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- PDB-3q09: Crystal Structure of Chlorite Dismutase from D. Aromatica at pH 9.0 -

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Basic information

Entry
Database: PDB / ID: 3q09
TitleCrystal Structure of Chlorite Dismutase from D. Aromatica at pH 9.0
ComponentsChlorite dismutase
KeywordsOXIDOREDUCTASE / Ferrodoxin Fold / Chlorite Decomposition / O2 generation / Periplasim
Function / homology
Function and homology information


chlorite O2-lyase / chlorite O2-lyase activity / periplasmic space / heme binding / metal ion binding
Similarity search - Function
Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRITE ION / Chlorite dismutase
Similarity search - Component
Biological speciesDechloromonas aromatica (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGoblirsch, B.R. / Wilmot, C.M.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2010
Title: Structural features promoting dioxygen production by Dechloromonas aromatica chlorite dismutase.
Authors: Goblirsch, B.R. / Streit, B.R. / DuBois, J.L. / Wilmot, C.M.
History
DepositionDec 15, 2010Deposition site: RCSB / Processing site: RCSB
SupersessionJan 5, 2011ID: 3M2S
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chlorite dismutase
B: Chlorite dismutase
C: Chlorite dismutase
D: Chlorite dismutase
E: Chlorite dismutase
F: Chlorite dismutase
G: Chlorite dismutase
H: Chlorite dismutase
I: Chlorite dismutase
J: Chlorite dismutase
K: Chlorite dismutase
L: Chlorite dismutase
M: Chlorite dismutase
N: Chlorite dismutase
O: Chlorite dismutase
P: Chlorite dismutase
Q: Chlorite dismutase
R: Chlorite dismutase
S: Chlorite dismutase
T: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)577,63880
Polymers563,58620
Non-polymers14,05160
Water36020
1
A: Chlorite dismutase
B: Chlorite dismutase
C: Chlorite dismutase
D: Chlorite dismutase
E: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,40920
Polymers140,8975
Non-polymers3,51315
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22660 Å2
ΔGint-204 kcal/mol
Surface area44080 Å2
MethodPISA
2
F: Chlorite dismutase
G: Chlorite dismutase
H: Chlorite dismutase
I: Chlorite dismutase
J: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,40920
Polymers140,8975
Non-polymers3,51315
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22720 Å2
ΔGint-207 kcal/mol
Surface area44140 Å2
MethodPISA
3
K: Chlorite dismutase
L: Chlorite dismutase
M: Chlorite dismutase
N: Chlorite dismutase
O: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,40920
Polymers140,8975
Non-polymers3,51315
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22760 Å2
ΔGint-207 kcal/mol
Surface area44160 Å2
MethodPISA
4
P: Chlorite dismutase
Q: Chlorite dismutase
R: Chlorite dismutase
S: Chlorite dismutase
T: Chlorite dismutase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,40920
Polymers140,8975
Non-polymers3,51315
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22980 Å2
ΔGint-207 kcal/mol
Surface area44110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.704, 202.850, 247.103
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
151O
161P
171Q
181R
191S
201T

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A8 - 3001
2115B8 - 3001
3115C8 - 3001
4115D8 - 3001
5115E8 - 3001
6115F8 - 3001
7115G8 - 3001
8115H8 - 3001
9115I8 - 3001
10115J8 - 3001
11115K8 - 3001
12115L8 - 3001
13115M8 - 3001
14115N8 - 3001
15115O8 - 3001
16115P8 - 3001
17115Q8 - 3001
18115R8 - 3001
19115S8 - 3001
20115T8 - 3001

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Components

#1: Protein
Chlorite dismutase


Mass: 28179.314 Da / Num. of mol.: 20 / Fragment: UNP residues 35-282
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dechloromonas aromatica (bacteria) / Strain: RCB / Gene: Daro_2580 / Plasmid: pBSCld / Production host: Escherichia coli (E. coli) / Strain (production host): Tuner(de3) / References: UniProt: Q47CX0, chlorite O2-lyase
#2: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-NO2 / NITRITE ION


Mass: 46.005 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: NO2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 16% PEG 8000, 200 mM calcium acetate (CaAc2), 22.5 mM sodium nitrite (NO2), 100 mM bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 20, 2007
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 123481 / Num. obs: 123152 / % possible obs: 99.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 3 / Redundancy: 8.3 % / Rmerge(I) obs: 0.089
Reflection shellResolution: 3→3.11 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 6 / % possible all: 99.5

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→48.31 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.887 / SU B: 38.308 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R Free: 0.416 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23393 6174 5 %RANDOM
Rwork0.18505 ---
obs0.18751 116905 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.871 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3→48.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms38560 0 940 20 39520
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02240500
X-RAY DIFFRACTIONr_angle_refined_deg1.7042.02655180
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.12854800
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.34824.0231740
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.511156940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.74515220
X-RAY DIFFRACTIONr_chiral_restr0.1070.26060
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02130320
X-RAY DIFFRACTIONr_mcbond_it0.5211.524100
X-RAY DIFFRACTIONr_mcangle_it1.004239160
X-RAY DIFFRACTIONr_scbond_it1.541316400
X-RAY DIFFRACTIONr_scangle_it2.5984.516020
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A967medium positional0.170.5
B967medium positional0.270.5
C967medium positional0.150.5
D967medium positional0.250.5
E967medium positional0.160.5
F967medium positional0.180.5
G967medium positional0.170.5
H967medium positional0.170.5
I967medium positional0.250.5
J967medium positional0.20.5
K967medium positional0.20.5
L967medium positional0.160.5
M967medium positional0.250.5
N967medium positional0.170.5
O967medium positional0.170.5
P967medium positional0.270.5
Q967medium positional0.290.5
R967medium positional0.230.5
S967medium positional0.240.5
T967medium positional0.260.5
A1009loose positional0.255
B1009loose positional0.325
C1009loose positional0.245
D1009loose positional0.315
E1009loose positional0.255
F1009loose positional0.285
G1009loose positional0.275
H1009loose positional0.265
I1009loose positional0.315
J1009loose positional0.285
K1009loose positional0.35
L1009loose positional0.255
M1009loose positional0.325
N1009loose positional0.275
O1009loose positional0.275
P1009loose positional0.385
Q1009loose positional0.45
R1009loose positional0.375
S1009loose positional0.355
T1009loose positional0.375
A967medium thermal0.532
B967medium thermal0.592
C967medium thermal0.522
D967medium thermal0.482
E967medium thermal0.532
F967medium thermal0.442
G967medium thermal0.482
H967medium thermal0.472
I967medium thermal0.52
J967medium thermal0.522
K967medium thermal0.462
L967medium thermal0.442
M967medium thermal0.492
N967medium thermal0.452
O967medium thermal0.452
P967medium thermal0.412
Q967medium thermal0.442
R967medium thermal0.352
S967medium thermal0.42
T967medium thermal0.412
A1009loose thermal0.8310
B1009loose thermal0.9710
C1009loose thermal0.810
D1009loose thermal0.8210
E1009loose thermal0.8610
F1009loose thermal0.6910
G1009loose thermal0.7810
H1009loose thermal0.7810
I1009loose thermal0.7510
J1009loose thermal0.7710
K1009loose thermal0.7310
L1009loose thermal0.7110
M1009loose thermal0.7710
N1009loose thermal0.6910
O1009loose thermal0.6310
P1009loose thermal0.6810
Q1009loose thermal0.7410
R1009loose thermal0.6510
S1009loose thermal0.6810
T1009loose thermal0.7210
LS refinement shellResolution: 3→3.08 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 445 -
Rwork0.26 8411 -
obs--98.54 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.1903-0.39990.19670.85030.0661.593-0.043-0.0876-0.14390.0741-0.02010.15670.4815-0.14790.06310.1655-0.03810.0280.02420.00830.0742-32.7524-44.389817.9961
21.1678-0.34090.48931.5657-0.33310.90280.00120.1701-0.0553-0.317-0.0192-0.07560.12960.1650.0180.15170.06080.07240.0810.03010.0531-10.8648-26.9534-18.5017
31.5841-0.7433-0.12471.0444-0.00841.52490.1609-0.02570.21140.0109-0.0408-0.1513-0.23440.282-0.12010.0656-0.04630.0570.0549-0.01360.1248-9.8229-7.73242.4219
41.7203-0.28130.2570.8616-0.2681.7275-0.03540.1393-0.1704-0.19790.0170.05690.5267-0.02950.01840.30080.0040.01850.0229-0.01860.0502-24.987-49.759-8.8407
51.5937-0.14080.24591.069-0.47841.47750.0434-0.21110.15230.1848-0.00950.0263-0.14480.1308-0.03390.0529-0.01570.02760.0545-0.02690.0344-23.3354-18.469324.9285
61.94680.4267-0.21251.3638-0.2071.64470.0966-0.5884-0.33020.467-0.2481-0.36170.00940.4290.15150.2002-0.1161-0.13630.37350.18330.20868.02015.6532-36.185
70.96180.383-0.09732.1220.45311.48810.1265-0.0758-0.14220.0602-0.1934-0.4637-0.05620.52050.06690.0539-0.0763-0.04720.31170.11270.241417.910815.0363-61.1169
81.73730.30890.10091.58330.43441.448-0.00490.3690.2557-0.07070.0272-0.0601-0.23920.1178-0.02220.0992-0.0712-0.03840.13830.10130.1038-3.265828.4986-74.398
91.33180.8016-0.01171.796-0.09391.78960.0346-0.03460.35970.13870.04720.3325-0.2877-0.235-0.08180.10520.02150.04360.06220.04550.2137-26.265827.5668-57.7246
101.39390.44340.03492.117-0.28691.66880.0836-0.36230.07240.4408-0.09550.1964-0.30140.06380.01190.2517-0.07020.0460.16480.03590.0835-19.349813.2395-34.0771
111.8051-0.28910.28750.9188-0.04311.95010.1582-0.0807-0.26910.1017-0.03030.06020.5277-0.166-0.1280.2617-0.1221-0.07970.15560.09820.165-59.8262-44.22-46.1322
121.650.30530.60741.5715-0.00121.72030.1465-0.19380.00820.2251-0.04450.245-0.0371-0.3704-0.1020.0668-0.04710.07150.27010.03390.1572-69.8623-17.8693-42.9568
131.80740.70130.06280.9999-0.32591.44470.0619-0.01510.2581-0.0833-0.00020.1975-0.2428-0.2671-0.06170.08970.07680.0170.15730.07440.212-64.122-3.4731-66.752
141.91090.05790.6571.7936-0.10571.29590.10690.48270.0219-0.5875-0.1183-0.16140.27410.21280.01140.28690.15710.05360.28840.04420.1044-50.6571-20.8879-84.6643
152.00790.08760.49251.24-0.17631.53660.20350.259-0.3428-0.3564-0.1784-0.10890.59990.1179-0.0250.43210.187-0.05170.1697-0.03390.2498-47.917-46.1445-71.8896
161.6013-0.25140.09881.7631-0.11391.67310.3264-0.0330.26360.0258-0.03770.3146-0.5883-0.7901-0.28870.50170.47730.25340.74860.12940.4458-80.315721.176926.2641
170.971-0.5468-0.21532.0549-0.23531.430.26660.1070.54710.20060.0803-0.0505-0.9374-0.1157-0.34690.73030.12170.29570.13380.05140.4553-41.948630.22022.5241
181.6618-0.72290.21022.2402-0.57641.47740.16920.54960.2144-0.2721-0.0170.1538-0.5832-0.5894-0.15220.48660.27780.06360.55950.1470.3159-60.538918.2151-15.1223
192.0319-1.0139-0.18161.5831-0.28352.09530.20580.3778-0.0612-0.1817-0.02690.4034-0.2445-1.0284-0.17890.32490.32150.01541.04190.15340.4704-84.253512.5187-0.4567
201.4828-0.266-0.47082.228-0.18691.73050.2184-0.43430.56740.25050.082-0.0523-0.9565-0.1094-0.30050.88270.21680.31320.3219-0.09850.4895-54.051432.169328.1826
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999
3X-RAY DIFFRACTION3C-10 - 9999
4X-RAY DIFFRACTION4D-10 - 9999
5X-RAY DIFFRACTION5E-10 - 9999
6X-RAY DIFFRACTION6F-10 - 9999
7X-RAY DIFFRACTION7G-10 - 9999
8X-RAY DIFFRACTION8H-10 - 9999
9X-RAY DIFFRACTION9I-10 - 9999
10X-RAY DIFFRACTION10J-10 - 9999
11X-RAY DIFFRACTION11K-10 - 9999
12X-RAY DIFFRACTION12L-10 - 9999
13X-RAY DIFFRACTION13M-10 - 9999
14X-RAY DIFFRACTION14N-10 - 9999
15X-RAY DIFFRACTION15O-10 - 9999
16X-RAY DIFFRACTION16P-10 - 9999
17X-RAY DIFFRACTION17Q-10 - 9999
18X-RAY DIFFRACTION18R-10 - 9999
19X-RAY DIFFRACTION19S-10 - 9999
20X-RAY DIFFRACTION20T-10 - 9999

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  • 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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