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- PDB-4gty: Crystal structure of mouse Enpp1 in complex with GMP -

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Basic information

Entry
Database: PDB / ID: 4gty
TitleCrystal structure of mouse Enpp1 in complex with GMP
ComponentsEctonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I
KeywordsHYDROLASE / Bone Mineralization / Phosphodiesterase
Function / homology
Function and homology information


dinucleotide phosphatase activity / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity ...dinucleotide phosphatase activity / alkylglycerophosphoethanolamine phosphodiesterase / sphingolipid catabolic process / phospholipid catabolic process / phosphatidylcholine catabolic process / lysophospholipase activity / positive regulation of lamellipodium morphogenesis / phosphodiesterase I activity / scavenger receptor activity / alkylglycerophosphoethanolamine phosphodiesterase activity / polysaccharide binding / positive regulation of oligodendrocyte differentiation / hydrolase activity, acting on ester bonds / negative regulation of cell-matrix adhesion / positive regulation of epithelial cell migration / positive regulation of focal adhesion assembly / estrous cycle / phospholipid metabolic process / positive regulation of substrate adhesion-dependent cell spreading / regulation of cell migration / cell chemotaxis / positive regulation of peptidyl-tyrosine phosphorylation / nucleic acid binding / immune response / calcium ion binding / positive regulation of cell population proliferation / extracellular space / zinc ion binding / extracellular region / membrane / metal ion binding / plasma membrane
Similarity search - Function
Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase ...Extracellular Endonuclease; Chain A / Extracellular Endonuclease, subunit A / Somatomedin B domain, chordata / Somatomedin B -like domains / Somatomedin B domain / Somatomedin B-like domain superfamily / Somatomedin B domain / Somatomedin B domain (SMB) signature. / Somatomedin B (SMB) domain profile. / Type I phosphodiesterase/nucleotide pyrophosphatase/phosphate transferase / Type I phosphodiesterase / nucleotide pyrophosphatase / Extracellular Endonuclease, subunit A / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease superfamily / DNA/RNA non-specific endonuclease / DNA/RNA non-specific endonuclease / His-Me finger superfamily / Alkaline Phosphatase, subunit A / Alkaline Phosphatase, subunit A / Alkaline-phosphatase-like, core domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-MONOPHOSPHATE / Ectonucleotide pyrophosphatase/phosphodiesterase 1 / Ectonucleotide pyrophosphatase/phosphodiesterase family member 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.19 Å
AuthorsKato, K. / Nishimasu, H. / Ishitani, R. / Nureki, O.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Crystal structure of Enpp1, an extracellular glycoprotein involved in bone mineralization and insulin signaling.
Authors: Kato, K. / Nishimasu, H. / Okudaira, S. / Mihara, E. / Ishitani, R. / Takagi, J. / Aoki, J. / Nureki, O.
History
DepositionAug 29, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Jun 20, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / 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_conn_angle / 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.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.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 / _struct_conn.conn_type_id / _struct_conn.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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
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: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,57116
Polymers189,1202
Non-polymers3,45014
Water0
1
A: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6108
Polymers94,5601
Non-polymers2,0497
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9618
Polymers94,5601
Non-polymers1,4017
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)104.863, 104.863, 174.831
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Ectonucleotide pyrophosphatase/phosphodiesterase family member 2, Alkaline phosphodiesterase I / E-NPP 2 / Autotaxin / Extracellular lysophospholipase D / LysoPLD / Ectonucleotide ...E-NPP 2 / Autotaxin / Extracellular lysophospholipase D / LysoPLD / Ectonucleotide pyrophosphatase/phosphodiesterase 1 / isoform CRA_d


Mass: 94560.203 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 51-59, 92-905 / Mutation: K59R
Source method: isolated from a genetically manipulated source
Details: THE FUSION PROTEIN OF ENPP2 (UNP RESIDUES 51-59) AND ENPP1 (UNP RESIDUES 92-905)
Source: (gene. exp.) Mus musculus (house mouse) / Cell: mammalian cells / Gene: Enpp2, Npps2, Pdnp2, Enpp1, mCG_9001 / Plasmid: modified pcDNA3.1 / Cell line (production host): HEK293S GnT1- / Production host: Homo sapiens (human)
References: UniProt: Q9R1E6, UniProt: G3X9S2, alkylglycerophosphoethanolamine phosphodiesterase

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Sugars , 3 types, 6 molecules

#2: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-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.: 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
#4: 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.: 4
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 , 3 types, 8 molecules

#5: Chemical ChemComp-5GP / GUANOSINE-5'-MONOPHOSPHATE / Guanosine monophosphate


Mass: 363.221 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14N5O8P
#6: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Details

Sequence detailsTHE FUSION PROTEIN OF ENPP2 (UNP RESIDUES 51-59) AND ENPP1 (UNP RESIDUES 92-905)

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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: 2.93 Å3/Da / Density % sol: 58.08 % / Mosaicity: 0.393 °
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: PEG 600, MgOAc, NaCl, ZnSO4, pH 4.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Jun 22, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.19→50 Å / Num. all: 35428 / Num. obs: 35428 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Rmerge(I) obs: 0.169 / Χ2: 1.507 / Net I/σ(I): 6.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.2-3.264.10.52117580.695198.4
3.26-3.314.20.51417860.73198.9
3.31-3.384.30.50517400.758198.3
3.38-3.454.10.51817261.044198.1
3.45-3.524.40.52918051.396198.4
3.52-3.64.50.47717520.985198.5
3.6-3.694.90.50817341.913198.4
3.69-3.794.70.42817671.285198.6
3.79-3.915.20.44817681.757197.8
3.91-4.035.50.38417571.598198.3
4.03-4.186.70.29317611.228199.5
4.18-4.347.10.25918131.385199.5
4.34-4.547.60.21417741.525199.7
4.54-4.787.90.18717711.559199.6
4.78-5.088.20.15817861.604199.9
5.08-5.478.10.16517721.433199.8
5.47-6.028.40.14917811.538199.7
6.02-6.898.80.12617931.768199.9
6.89-8.679.80.07817891.829199.9
8.67-5010.80.04617952.044199.6

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
BSSdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GTW

4gtw


Resolution: 3.19→49.047 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7755 / SU ML: 1.01 / σ(F): 2 / Phase error: 30.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2808 1759 4.97 %
Rwork0.2581 --
all0.2593 35397 -
obs0.2593 35397 98.96 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 17.658 Å2 / ksol: 0.295 e/Å3
Displacement parametersBiso max: 208.4 Å2 / Biso mean: 92.8261 Å2 / Biso min: 34.94 Å2
Baniso -1Baniso -2Baniso -3
1-6.4465 Å20 Å2-0 Å2
2--6.4465 Å2-0 Å2
3----12.893 Å2
Refinement stepCycle: LAST / Resolution: 3.19→49.047 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10971 0 210 0 11181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611560
X-RAY DIFFRACTIONf_angle_d0.85415756
X-RAY DIFFRACTIONf_chiral_restr0.0441761
X-RAY DIFFRACTIONf_plane_restr0.0042002
X-RAY DIFFRACTIONf_dihedral_angle_d15.5644140
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1903-3.27660.44511370.42132554269198
3.2766-3.3730.41081310.38762549268098
3.373-3.48180.36621390.38552562270198
3.4818-3.60620.35691450.34122581272698
3.6062-3.75060.33361320.33452571270398
3.7506-3.92120.35081360.29172549268598
3.9212-4.12780.27791360.24552590272699
4.1278-4.38630.24841370.212626002737100
4.3863-4.72470.21291340.193526292763100
4.7247-5.19970.23141400.190726072747100
5.1997-5.9510.26871370.221925902727100
5.951-7.49330.23821310.208826402771100
7.4933-49.05250.20871240.209326162740100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3673-0.1156-1.12830.2039-0.05560.999-0.01220.47820.2864-0.17170.17450.0701-0.11240.118300.7593-0.0792-0.03440.51170.07350.656-3.394731.6789-25.0118
20.7986-0.67180.64140.963-1.35592.07230.08190.65340.4314-0.58610.033-0.1656-0.6037-0.3826-0.00390.7069-0.1080.09770.64570.08620.7012-0.840838.3422-29.1731
30.77740.1118-0.29790.7580.37330.330.05510.35780.2424-0.4617-0.12690.06370.2987-0.55690.03170.9757-0.3327-0.25161.1147-0.05120.4304-20.20911.5384-41.5914
40.6577-0.2932-0.88710.15610.40151.10230.09880.5413-0.0037-0.47780.263-0.11310.4604-0.99280.16350.59340.0427-0.2560.25460.06660.3531-9.726924.235-25.8193
50.5131-0.0961-0.4390.00360.09840.38780.19040.50680.25960.0670.31540.2335-0.2004-0.53460.2630.368-0.2947-0.09230.72930.04820.8053-31.371618.0591-3.9346
60.77780.1464-0.98930.3551-0.13481.17550.18210.4253-0.31330.03270.2519-0.18540.9689-0.76640.02150.703-0.3086-0.25290.95930.15530.7918-34.97064.623-7.4614
70.8598-0.1267-0.80720.2052-0.18131.0588-0.07220.2637-0.12490.19940.22720.07410.2916-0.02820.00090.4591-0.1186-0.21280.45120.0490.4389-23.107910.8435-14.5174
80.94270.069-0.82461.4485-0.23292.17840.2594-0.54340.26260.7850.08260.184-0.3658-0.33040.0580.43160.28290.07650.5569-0.06340.4807-22.672727.504327.58
90.1528-0.1237-0.00870.7629-0.54850.4618-0.1161-0.34480.13690.41210.1466-0.0432-0.40470.50450.00610.92520.0598-0.21431.1934-0.15560.49613.362622.10939.8401
101.12590.213-0.51020.422-0.35681.8394-0.0015-0.2493-0.09960.0326-0.0019-0.1244-0.21330.62160.00230.3598-0.0791-0.12280.6116-0.17970.537410.673127.658611.4753
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 170:278)A170 - 278
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 279:415)A279 - 415
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 416:481)A416 - 481
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 482:573)A482 - 573
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 574:628)A574 - 628
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 629:758)A629 - 758
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 759:902)A759 - 902
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 170:415)B170 - 415
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 416:526)B416 - 526
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 527:902)B527 - 902

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Yorodumi

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  • 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

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