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- PDB-3ala: Crystal structure of vascular adhesion protein-1 in space group C2 -

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Basic information

Entry
Database: PDB / ID: 3ala
TitleCrystal structure of vascular adhesion protein-1 in space group C2
ComponentsMembrane primary amine oxidase
KeywordsOXIDOREDUCTASE / membrane primary amine oxidase / vascular adhesion protein-1 / VAP-1 / semicarbazide-sensitive amine oxidase / SSAO / copper containing amine oxidase
Function / homology
Function and homology information


negative regulation of primary amine oxidase activity / primary amine oxidase activity / : / primary-amine oxidase / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion ...negative regulation of primary amine oxidase activity / primary amine oxidase activity / : / primary-amine oxidase / amine metabolic process / Phase I - Functionalization of compounds / microvillus / quinone binding / early endosome / cell adhesion / inflammatory response / copper ion binding / protein heterodimerization activity / response to antibiotic / calcium ion binding / Golgi apparatus / cell surface / endoplasmic reticulum / membrane / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain ...Copper amine oxidase, N3-terminal / Copper amine oxidase, N2-terminal / Copper amine oxidase, N2 domain / Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain / Beta-galactosidase; Chain A, domain 5 / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Amine oxidase [copper-containing] 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsErnberg, K.E. / McGrath, A.P. / Guss, J.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: A new crystal form of human vascular adhesion protein 1
Authors: Ernberg, K. / McGrath, A.P. / Peat, T.S. / Adams, T.E. / Xiao, X. / Pham, T. / Newman, J. / McDonald, I.A. / Collyer, C.A. / Guss, J.M.
History
DepositionJul 29, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_conn_angle / pdbx_unobs_or_zero_occ_residues / pdbx_validate_chiral / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Membrane primary amine oxidase
B: Membrane primary amine oxidase
C: Membrane primary amine oxidase
D: Membrane primary amine oxidase
E: Membrane primary amine oxidase
F: Membrane primary amine oxidase
G: Membrane primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)595,57651
Polymers584,6097
Non-polymers10,96744
Water4,143230
1
A: Membrane primary amine oxidase
B: Membrane primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,16715
Polymers167,0312
Non-polymers3,13613
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16430 Å2
ΔGint-101 kcal/mol
Surface area45230 Å2
MethodPISA
2
C: Membrane primary amine oxidase
D: Membrane primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,29615
Polymers167,0312
Non-polymers3,26513
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16720 Å2
ΔGint-103 kcal/mol
Surface area45670 Å2
MethodPISA
3
E: Membrane primary amine oxidase
hetero molecules

E: Membrane primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,07514
Polymers167,0312
Non-polymers3,04412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area16430 Å2
ΔGint-103 kcal/mol
Surface area44920 Å2
MethodPISA
4
F: Membrane primary amine oxidase
G: Membrane primary amine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,07514
Polymers167,0312
Non-polymers3,04412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16390 Å2
ΔGint-99 kcal/mol
Surface area45140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)394.468, 115.826, 179.286
Angle α, β, γ (deg.)90.00, 112.34, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
12A
22B
32C
42D
52E
62G

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1112A57 - 77
2112B57 - 77
3112C57 - 77
4112D57 - 77
5112E57 - 77
6112F57 - 77
7112G57 - 77
1212A90 - 269
2212B90 - 269
3212C90 - 269
4212D90 - 269
5212E90 - 269
6212F90 - 269
7212G90 - 269
1312A291 - 467
2312B291 - 467
3312C291 - 467
4312D291 - 467
5312E291 - 467
6312F291 - 467
7312G291 - 467
1412A475 - 502
2412B475 - 502
3412C475 - 502
4412D475 - 502
5412E475 - 502
6412F475 - 502
7412G475 - 502
1512A506 - 532
2512B506 - 532
3512C506 - 532
4512D506 - 532
5512E506 - 532
6512F506 - 532
7512G506 - 532
1614A533 - 577
2614B533 - 577
3614C533 - 577
4614D533 - 577
5614E533 - 577
6614F533 - 577
7614G533 - 577
1712A578 - 582
2712B578 - 582
3712C578 - 582
4712D578 - 582
5712E578 - 582
6712F578 - 582
7712G578 - 582
1814A583 - 602
2814B583 - 602
3814C583 - 602
4814D583 - 602
5814E583 - 602
6814F583 - 602
7814G583 - 602
1912A603 - 690
2912B603 - 690
3912C603 - 690
4912D603 - 690
5912E603 - 690
6912F603 - 690
7912G603 - 690
11014A691 - 750
21014B691 - 750
31014C691 - 750
41014D691 - 750
51014E691 - 750
61014F691 - 750
71014G691 - 750
11112A751 - 761
21112B751 - 761
31112C751 - 761
41112D751 - 761
51112E751 - 761
61112F751 - 761
71112G751 - 761
1124A78 - 89
2124B78 - 89
3124C78 - 89
4124D78 - 89
5124E78 - 89
6124G78 - 89

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 7 molecules ABCDEFG

#1: Protein
Membrane primary amine oxidase / Copper amine oxidase / Semicarbazide-sensitive amine oxidase / SSAO / Vascular adhesion protein 1 / ...Copper amine oxidase / Semicarbazide-sensitive amine oxidase / SSAO / Vascular adhesion protein 1 / VAP-1 / HPAO


Mass: 83515.586 Da / Num. of mol.: 7 / Fragment: Extracellular domain, UNP residues 33-763
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AOC3, VAP1 / Plasmid: pLO-CMV / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec8 / References: UniProt: Q16853, primary-amine oxidase

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Sugars , 6 types, 22 molecules

#2: Polysaccharide
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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.: 6
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
#4: Polysaccharide
beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 5
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)][a-D-GlcpNAc]{[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#5: 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.: 1
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
#6: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
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)][a-L-Fucp]{}}}LINUCSPDB-CARE
#10: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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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Non-polymers , 4 types, 252 molecules

#7: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cu
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#11: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O

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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: 3.24 Å3/Da / Density % sol: 62.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.9→110.43 Å / Num. all: 163097 / Num. obs: 163097 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.192 / Rsym value: 0.192 / Net I/σ(I): 9.4
Reflection shellResolution: 2.9→3.06 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.883 / Mean I/σ(I) obs: 1.9 / Rsym value: 0.883 / % possible all: 98.1

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2c10

2c10


Resolution: 2.9→110.4 Å / Cor.coef. Fo:Fc: 0.875 / Cor.coef. Fo:Fc free: 0.831 / Occupancy max: 1 / Occupancy min: 0 / SU B: 18.919 / SU ML: 0.353 / SU R Cruickshank DPI: 0.7645
Isotropic thermal model: Initially isotropic B-factors were refined. Thereafter B-factors for solvent water molecules were set to 43.1 and an overall B-factor was refined.
Cross valid method: THROUGHOUT / ESU R: 0.759 / ESU R Free: 0.427 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28621 8187 5 %RANDOM
Rwork0.25001 ---
obs0.25183 154651 98.26 %-
all-162838 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 40.0431 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20.87 Å2
2--1.35 Å20 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.9→110.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38113 0 678 230 39021
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02240158
X-RAY DIFFRACTIONr_bond_other_d0.0040.0226455
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.96354920
X-RAY DIFFRACTIONr_angle_other_deg0.9833.00163936
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.08954935
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.4323.3261807
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.513155429
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.20415214
X-RAY DIFFRACTIONr_chiral_restr0.0980.25923
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02145274
X-RAY DIFFRACTIONr_gen_planes_other0.0030.028649
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
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
11A3088tight positional0.040.05
11B3088tight positional0.040.05
11C3088tight positional0.040.05
11D3088tight positional0.040.05
11E3088tight positional0.040.05
11F3088tight positional0.050.05
11G3088tight positional0.050.05
11A5128medium positional0.040.5
11B5128medium positional0.050.5
11C5128medium positional0.050.5
11D5128medium positional0.050.5
11E5128medium positional0.040.5
11F5128medium positional0.050.5
11G5128medium positional0.060.5
22A96medium positional0.360.5
22B96medium positional0.380.5
22C96medium positional0.480.5
22D96medium positional0.330.5
22E96medium positional0.460.5
22G96medium positional0.70.5
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 584 -
Rwork0.317 11137 -
obs--96.14 %

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