[English] 日本語
Yorodumi
- PDB-1w1i: Crystal structure of dipeptidyl peptidase IV (DPPIV or CD26) in c... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w1i
TitleCrystal structure of dipeptidyl peptidase IV (DPPIV or CD26) in complex with adenosine deaminase
Components
  • ADENOSINE DEAMINASE
  • DIPEPTIDYL PEPTIDASE IV
KeywordsHYDROLASE / HYDROLASE-COMPLEX / DIPETIDYL PEPTIDASE IV / DPPIV / CD26 / ALPHA/BETA-HYDROLASE FOLD / BETA-PROPELLER FOLD / PROTEIN-PROTEIN COMPLEX / ADENOSINE DEAMINASE / ADA / SERINE PROTEASE / AMINOPEPTIDASE
Function / homology
Function and homology information


negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / inosine biosynthetic process / purine ribonucleoside monophosphate biosynthetic process / adenosine deaminase / hypoxanthine salvage / adenosine catabolic process / glucagon processing / adenosine deaminase activity ...negative regulation of adenosine receptor signaling pathway / cytoplasmic vesicle lumen / 2'-deoxyadenosine deaminase activity / inosine biosynthetic process / purine ribonucleoside monophosphate biosynthetic process / adenosine deaminase / hypoxanthine salvage / adenosine catabolic process / glucagon processing / adenosine deaminase activity / negative regulation of neutrophil chemotaxis / regulation of cell-cell adhesion mediated by integrin / Synthesis, secretion, and inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) / negative regulation of extracellular matrix disassembly / dipeptidyl-peptidase IV / chemorepellent activity / psychomotor behavior / intercellular canaliculus / nucleotide metabolic process / dipeptidyl-peptidase activity / peptide hormone processing / anchoring junction / locomotory exploration behavior / lamellipodium membrane / endocytic vesicle / behavioral fear response / endothelial cell migration / aminopeptidase activity / receptor-mediated endocytosis of virus by host cell / T cell costimulation / serine-type peptidase activity / T cell activation / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / lamellipodium / virus receptor activity / protease binding / membrane fusion / response to hypoxia / lysosome / receptor-mediated virion attachment to host cell / cell adhesion / apical plasma membrane / membrane raft / symbiont entry into host cell / external side of plasma membrane / signaling receptor binding / lysosomal membrane / serine-type endopeptidase activity / focal adhesion / positive regulation of cell population proliferation / cell surface / protein homodimerization activity / proteolysis / extracellular exosome / extracellular region / zinc ion binding / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
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 / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / : ...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 / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / 8 Propeller / Methanol Dehydrogenase; Chain A / 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
Dipeptidyl peptidase 4 / Adenosine deaminase
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
BOS TAURUS (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.03 Å
AuthorsWeihofen, W.A. / Liu, J. / Reutter, W. / Saenger, W. / Fan, H.
CitationJournal: J. Biol. Chem. / Year: 2004
Title: Crystal structure of CD26/dipeptidyl-peptidase IV in complex with adenosine deaminase reveals a highly amphiphilic interface.
Authors: Weihofen, W.A. / Liu, J. / Reutter, W. / Saenger, W. / Fan, H.
History
DepositionJun 22, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 2, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 25, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / database_PDB_caveat / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / 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_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 3.0Jul 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_chiral / 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 / _database_PDB_caveat.text / _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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_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.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 3.1Dec 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 3.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)511,95244
Polymers499,6828
Non-polymers12,27036
Water00
1
A: DIPEPTIDYL PEPTIDASE IV
B: DIPEPTIDYL PEPTIDASE IV
E: ADENOSINE DEAMINASE
F: ADENOSINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)255,87422
Polymers249,8414
Non-polymers6,03318
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: DIPEPTIDYL PEPTIDASE IV
D: DIPEPTIDYL PEPTIDASE IV
G: ADENOSINE DEAMINASE
H: ADENOSINE DEAMINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)256,07822
Polymers249,8414
Non-polymers6,23718
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)158.065, 168.504, 236.842
Angle α, β, γ (deg.)90.00, 100.54, 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:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGTYRTYRAA40 - 702 - 32
211ARGARGTYRTYRBB40 - 702 - 32
311ARGARGTYRTYRCC40 - 702 - 32
411ARGARGTYRTYRDD40 - 702 - 32
121ASNASNASNASNAA74 - 28136 - 243
221ASNASNASNASNBB74 - 28136 - 243
321ASNASNASNASNCC74 - 28136 - 243
421ASNASNASNASNDD74 - 28136 - 243
131GLYGLYASPASPAA296 - 331258 - 293
231GLYGLYASPASPBB296 - 331258 - 293
331GLYGLYASPASPCC296 - 331258 - 293
431GLYGLYASPASPDD296 - 331258 - 293
141GLUGLUSERSERAA347 - 764309 - 726
241GLUGLUSERSERBB347 - 764309 - 726
341GLUGLUSERSERCC347 - 764309 - 726
441GLUGLUSERSERDD347 - 764309 - 726
112ALAALAPROPROEE6 - 556 - 55
212ALAALAPROPROFF6 - 556 - 55
312ALAALAPROPROGG6 - 556 - 55
412ALAALAPROPROHH6 - 556 - 55
122GLUGLUGLYGLYEE217 - 237217 - 237
222GLUGLUGLYGLYFF217 - 237217 - 237
322GLUGLUGLYGLYGG217 - 237217 - 237
422GLUGLUGLYGLYHH217 - 237217 - 237
132GLUGLUALAALAEE85 - 10885 - 108
232GLUGLUALAALAFF85 - 10885 - 108
332GLUGLUALAALAGG85 - 10885 - 108
432GLUGLUALAALAHH85 - 10885 - 108
142PHEPHEALAALAEE144 - 215144 - 215
242PHEPHEALAALAFF144 - 215144 - 215
342PHEPHEALAALAGG144 - 215144 - 215
442PHEPHEALAALAHH144 - 215144 - 215
152GLNGLNPROPROEE119 - 126119 - 126
252GLNGLNPROPROFF119 - 126119 - 126
352GLNGLNPROPROGG119 - 126119 - 126
452GLNGLNPROPROHH119 - 126119 - 126
162THRTHRILEILEEE57 - 7257 - 72
262THRTHRILEILEFF57 - 7257 - 72
362THRTHRILEILEGG57 - 7257 - 72
462THRTHRILEILEHH57 - 7257 - 72
172HISHISVALVALEE241 - 280241 - 280
272HISHISVALVALFF241 - 280241 - 280
372HISHISVALVALGG241 - 280241 - 280
472HISHISVALVALHH241 - 280241 - 280
182ASPASPTYRTYREE338 - 351338 - 351
282ASPASPTYRTYRFF338 - 351338 - 351
382ASPASPTYRTYRGG338 - 351338 - 351
482ASPASPTYRTYRHH338 - 351338 - 351
192LYSLYSLEULEUEE284 - 335284 - 335
292LYSLYSLEULEUFF284 - 335284 - 335
392LYSLYSLEULEUGG284 - 335284 - 335
492LYSLYSLEULEUHH284 - 335284 - 335

NCS ensembles :
ID
1
2
DetailsTHE COMPLEX DESCRIBED BY REMARK 350 BELOW IS OF THETYPE A2B2, WHERE CHAINS A AND B ARE IN CONTACTWITH EACH OTHER, AND EACH OF THESE CHAINS IS IN TURNIN COMPLEX WITH CHAINS F AND E RESPECTIVELY.

-
Components

-
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 39 - 766
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Organ: KIDNEY / Plasmid: PFASTBACHTC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P27487, dipeptidyl-peptidase IV
#2: Protein
ADENOSINE DEAMINASE / ADENOSINE AMINOHYDROLASE


Mass: 40457.898 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) / Tissue: INTESTINAL MUCOSA / References: UniProt: P56658, adenosine deaminase

-
Sugars , 5 types, 32 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-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[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_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
#4: 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.: 9
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
#5: 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
#6: Polysaccharide alpha-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
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#7: 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.: 15
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

-
Non-polymers , 1 types, 4 molecules

#8: Chemical
ChemComp-ZN / ZINC ION


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

-
Details

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.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 60.36 %
Crystal growpH: 8 / Details: pH 8.00

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.914
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 30, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.914 Å / Relative weight: 1
ReflectionResolution: 3.03→30 Å / Num. obs: 100817 / % possible obs: 85.3 % / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shellResolution: 3.03→3.15 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.1 / % possible all: 81.3

-
Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1N1M AND 1KRM

1n1m

1krm


Resolution: 3.03→30 Å / Cor.coef. Fo:Fc: 0.906 / Cor.coef. Fo:Fc free: 0.867 / SU B: 21.957 / SU ML: 0.378 / Cross valid method: THROUGHOUT / ESU R Free: 0.498 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-3 OF CHAINS E,F,G,H OF ADA ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.257 2048 2 %RANDOM
Rwork0.224 ---
obs0.224 98926 85.5 %-
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: 52.46 Å2
Baniso -1Baniso -2Baniso -3
1-4.45 Å20 Å21.75 Å2
2---2.35 Å20 Å2
3----1.47 Å2
Refinement stepCycle: LAST / Resolution: 3.03→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35087 0 790 0 35877
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02141313
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.341.9363508
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9637.58614
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.82724.1081772
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.946155999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7915184
X-RAY DIFFRACTIONr_chiral_restr0.1160.25519
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.317208
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.51927
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.358
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2820.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.646221822
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.141334915
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.608217155
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.053315310
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
11A5696tight positional0.020.05
12B5696tight positional0.020.05
13C5696tight positional0.020.05
14D5696tight positional0.020.05
21E2372tight positional0.020.05
22F2372tight positional0.020.05
23G2372tight positional0.020.05
24H2372tight positional0.020.05
11A5696tight thermal0.040.5
12B5696tight thermal0.040.5
13C5696tight thermal0.040.5
14D5696tight thermal0.040.5
21E2372tight thermal0.060.5
22F2372tight thermal0.040.5
23G2372tight thermal0.030.5
24H2372tight thermal0.030.5
LS refinement shellResolution: 3.03→3.11 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.417 154
Rwork0.367 6906

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more