, H.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structures of HIV-1 Tat-Derived Nonapeptides Tat-(1-9) and Trp2-Tat-(1-9) Bound to the Active Site of Dipeptidyl-Peptidase Iv (Cd26)
Authors: Weihofen, W.A. / Liu, J. / Reutter, W. / Saenger, W. / Fan, H.
History
DepositionJan 3, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_conn_angle / pdbx_validate_close_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 / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / 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_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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
Revision 3.0Oct 1, 2025Group: 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_validate_chiral / pdbx_validate_close_contact / struct_conn
Item: _atom_site.auth_seq_id / _pdbx_entry_details.has_protein_modification ..._atom_site.auth_seq_id / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_validate_chiral.auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIPEPTIDYL PEPTIDASE IV
B: DIPEPTIDYL PEPTIDASE IV
C: DIPEPTIDYL PEPTIDASE IV
D: DIPEPTIDYL PEPTIDASE IV
E: ADENOSINE DEAMINASE
F: ADENOSINE DEAMINASE
G: ADENOSINE DEAMINASE
H: ADENOSINE DEAMINASE
W: TAT PROTEIN
X: TAT PROTEIN
Y: TAT PROTEIN
Z: TAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)519,08348
Polymers506,61012
Non-polymers12,47336
Water00
1
A: DIPEPTIDYL PEPTIDASE IV
B: DIPEPTIDYL PEPTIDASE IV
E: ADENOSINE DEAMINASE
F: ADENOSINE DEAMINASE
W: TAT PROTEIN
X: TAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,54124
Polymers253,3056
Non-polymers6,23718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: DIPEPTIDYL PEPTIDASE IV
D: DIPEPTIDYL PEPTIDASE IV
G: ADENOSINE DEAMINASE
H: ADENOSINE DEAMINASE
Y: TAT PROTEIN
Z: TAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)259,54124
Polymers253,3056
Non-polymers6,23718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)158.945, 170.273, 239.200
Angle α, β, γ (deg.)90.00, 100.93, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12E
22F
32G
42H

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGTYRTYR1AA40 - 702 - 32
211ARGARGTYRTYR1BB40 - 702 - 32
311ARGARGTYRTYR1CC40 - 702 - 32
411ARGARGTYRTYR1DD40 - 702 - 32
121ASNASNASNASN1AA74 - 28136 - 243
221ASNASNASNASN1BB74 - 28136 - 243
321ASNASNASNASN1CC74 - 28136 - 243
421ASNASNASNASN1DD74 - 28136 - 243
131GLYGLYASPASP1AA296 - 331258 - 293
231GLYGLYASPASP1BB296 - 331258 - 293
331GLYGLYASPASP1CC296 - 331258 - 293
431GLYGLYASPASP1DD296 - 331258 - 293
141GLUGLUSERSER1AA347 - 764309 - 726
241GLUGLUSERSER1BB347 - 764309 - 726
341GLUGLUSERSER1CC347 - 764309 - 726
441GLUGLUSERSER1DD347 - 764309 - 726
112ALAALAPROPRO1EE6 - 556 - 55
212ALAALAPROPRO1FF6 - 556 - 55
312ALAALAPROPRO1GG6 - 556 - 55
412ALAALAPROPRO1HH6 - 556 - 55
122GLUGLUGLYGLY1EE217 - 237217 - 237
222GLUGLUGLYGLY1FF217 - 237217 - 237
322GLUGLUGLYGLY1GG217 - 237217 - 237
422GLUGLUGLYGLY1HH217 - 237217 - 237
132GLUGLUALAALA1EE85 - 10885 - 108
232GLUGLUALAALA1FF85 - 10885 - 108
332GLUGLUALAALA1GG85 - 10885 - 108
432GLUGLUALAALA1HH85 - 10885 - 108
142PHEPHEALAALA1EE144 - 215144 - 215
242PHEPHEALAALA1FF144 - 215144 - 215
342PHEPHEALAALA1GG144 - 215144 - 215
442PHEPHEALAALA1HH144 - 215144 - 215
152GLNGLNPROPRO1EE119 - 126119 - 126
252GLNGLNPROPRO1FF119 - 126119 - 126
352GLNGLNPROPRO1GG119 - 126119 - 126
452GLNGLNPROPRO1HH119 - 126119 - 126
162THRTHRILEILE1EE57 - 7257 - 72
262THRTHRILEILE1FF57 - 7257 - 72
362THRTHRILEILE1GG57 - 7257 - 72
462THRTHRILEILE1HH57 - 7257 - 72
172HISHISGLUGLU1EE241 - 277241 - 277
272HISHISGLUGLU1FF241 - 277241 - 277
372HISHISGLUGLU1GG241 - 277241 - 277
472HISHISGLUGLU1HH241 - 277241 - 277
182ASPASPTYRTYR1EE338 - 351338 - 351
282ASPASPTYRTYR1FF338 - 351338 - 351
382ASPASPTYRTYR1GG338 - 351338 - 351
482ASPASPTYRTYR1HH338 - 351338 - 351
192LYSLYSASNASN1EE284 - 293284 - 293
292LYSLYSASNASN1FF284 - 293284 - 293
392LYSLYSASNASN1GG284 - 293284 - 293
492LYSLYSASNASN1HH284 - 293284 - 293
1102PROPROLEULEU4EE297 - 335297 - 335
2102PROPROLEULEU4FF297 - 335297 - 335
3102PROPROLEULEU4GG297 - 335297 - 335
4102PROPROLEULEU4HH297 - 335297 - 335

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.78, -0.593, -0.203), (-0.586, 0.577, 0.568), (-0.22, 0.562, -0.797)56.66322, -47.59455, 192.04016
2given(-0.997, -0.032, 0.072), (0.031, -0.999, -0.018), (0.072, -0.016, 0.997)-4.96595, 14.8425, -116.32928
3given(0.744, 0.62, -0.251), (0.648, -0.575, 0.5), (0.165, -0.534, -0.829)76.30225, -98.93713, 295.61942
4given(-0.772, 0.577, -0.264), (0.61, 0.558, -0.563), (-0.178, -0.596, -0.783)-70.63954, 17.53247, 286.85556
5given(-0.757, -0.597, 0.264), (0.634, -0.575, 0.517), (-0.157, 0.559, 0.814)-37.5231, 88.54301, 80.94585
6given(0.989, 0.073, -0.125), (0.066, -0.996, -0.059), (-0.129, 0.05, -0.99)-28.64116, 22.80677, 350.30649
DetailsTHE COMPLEX DESCRIBED BY REMARK 350 BELOW IS OF THETYPE A2B2, WHERE CHAINS A AND B ARE IN CONTACT WITHEACH OTHER, AND EACH OF THESE CHAINS IS IN TURN INCOMPLEX WITH CHAINS F AND E RESPECTIVELY.

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Components

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Protein , 2 types, 8 molecules ABCDEFGH

#1: Protein
DIPEPTIDYL PEPTIDASE IV / DPP IV / T-CELL ACTIVATION ANTIGEN CD26 / TP103 / ADENOSINE DEAMINASE COMPLEXING PROTEIN-2 / ADABP


Mass: 84462.617 Da / Num. of mol.: 4 / Fragment: EXTRACELLULAR DOMAIN, RESIDUES 39-766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: KIDNEY / Plasmid: PFASTBACHTC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 CELLS / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Protein
ADENOSINE DEAMINASE / ADENOSINE AMINOHYDROLASE


Mass: 41089.594 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: SIGMA, TYPE VI, FROM CALF INTESTINAL MUCOSA / Source: (natural) BOS TAURUS (domestic cattle) / Organ: INTESTINAL MUCOSA / References: UniProt: P56658, adenosine deaminase

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Protein/peptide / Non-polymers , 2 types, 8 molecules WXYZ

#3: Protein/peptide
TAT PROTEIN / TRANSACTIVATING REGULATORY PROTEIN


Mass: 1100.244 Da / Num. of mol.: 4
Fragment: HIV-1 TAT PROTEIN DERIVED N-TERMINAL NONAPEPTIDE, RESIDUES 1-9
Mutation: YES / Source method: obtained synthetically
Details: ASP2TRP VARIANT OF HIV-1 TAT PROTEIN DERIVED N-TERMINAL NONAPEPTIDE
Source: (synth.) HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 / References: UniProt: P12506
#9: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn

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Sugars , 5 types, 32 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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.: 10
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
#6: Polysaccharide
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpb1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1b_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#8: 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.: 14
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

Compound detailsENGINEERED MUTATION ASP 2 TRP, CHAINS W, X, Y AND Z
Has protein modificationY
Sequence detailsTHE CONFLICTS DESCRIBED WITH ANNOTATION FOR THIS REMARK HAS BEEN DESCRIBED IN J. PHARM. BIOMED. ...THE CONFLICTS DESCRIBED WITH ANNOTATION FOR THIS REMARK HAS BEEN DESCRIBED IN J. PHARM. BIOMED. ANAL. 14:1513-1519(1996). PUBMED ID: 8877857.

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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: 3.14 Å3/Da / Density % sol: 60.79 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 3.15→30 Å / Num. obs: 97782 / % possible obs: 89 % / Observed criterion σ(I): 2.6 / Redundancy: 2.5 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.7
Reflection shellResolution: 3.15→3.26 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.6 / % possible all: 81

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W1I

1w1i


Resolution: 3.15→30 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.887 / SU B: 21.415 / SU ML: 0.346 / Cross valid method: THROUGHOUT / ESU R Free: 0.502 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1925 2 %RANDOM
Rwork0.227 ---
obs0.227 94691 89.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.38 Å20 Å21.4 Å2
2---1.9 Å20 Å2
3----2.95 Å2
Refinement stepCycle: LAST / Resolution: 3.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35292 0 804 0 36096
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02141545
X-RAY DIFFRACTIONr_bond_other_d0.0020.0232136
X-RAY DIFFRACTIONr_angle_refined_deg1.5181.9363863
X-RAY DIFFRACTIONr_angle_other_deg0.948378891
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1767.58652
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.56624.1121780
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.616156022
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.10515184
X-RAY DIFFRACTIONr_chiral_restr0.1050.25544
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0270962
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0211766
X-RAY DIFFRACTIONr_nbd_refined0.2160.37198
X-RAY DIFFRACTIONr_nbd_other0.2090.331675
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0960.520330
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.51179
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1780.513
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3020.324
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.3107
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4030.512
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5561.522111
X-RAY DIFFRACTIONr_mcbond_other0.3271.58756
X-RAY DIFFRACTIONr_mcangle_it1.013235120
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.102317274
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8984.515399
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A10693tight positional0.010.05
12B10693tight positional0.010.05
13C10693tight positional0.010.05
14D10693tight positional0.010.05
21E3859tight positional0.010.05
22F3859tight positional0.010.05
23G3859tight positional0.010.05
24H3859tight positional0.010.05
21E610medium positional0.230.5
22F610medium positional0.260.5
23G610medium positional0.260.5
24H610medium positional0.230.5
11A10693tight thermal0.020.5
12B10693tight thermal0.020.5
13C10693tight thermal0.020.5
14D10693tight thermal0.020.5
21E3859tight thermal0.030.5
22F3859tight thermal0.020.5
23G3859tight thermal0.020.5
24H3859tight thermal0.020.5
21E610medium thermal0.272
22F610medium thermal0.122
23G610medium thermal0.122
24H610medium thermal0.132
LS refinement shellResolution: 3.15→3.23 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.384 135
Rwork0.356 6358

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