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- PDB-2x85: Tailspike protein of E. coli bacteriophage HK620 in complex with ... -

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Basic information

Entry
Database: PDB / ID: 2x85
TitleTailspike protein of E. coli bacteriophage HK620 in complex with hexasaccharide
ComponentsTAILSPIKE PROTEIN HK620
KeywordsVIRAL PROTEIN / VIRAL ADHESION PROTEIN / ENDO-N-ACETYLGLUCOSAMINIDASE / HYDROLASE / TAILSPIKE
Function / homology
Function and homology information


biological process involved in interaction with host / viral life cycle / virion component / metal ion binding
Similarity search - Function
Elongation Factor Tu (Ef-tu); domain 3 - #250 / Hk620 tailspike protein, N-terminal domain-like / Phage spike trimer 2 / Phage spike trimer / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Arc Repressor Mutant, subunit A / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like ...Elongation Factor Tu (Ef-tu); domain 3 - #250 / Hk620 tailspike protein, N-terminal domain-like / Phage spike trimer 2 / Phage spike trimer / Bacteriophage P22 tailspike, N-terminal / Phage P22 tailspike-like, N-terminal domain superfamily / Head binding / Arc Repressor Mutant, subunit A / Single-stranded right-handed beta-helix, Pectin lyase-like / Pectate Lyase C-like / Pectin lyase fold / Pectin lyase fold/virulence factor / 3 Solenoid / Elongation Factor Tu (Ef-tu); domain 3 / Helix non-globular / Special / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesENTEROBACTERIA PHAGE HK620 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsLorenzen, N.K. / Mueller, J.J. / Heinemann, U. / Seckler, R. / Barbirz, S.
Citation
Journal: Glycobiology / Year: 2013
Title: Single Amino Acid Exchange in Bacteriophage Hk620 Tailspike Protein Results in Thousand-Fold Increase of its Oligosaccharide Affinity.
Authors: Broeker, N.K. / Gohlke, U. / Muller, J.J. / Uetrecht, C. / Heinemann, U. / Seckler, R. / Barbirz, S.
#1: Journal: Mol.Microbiol. / Year: 2008
Title: Crystal Structure of Escherichia Coli Phage Hk620 Tailspike: Podoviral Tailspike Endoglycosidase Modules are Evolutionarily Related
Authors: Barbirz, S. / Mueller, J.J. / Uetrecht, C. / Clark, A.J. / Heinemann, U. / Seckler, R.
History
DepositionMar 5, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references / Version format compliance
Revision 1.2Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.3Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / 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 / struct_asym / struct_conn / struct_conn_type / 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.pdbx_formal_charge / _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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TAILSPIKE PROTEIN HK620
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9767
Polymers64,7051
Non-polymers1,2716
Water12,448691
1
A: TAILSPIKE PROTEIN HK620
hetero molecules

A: TAILSPIKE PROTEIN HK620
hetero molecules

A: TAILSPIKE PROTEIN HK620
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,92921
Polymers194,1163
Non-polymers3,81318
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
Buried area30700 Å2
ΔGint-118.2 kcal/mol
Surface area48030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.250, 74.250, 174.440
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein TAILSPIKE PROTEIN HK620


Mass: 64705.355 Da / Num. of mol.: 1
Fragment: LACKING THE N-TERMINAL HEAD-BINDING DOMAIN, RESIDUES 111-710
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ENTEROBACTERIA PHAGE HK620 (virus) / Plasmid: PET11D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: Q9AYY6
#2: Polysaccharide alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose- ...alpha-L-rhamnopyranose-(1-6)-alpha-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]alpha-D-galactopyranose-(1-3)-[alpha-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LRhapa1-6DGlcpa1-4[DGlcpNAcb1-3]DGalpa1-3[DGlcpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1a_1-5][a2122h-1a_1-5][a2211m-1a_1-5]/1-2-1-3-4-3/a3-b1_a6-f1_b3-c1_b4-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-D-Galp]{[(3+1)][b-D-GlcpNAc]{}[(4+1)][a-D-Glcp]{[(6+1)][a-L-Rhap]{}}}[(6+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsDELETION 1-110

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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: 2.13 Å3/Da / Density % sol: 42.2 % / Description: NONE
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: VAPOR DIFFUSION, HANGING DROP: PROTEIN CONCENTRATION 8MG/ML. BUFFER: 40MM TRIS, PH7.8, 2MM EDTA, 0.2M NACL. RESERVOIR: 100MM TRIS PH8.5, 3.5M NA-FORMIATE. DROPLET 1.5:1.5 MICROLITER, 0.3 ...Details: VAPOR DIFFUSION, HANGING DROP: PROTEIN CONCENTRATION 8MG/ML. BUFFER: 40MM TRIS, PH7.8, 2MM EDTA, 0.2M NACL. RESERVOIR: 100MM TRIS PH8.5, 3.5M NA-FORMIATE. DROPLET 1.5:1.5 MICROLITER, 0.3 MICROLITER 33MM HEXASACCHARIDE. TEMPERATURE 20 DEGREE CELSIUS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 2, 2009 / Details: GLAS MIRROR
RadiationMonochromator: SI-111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.5→36.31 Å / Num. obs: 77347 / % possible obs: 90.4 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 19.6 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.2
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.8 / % possible all: 66

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VJI

2vji


Resolution: 1.5→37.13 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.982 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.19825 4112 5 %RANDOM
Rwork0.16491 ---
obs0.16659 77347 90.4 %-
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: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20.31 Å20 Å2
2--0.61 Å20 Å2
3----0.92 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4532 0 84 691 5307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0214819
X-RAY DIFFRACTIONr_bond_other_d0.0010.023069
X-RAY DIFFRACTIONr_angle_refined_deg1.331.9346565
X-RAY DIFFRACTIONr_angle_other_deg1.04137432
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1195596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54324.459231
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.09615688
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8211523
X-RAY DIFFRACTIONr_chiral_restr0.0910.2753
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025443
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021011
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_it0.77822971
X-RAY DIFFRACTIONr_mcbond_other0.25521234
X-RAY DIFFRACTIONr_mcangle_it1.22134810
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.014.51848
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.7361755
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
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 221 -
Rwork0.2 4510 -
obs--71.77 %
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)
13.4127-0.6282-1.45327.71023.0213.24330.03320.35380.0254-0.35710.04780.0441-0.0683-0.212-0.0810.08350.0063-0.0160.0810.0430.0445-3.9324-36.3035-18.2926
20.45190.3365-0.34741.5743-0.37040.8114-0.02970.0807-0.0325-0.1022-0.0141-0.03260.0992-0.02870.04380.092-0.0039-0.00430.0935-0.02090.0478-6.5099-48.5065-5.3848
30.3825-0.12130.01570.41940.11671.0336-0.03010.08740.0358-0.0596-0.0301-0.0051-0.1266-0.0220.06020.10660.0163-0.03220.06940.01280.06-3.1184-23.87327.2446
40.54150.208-0.18960.32410.23020.613-0.02030.04640.0139-0.0982-0.0129-0.0355-0.16450.01850.03320.13290.0153-0.03470.05870.03310.05930.472-20.069216.7847
58.8527-1.1142-2.52310.16670.21151.17680.12790.379-0.12030.0598-0.04540.0365-0.457-0.4625-0.08260.37220.3187-0.0130.29080.02050.0908-18.7333-20.861321.31
61.96720.96110.12310.83390.0530.37770.01230.2244-0.1182-0.0803-0.0504-0.04250.0007-0.02390.03810.09920.0131-0.01410.1125-0.00620.0695-2.0466-33.68618.4482
70.3930.066-0.15060.5410.1160.425-0.01290.05310.0329-0.0814-0.03020.0021-0.107-0.02840.04320.09140.0142-0.02820.06070.01120.0537-3.5839-22.30425.8147
81.19130.3072-0.19842.67420.23010.4840.00870.00590.0477-0.0007-0.0205-0.0086-0.05310.02080.01180.0972-0.0062-0.020.08220.02050.05985.0692-21.381330.1392
91.06660.1868-0.17280.28670.02550.4907-0.01240.01510.0221-0.0318-0.03-0.0175-0.08340.0140.04240.06960.0027-0.01730.04960.01180.0583-1.0936-25.443835.3182
101.2575-0.3088-0.10810.39080.1080.3618-0.00420.0227-0.0077-0.0344-0.03190.0588-0.0586-0.0530.03610.06460.0087-0.01790.05720.00050.0592-6.3794-26.008839.4899
116.8752-0.25810.60250.1838-0.28370.47450.08930.2072-0.4075-0.0564-0.03590.03760.0845-0.0015-0.05340.07040.0072-0.01720.099-0.03030.0898-7.3518-35.307742.5805
120.4360.0652-0.01780.38640.06820.4454-0.00410.02310.0625-0.0225-0.02370.0206-0.0732-0.0170.02790.06170.0043-0.01070.04420.00230.0629-1.2391-24.432350.0052
131.4624-0.0837-0.28190.0129-0.03290.3954-0.0182-0.0120.18010.0126-0.0068-0.0262-0.09840.0480.0250.0674-0.0012-0.00810.0403-0.00250.08641.9199-21.054459.2273
141.2150.2944-0.19340.37020.00450.5102-0.0243-0.0069-0.02650.00190.0018-0.012-0.0215-0.01440.02260.05780.0024-0.0030.05560.00410.06281.7856-32.080661.107
150.9266-0.22020.05290.19580.00120.234-0.004-0.00320.08610.0035-0.0073-0.0342-0.04750.02370.01130.0561-0.0051-0.00680.04940.00050.07254.0645-24.231567.0831
161.1781-0.35190.00020.29050.01660.0641-0.0118-0.07030.09810.01580.002-0.0344-0.05950.00020.00980.0608-0.0008-0.00320.0571-0.00040.06650.9158-27.027973.9847
170.7897-0.1310.52550.2571-0.05020.3862-0.0215-0.03260.07960.04-0.0081-0.0425-0.0537-0.01810.02960.074-0.00640.00870.059-0.00160.0705-1.5023-29.195280.4149
181.3103-0.51230.65350.58320.08630.6664-0.0661-0.02160.0904-0.00290.0177-0.0156-0.11710.00060.04840.0909-0.01140.00960.0612-0.00790.10082.9534-30.097796.456
190.5172-0.06350.62030.1004-0.16940.84030.00140.0034-0.01990.0520.0127-0.0072-0.05510.0045-0.01410.0427-0.0007-0.00490.05-0.00780.07496.2401-37.131190.7779
200.39790.10570.14580.0478-0.06980.65880.043-0.0156-0.02010.0113-0.0133-0.00370.00810.0256-0.02970.0539-0.0006-0.00490.0513-0.00790.08534.3177-33.837492.4446
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A113 - 122
2X-RAY DIFFRACTION2A123 - 148
3X-RAY DIFFRACTION3A149 - 221
4X-RAY DIFFRACTION4A222 - 247
5X-RAY DIFFRACTION5A248 - 259
6X-RAY DIFFRACTION6A260 - 268
7X-RAY DIFFRACTION7A269 - 323
8X-RAY DIFFRACTION8A324 - 341
9X-RAY DIFFRACTION9A342 - 377
10X-RAY DIFFRACTION10A378 - 408
11X-RAY DIFFRACTION11A409 - 415
12X-RAY DIFFRACTION12A416 - 516
13X-RAY DIFFRACTION13A517 - 535
14X-RAY DIFFRACTION14A536 - 550
15X-RAY DIFFRACTION15A551 - 593
16X-RAY DIFFRACTION16A594 - 621
17X-RAY DIFFRACTION17A622 - 636
18X-RAY DIFFRACTION18A637 - 656
19X-RAY DIFFRACTION19A657 - 680
20X-RAY DIFFRACTION20A681 - 709

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  • 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

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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

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