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- PDB-1uxm: A4V mutant of human SOD1 -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1uxm
TitleA4V mutant of human SOD1
ComponentsSUPEROXIDE DISMUTASE [CU-ZN]
KeywordsOXIDOREDUCTASE / HUMAN CU / ZN SUPEROXIDE DISMUTASE / ANTIOXIDANT / METAL- BINDING / AMYOTROPHIC LATERAL SCLEROSIS / DISEASE MUTATION
Function / homology
Function and homology information


action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance ...action potential initiation / neurofilament cytoskeleton organization / anterograde axonal transport / retrograde axonal transport / positive regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / protein phosphatase 2B binding / regulation of organ growth / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / regulation of T cell differentiation in thymus / superoxide anion generation / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / regulation of GTPase activity / superoxide metabolic process / heart contraction / positive regulation of catalytic activity / superoxide dismutase / Detoxification of Reactive Oxygen Species / transmission of nerve impulse / negative regulation of reproductive process / negative regulation of developmental process / superoxide dismutase activity / neuronal action potential / regulation of multicellular organism growth / response to axon injury / ectopic germ cell programmed cell death / glutathione metabolic process / positive regulation of phagocytosis / ovarian follicle development / axon cytoplasm / embryo implantation / reactive oxygen species metabolic process / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / dendrite cytoplasm / removal of superoxide radicals / positive regulation of superoxide anion generation / regulation of mitochondrial membrane potential / thymus development / locomotory behavior / placenta development / response to organic substance / determination of adult lifespan / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / mitochondrial intermembrane space / small GTPase binding / regulation of blood pressure / negative regulation of inflammatory response / peroxisome / Platelet degranulation / gene expression / response to heat / protein-folding chaperone binding / cytoplasmic vesicle / spermatogenesis / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / mitochondrial matrix / response to xenobiotic stimulus / positive regulation of apoptotic process / copper ion binding / neuronal cell body / apoptotic process / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / extracellular region / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Superoxide dismutase, copper/zinc binding domain / Copper/Zinc superoxide dismutase signature 1. / Superoxide dismutase, copper/zinc, binding site / Copper/Zinc superoxide dismutase signature 2. / Superoxide dismutase, copper/zinc binding domain / Superoxide dismutase (Cu/Zn) / superoxide dismutase copper chaperone / Copper/zinc superoxide dismutase (SODC) / Superoxide dismutase-like, copper/zinc binding domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Superoxide dismutase [Cu-Zn]
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHough, M.A. / Grossmann, J.G. / Antonyuk, S.V. / Strange, R.W. / Doucette, P.A. / Rodriguez, J.A. / Whitson, L.J. / Hart, P.J. / Hayward, L.J. / Valentine, J.S. / Hasnain, S.S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2004
Title: Dimer Destabilization in Superoxide Dismutase May Result in Disease-Causing Properties: Structures of Motor Neuron Disease Mutants
Authors: Hough, M.A. / Grossmann, J.G. / Antonyuk, S.V. / Strange, R.W. / Doucette, P.A. / Rodriguez, J.A. / Whitson, L.J. / Hart, P.J. / Hayward, L.J. / Valentine, J.S. / Hasnain, S.S.
History
DepositionFeb 26, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2004Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_database_status.status_code_sf / _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.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_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_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
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA DA GA HA KA LA" IN EACH CHAIN ON ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA DA GA HA KA LA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 9-STRANDED BARREL THIS IS REPRESENTED BY A 10-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUPEROXIDE DISMUTASE [CU-ZN]
B: SUPEROXIDE DISMUTASE [CU-ZN]
C: SUPEROXIDE DISMUTASE [CU-ZN]
D: SUPEROXIDE DISMUTASE [CU-ZN]
E: SUPEROXIDE DISMUTASE [CU-ZN]
F: SUPEROXIDE DISMUTASE [CU-ZN]
G: SUPEROXIDE DISMUTASE [CU-ZN]
H: SUPEROXIDE DISMUTASE [CU-ZN]
I: SUPEROXIDE DISMUTASE [CU-ZN]
J: SUPEROXIDE DISMUTASE [CU-ZN]
K: SUPEROXIDE DISMUTASE [CU-ZN]
L: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)191,81536
Polymers190,26712
Non-polymers1,54724
Water19,7441096
1
A: SUPEROXIDE DISMUTASE [CU-ZN]
B: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9696
Polymers31,7112
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: SUPEROXIDE DISMUTASE [CU-ZN]
D: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9696
Polymers31,7112
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
E: SUPEROXIDE DISMUTASE [CU-ZN]
F: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9696
Polymers31,7112
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
G: SUPEROXIDE DISMUTASE [CU-ZN]
H: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9696
Polymers31,7112
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
5
I: SUPEROXIDE DISMUTASE [CU-ZN]
J: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9696
Polymers31,7112
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
6
K: SUPEROXIDE DISMUTASE [CU-ZN]
L: SUPEROXIDE DISMUTASE [CU-ZN]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9696
Polymers31,7112
Non-polymers2584
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)112.374, 145.582, 112.497
Angle α, β, γ (deg.)90.00, 120.05, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.99809, -0.06173, -0.00108), (-0.06134, 0.98939, 0.13168), (-0.00706, 0.1315, -0.99129)22.19083, -0.27397, 14.30155
2given(0.50008, -0.00114, 0.86598), (0.00861, -0.99994, -0.00629), (0.86594, 0.0106, -0.50004)5.53139, -96.49535, 3.50316
3given(0.50008, -0.00114, 0.86598), (0.00861, -0.99994, -0.00629), (0.86594, 0.0106, -0.50004)5.53139, -96.49535, 3.50316
4given(0.49767, 0.04304, -0.8663), (-0.01181, -0.99834, -0.05639), (-0.86729, 0.0383, -0.49633)11.4713, -24.22828, 51.82755
5given(-0.49676, -0.10343, 0.8617), (0.03717, -0.9945, -0.09794), (0.86709, -0.01662, 0.49787)10.20352, -24.47743, 24.2059
6given(0.99931, 0.03714, -0.00022), (0.03705, -0.99733, -0.06299), (-0.00256, 0.06293, -0.99801)29.20916, -24.06009, -3.92607
7given(-0.99975, 0.02248, 0.00197), (-0.02254, -0.99882, -0.04306), (0.001, -0.0431, 0.99907)52.84855, -23.35865, -17.472
8given(-0.50514, 0.03602, -0.86229), (0.0295, 0.99927, 0.02446), (0.86254, -0.01308, -0.50583)55.65426, 73.59691, -13.55712
9given(0.5052, -0.10066, 0.85711), (-0.02225, 0.99132, 0.12954), (-0.86271, -0.08451, 0.49858)30.64955, 73.3299, 0.01541
10given(-0.48945, -0.07168, 0.86908), (0.00127, 0.99656, 0.0829), (-0.87203, 0.04168, -0.48767)15.39836, 72.11509, 57.78385
11given(0.49486, 0.06613, -0.86645), (-0.0337, 0.99781, 0.05691), (0.86832, 0.00104, 0.496)16.56118, 72.75935, 30.56594

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Components

#1: Protein
SUPEROXIDE DISMUTASE [CU-ZN]


Mass: 15855.613 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / Strain (production host): EG118 / Variant (production host): YEP351 / References: UniProt: P00441, superoxide dismutase
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cu
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1096 / Source method: isolated from a natural source / Formula: H2O
Compound detailsDESTROYS RADICALS WHICH ARE NORMALLY PRODUCED WITHIN THE CELLS AND WHICH ARE TOXIC TO BIOLOGICAL ...DESTROYS RADICALS WHICH ARE NORMALLY PRODUCED WITHIN THE CELLS AND WHICH ARE TOXIC TO BIOLOGICAL SYSTEMS. ENGINEERED MUTATION ALA 4 TO VAL 4 IN CHAINS A TO L

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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: 4.2 Å3/Da / Density % sol: 70 %
Crystal growpH: 6 / Details: 0.2 M CA ACET, 15% PEG 2000, 0.1 M TRIS PH 8.0
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
215 %PEG20001reservoir
30.2 Mcalcium acetate1reservoir
40.1 MTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.97
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2002 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 246133 / % possible obs: 97 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.2 / % possible all: 82.4
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Num. obs: 245475 / % possible obs: 96.7 % / Rmerge(I) obs: 0.063
Reflection shell
*PLUS
Lowest resolution: 1.95 Å / % possible obs: 70.7 % / Rmerge(I) obs: 0.256 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HL5

1hl5


Resolution: 1.9→27 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.366 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS SOME ATOMS THAT HAVE BEEN REFINED WITH AN OCCUPANCY OF 0.00
RfactorNum. reflection% reflectionSelection details
Rfree0.25 11944 5 %RANDOM
Rwork0.228 ---
obs0.229 225403 96.7 %-
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: 18.92 Å2
Baniso -1Baniso -2Baniso -3
1--2.4 Å20 Å2-1.35 Å2
2--3.24 Å20 Å2
3----2.19 Å2
Refinement stepCycle: LAST / Resolution: 1.9→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13344 0 24 1096 14464
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02113572
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7861.94518312
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.79231824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.379152331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1290.22028
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0210344
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3190.37656
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2420.52194
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.130.542
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4020.3129
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3550.544
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9021.58940
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.556214220
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.63734632
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.24.54092
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: 1.9→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.308 734
Rwork0.292 13965
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)
12.6422-0.18220.48560.8793-0.10711.22720.04860.19130.002-0.0367-0.01730.0139-0.0323-0.0286-0.03130.13520.0089-0.02080.05710.00930.13570.042-29.119-1.883
22.28510.11820.9340.6703-0.0841.641-0.04690.14560.05590.0832-0.00720.0002-0.09720.12480.05410.1540.0006-0.02750.04840.01120.142923.995-29.33612.357
31.93150.13840.84630.72420.08491.4761-0.04330.0414-0.00820.01830.02450.05470.0119-0.01010.01880.1523-0.0207-0.01870.02680.0030.13453.956-67.4664.165
42.6553-0.09330.64610.62760.02091.4533-0.0354-0.081-0.1196-0.02380.0123-0.07180.02030.02740.02320.13940.0022-0.01340.03140.0060.147128.227-67.05317.8
51.4518-0.10450.29280.6762-0.1276.41020.0619-0.1033-0.09460.01180.0238-0.0477-0.0218-0.183-0.08570.1563-0.0096-0.01590.17790.00790.111811.9534.93451.645
61.5595-0.24331.38670.3623-0.224110.7670.13650.093-0.0444-0.013-0.01990.07920.05950.3076-0.11660.1590.0235-0.0250.124-0.01740.112311.6284.69823.783
74.86870.396-1.09540.9088-0.37651.8924-0.119-0.37290.0238-0.00510.0136-0.08360.14090.39790.10540.16890.03470.01970.27970.02650.162428.1955.07-3.885
87.02430.5342-0.7296-0.2740.0811.3593-0.06990.4753-0.11560.0270.0512-0.08540.0249-0.12890.01870.1721-0.01940.02150.31760.02240.227552.2155.753-18.126
96.45160.4821-0.96620.668-0.1772.4921-0.14690.86720.02120.04820.1092-0.0436-0.0167-0.00350.03770.091-0.00540.00820.393-0.02240.167456.32344.445-12.203
107.40310.2749-0.39440.3809-0.04682.1133-0.0055-0.25890.2263-0.0684-0.02340.02150.0397-0.11380.02890.09530.0138-0.00680.2355-0.04210.163432.00844.291.515
111.0991-0.3721.93630.5256-1.164213.3599-0.0522-0.15960.02040.05340.19240.0043-0.1363-1.675-0.14020.19220.0125-0.02640.4020.02110.140715.89943.04457.474
121.6275-0.21852.64140.5399-0.61396.59420.0699-0.088-0.03090.07940.0065-0.0874-0.0135-0.4014-0.07650.1646-0.0295-0.02030.3025-0.01170.135416.33543.67729.613
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 153
2X-RAY DIFFRACTION2B1 - 153
3X-RAY DIFFRACTION3C1 - 153
4X-RAY DIFFRACTION4D1 - 153
5X-RAY DIFFRACTION5E1 - 153
6X-RAY DIFFRACTION6F1 - 153
7X-RAY DIFFRACTION7G1 - 153
8X-RAY DIFFRACTION8H1 - 153
9X-RAY DIFFRACTION9I1 - 153
10X-RAY DIFFRACTION10J1 - 153
11X-RAY DIFFRACTION11K1 - 153
12X-RAY DIFFRACTION12L1 - 153
Refinement
*PLUS
Num. reflection Rfree: 11954 / Rfactor Rfree: 0.249 / Rfactor Rwork: 0.227
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.78

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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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