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- PDB-4arf: CRYSTAL STRUCTURE OF THE PEPTIDASE DOMAIN OF COLLAGENASE H FROM C... -

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Basic information

Entry
Database: PDB / ID: 4arf
TitleCRYSTAL STRUCTURE OF THE PEPTIDASE DOMAIN OF COLLAGENASE H FROM CLOSTRIDIUM HISTOLYTICUM IN COMPLEX WITH THE PEPTIDIC INHIBITOR ISOAMYLPHOSPHONYL-GLY-PRO-ALA AT 1.77 ANGSTROM RESOLUTION.
Components
  • COLH PROTEIN
  • ISOAMYLPHOSPHONYL-GLY-PRO-ALA
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR COMPLEX / COLLAGENOLYSIS / HYDROLYSE / METALLOPROTEASE / HEXXH
Function / homology
Function and homology information


tripeptidase activity / microbial collagenase / collagen metabolic process / collagen binding / metalloendopeptidase activity / endopeptidase activity / calcium ion binding / proteolysis / zinc ion binding / extracellular region
Similarity search - Function
Neutral Protease; domain 2 - #20 / Collagenase ColT, N-terminal domain / Threonyl-tRNA Synthetase; Chain A, domain 2 - #50 / Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Threonyl-tRNA Synthetase; Chain A, domain 2 / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal ...Neutral Protease; domain 2 - #20 / Collagenase ColT, N-terminal domain / Threonyl-tRNA Synthetase; Chain A, domain 2 - #50 / Collagenase ColG, catalytic helper subdomain / Collagenase G catalytic helper subdomain / Threonyl-tRNA Synthetase; Chain A, domain 2 / Peptidase M9A/M9B, collagenase, bacterial / Peptidase M9, collagenase, N-terminal domain / Collagenase / Peptidase family M9 N-terminal / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / PKD domain / Polycystic kidney disease (PKD) domain profile. / PKD domain / PKD domain superfamily / PKD/Chitinase domain / Repeats in polycystic kidney disease 1 (PKD1) and other proteins / Neutral Protease; domain 2 / Glutaredoxin / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily / Immunoglobulin-like fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesCLOSTRIDIUM HISTOLYTICUM (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.77 Å
AuthorsEckhard, U. / Brandstetter, H.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis for Activity Regulation and Substrate Preference of Clostridial Collagenases G, H, and T.
Authors: Eckhard, U. / Schonauer, E. / Brandstetter, H.
History
DepositionApr 23, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Database references
Revision 1.2Feb 8, 2017Group: Source and taxonomy
Revision 2.0Feb 7, 2018Group: Advisory / Atomic model / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_distant_solvent_atoms / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_polymer_linkage / pdbx_validate_symm_contact / struct_conf / struct_conn / struct_sheet / struct_sheet_order / struct_sheet_range / 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_seq_id / _atom_site.label_asym_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _pdbx_distant_solvent_atoms.auth_seq_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_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_struct_sheet_hbond.range_1_auth_atom_id / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_atom_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_atom_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_atom_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_sheet_hbond.sheet_id / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conf.pdbx_PDB_helix_id / _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_sheet.id / _struct_sheet_order.sheet_id / _struct_sheet_range.sheet_id
Revision 3.0Dec 20, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: COLH PROTEIN
B: ISOAMYLPHOSPHONYL-GLY-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3744
Polymers46,2682
Non-polymers1052
Water4,810267
1
A: COLH PROTEIN
B: ISOAMYLPHOSPHONYL-GLY-PRO-ALA
hetero molecules

A: COLH PROTEIN
B: ISOAMYLPHOSPHONYL-GLY-PRO-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,7478
Polymers92,5364
Non-polymers2114
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area4330 Å2
ΔGint-119.9 kcal/mol
Surface area30960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.870, 106.780, 51.350
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-1130-

HOH

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Components

#1: Protein COLH PROTEIN / COLLAGENASE


Mass: 45876.820 Da / Num. of mol.: 1 / Fragment: PEPTIDASE DOMAIN, RESIDUES 331-721
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM HISTOLYTICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q46085, microbial collagenase
#2: Protein/peptide ISOAMYLPHOSPHONYL-GLY-PRO-ALA


Mass: 391.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.48 Å3/Da / Density % sol: 50.37 % / Description: NONE
Crystal growpH: 7.25 / Details: 22.5% PEG3350, 0.15M SODIUM FORMATE, PH 7.25

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8856
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.77→40 Å / Num. obs: 42481 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 4.4 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 10
Reflection shellResolution: 1.77→1.87 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / % possible all: 86.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Y3U

2y3u


Resolution: 1.77→40 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.955 / SU B: 5.339 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.105 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.20007 2150 5.1 %RANDOM
Rwork0.15019 ---
obs0.15272 40273 97.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.437 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2--1.5 Å20 Å2
3----1.81 Å2
Refinement stepCycle: LAST / Resolution: 1.77→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3105 0 2 267 3374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023190
X-RAY DIFFRACTIONr_bond_other_d0.0010.022167
X-RAY DIFFRACTIONr_angle_refined_deg1.1471.9494304
X-RAY DIFFRACTIONr_angle_other_deg0.82335220
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3975379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.68924.337166
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.92815525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2791515
X-RAY DIFFRACTIONr_chiral_restr0.0730.2445
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023595
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02695
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.96135357
X-RAY DIFFRACTIONr_sphericity_free23.143585
X-RAY DIFFRACTIONr_sphericity_bonded13.0455463
LS refinement shellResolution: 1.77→1.816 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 117 -
Rwork0.254 2292 -
obs--79.93 %
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)
12.12882.0724-1.75063.3866-1.68432.2718-0.0234-0.1249-0.1443-0.0472-0.0161-0.09760.0744-0.04420.03940.0168-0.0033-0.00930.06530.03960.0345-13.99814.7608-28.5202
20.0286-0.2519-0.06435.87351.02950.2119-0.01990.0037-0.0297-0.0236-0.05090.32760.032-0.03610.07080.0555-0.01890.00390.08590.00670.0403-20.826815.5684-21.8204
30.241-0.0616-0.05390.16830.2190.29270.0055-0.0292-0.00820.0072-0.0046-0.00990.0011-0.0124-0.00090.03930.0012-0.01240.0590.01530.0355-5.800718.5219-18.8348
423.01890.33586.171512.1256-0.22481.66280.6745-0.30072.42230.4313-1.25910.2490.187-0.04820.58460.12360.01260.06440.2435-0.06960.2635-7.4681-2.0062-19.2159
51.361.16890.437219.28832.81783.636-0.1538-0.0351-0.32750.50870.0926-1.2030.5210.31410.06130.11560.06590.04690.10160.0160.1548-6.54931.6723-12.2576
63.4921.1037-1.65761.27320.11021.326-0.0962-0.0129-0.20640.0604-0.039-0.04010.0377-0.07090.13510.06370.0164-0.01130.08640.01190.025-11.55238.1862-15.7892
70.73230.1990.0280.36730.17440.0948-0.0022-0.01610.03980.03970.00050.00010.0063-0.00290.00180.0540.0056-0.01680.06480.00560.0118-6.731616.8135-13.8895
83.74020.02942.90363.62783.00917.6564-0.00890.1122-0.19910.22760.09760.22140.33180.2673-0.08870.0516-0.0186-0.01020.04260.02010.04939.13410.2915-14.346
91.51130.6572-1.03720.3337-0.23261.7072-0.08330.0534-0.0786-0.04470.0639-0.04210.020.14760.01940.0247-0.0116-0.00470.0907-0.00850.02195.91212.8602-5.5268
100.2220.3457-0.37220.5602-0.46881.199-0.00680.01720.01170.00760.02360.01760.0583-0.0228-0.01680.04640.0085-0.01660.05910.00140.0303-11.536420.5016-0.5684
110.59060.1569-0.11510.7170.66941.34250.0026-0.0279-0.0383-0.0219-0.00690.00360.08760.09920.00430.03160.00650.00070.0531-0.00280.0237-1.434613.07063.5524
121.6648-0.9335-0.92250.79490.68990.66130.0087-0.08770.0766-0.06030.0597-0.0073-0.05030.068-0.06840.0397-0.01330.00410.0697-0.01410.05827.982324.5009-4.0794
135.9325-5.2517-9.0796.20687.719317.2498-0.0071-0.310.078-0.00270.1537-0.04560.19340.6644-0.14660.0131-0.005-0.00070.1083-0.00480.02169.996720.66717.7092
141.2946-0.2811.11280.1022-0.31552.08730.01550.00850.0473-0.03460.02580.0096-0.0602-0.0723-0.04130.0423-0.0121-0.01430.0467-0.00170.0358-10.008922.5017.6496
155.2505-1.82784.69122.6942-2.77164.8245-0.0153-0.2157-0.0804-0.02320.13290.08840.0175-0.2172-0.11760.05470.0209-0.00930.0703-0.01490.0158-24.725227.0199-18.5463
161.45511.08080.24511.33110.17380.0416-0.10140.09460.3112-0.06770.04410.0058-0.01570.01490.05730.0264-0.029-0.01620.04250.01840.1678-14.543843.8463-24.9842
171.1480.17341.01490.49760.6831.4968-0.00620.0013-0.03950.04330.047-0.02250.0370.06-0.04080.046-0.01410.00730.05740.00790.0435-6.931935.8299-20.7734
187.49150.04252.46920.05970.24011.7769-0.0756-0.18080.17780.0115-0.0216-0.01010.0002-0.15470.09720.0429-0.0068-0.01860.0486-0.02650.074-12.059340.6985-10.3413
191.77890.37940.86140.46130.65070.9949-0.02770.06950.06640.00780.0476-0.0410.00910.0645-0.01990.0305-0.01530.00210.04960.00480.0546-5.713739.3054-16.4664
209.8626-0.29448.55610.9012-3.350218.1945-0.16510.3651-0.0527-0.07780.14-0.03450.1055-0.23340.02520.07750.01330.04850.0838-0.01510.0636-20.49733.4497-31.8078
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A342 - 356
2X-RAY DIFFRACTION2A357 - 372
3X-RAY DIFFRACTION3A373 - 412
4X-RAY DIFFRACTION4A413 - 419
5X-RAY DIFFRACTION5A420 - 427
6X-RAY DIFFRACTION6A428 - 445
7X-RAY DIFFRACTION7A446 - 469
8X-RAY DIFFRACTION8A470 - 477
9X-RAY DIFFRACTION9A478 - 487
10X-RAY DIFFRACTION10A488 - 517
11X-RAY DIFFRACTION11A518 - 547
12X-RAY DIFFRACTION12A548 - 574
13X-RAY DIFFRACTION13A575 - 584
14X-RAY DIFFRACTION14A585 - 605
15X-RAY DIFFRACTION15A606 - 615
16X-RAY DIFFRACTION16A616 - 636
17X-RAY DIFFRACTION17A637 - 665
18X-RAY DIFFRACTION18A666 - 685
19X-RAY DIFFRACTION19A686 - 715
20X-RAY DIFFRACTION20A716 - 721

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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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