[English] 日本語
Yorodumi
- PDB-8ecx: PA0709 with glyoxal and BME modifications -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ecx
TitlePA0709 with glyoxal and BME modifications
ComponentsAntibiotic biosynthesis monooxygenase
KeywordsCYTOSOLIC PROTEIN / glyoxal
Function / homologyABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Dimeric alpha-beta barrel / monooxygenase activity / cytosol / ACETATE ION / Antibiotic biosynthesis monooxygenase
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsCuthbert, B.J. / Goulding, C.W.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: To Be Published
Title: Structural characterization of PA0709
Authors: Cuthbert, B.J. / Goulding, C.W. / Ulijasz, A.T.
History
DepositionSep 2, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Dec 27, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Derived calculations / Polymer sequence / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / chem_comp_atom / chem_comp_bond / entity_poly_seq / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_poly_seq_scheme / pdbx_refine_tls / pdbx_struct_assembly / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / struct_conn / struct_mon_prot_cis
Item: _pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] ..._pdbx_refine_tls.L[1][1] / _pdbx_refine_tls.L[1][2] / _pdbx_refine_tls.L[1][3] / _pdbx_refine_tls.L[2][2] / _pdbx_refine_tls.L[2][3] / _pdbx_refine_tls.L[3][3] / _pdbx_refine_tls.S[1][1] / _pdbx_refine_tls.S[1][2] / _pdbx_refine_tls.S[1][3] / _pdbx_refine_tls.S[2][1] / _pdbx_refine_tls.S[2][2] / _pdbx_refine_tls.S[2][3] / _pdbx_refine_tls.S[3][1] / _pdbx_refine_tls.S[3][2] / _pdbx_refine_tls.S[3][3] / _pdbx_refine_tls.T[1][1] / _pdbx_refine_tls.T[1][2] / _pdbx_refine_tls.T[1][3] / _pdbx_refine_tls.T[2][2] / _pdbx_refine_tls.T[2][3] / _pdbx_refine_tls.T[3][3] / _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_struct_assembly.details / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_mean / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_protein / _refine_ls_restr.dev_ideal / _refine_ls_restr.number / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_work / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model completeness
Details: We wanted to model two different adducts alongside wt Arg at position 49 for three of the chains. Previously only one adduct was modeled.
Provider: author / Type: Coordinate replacement

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Antibiotic biosynthesis monooxygenase
B: Antibiotic biosynthesis monooxygenase
C: Antibiotic biosynthesis monooxygenase
D: Antibiotic biosynthesis monooxygenase
E: Antibiotic biosynthesis monooxygenase
F: Antibiotic biosynthesis monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,57620
Polymers70,7166
Non-polymers86014
Water13,944774
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15640 Å2
ΔGint-47 kcal/mol
Surface area23300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.013, 148.984, 120.184
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-314-

HOH

-
Components

#1: Protein
Antibiotic biosynthesis monooxygenase / Quinol monooxygenase YgiN


Mass: 11786.025 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: C/D/E subunits have HEM/CAR modifications modelled alongside unmodified ARG at Arg49 position
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A072ZNL3
#2: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 774 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.45 Å3/Da / Density % sol: 64.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 12 % PEG 4000, 0.1 M sodium acetate pH 5 / Temp details: room temperature

-
Data collection

DiffractionMean temperature: 100 K / Ambient temp details: cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 22, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.03→49.64 Å / Num. obs: 63379 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 29.36 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.061 / Rrim(I) all: 0.162 / Χ2: 1 / Net I/σ(I): 13.5
Reflection shellResolution: 2.03→2.08 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.302 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 4439 / CC1/2: 0.682 / Rpim(I) all: 0.536 / Rrim(I) all: 1.409 / Χ2: 0.99 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: unpublished

Resolution: 2.03→49.64 Å / SU ML: 0.2026 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.2779
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1887 6335 10 %
Rwork0.1648 57009 -
obs0.1672 63344 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.39 Å2
Refinement stepCycle: LAST / Resolution: 2.03→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 58 774 5800
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00335271
X-RAY DIFFRACTIONf_angle_d0.77467116
X-RAY DIFFRACTIONf_chiral_restr0.0439706
X-RAY DIFFRACTIONf_plane_restr0.0041973
X-RAY DIFFRACTIONf_dihedral_angle_d24.5558763
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.03-2.050.26572110.24761896X-RAY DIFFRACTION100
2.05-2.080.28092090.24011887X-RAY DIFFRACTION100
2.08-2.10.25792090.22051881X-RAY DIFFRACTION100
2.1-2.130.27422080.22431872X-RAY DIFFRACTION100
2.13-2.160.2292090.21771873X-RAY DIFFRACTION100
2.16-2.190.2372080.19811876X-RAY DIFFRACTION100
2.19-2.220.21212100.19311887X-RAY DIFFRACTION100
2.22-2.250.23932100.17681893X-RAY DIFFRACTION100
2.25-2.290.22092060.17841858X-RAY DIFFRACTION100
2.29-2.320.23062120.1851904X-RAY DIFFRACTION100
2.32-2.360.21412110.19031896X-RAY DIFFRACTION100
2.36-2.410.22592060.18781861X-RAY DIFFRACTION100
2.41-2.450.21342100.18911889X-RAY DIFFRACTION100
2.45-2.50.21832110.18481893X-RAY DIFFRACTION99.95
2.5-2.560.22142090.17221890X-RAY DIFFRACTION100
2.56-2.620.18722120.16861900X-RAY DIFFRACTION100
2.62-2.680.19192060.16391860X-RAY DIFFRACTION100
2.68-2.760.1862110.16231899X-RAY DIFFRACTION100
2.76-2.840.20592100.16261885X-RAY DIFFRACTION100
2.84-2.930.18412120.15871909X-RAY DIFFRACTION100
2.93-3.030.17842130.16331917X-RAY DIFFRACTION100
3.03-3.150.18892100.16711892X-RAY DIFFRACTION100
3.15-3.30.16942130.1561917X-RAY DIFFRACTION100
3.3-3.470.17882100.14251887X-RAY DIFFRACTION100
3.47-3.690.1672140.14251926X-RAY DIFFRACTION100
3.69-3.970.16872110.13821901X-RAY DIFFRACTION100
3.97-4.370.16592150.13421936X-RAY DIFFRACTION100
4.37-50.13182160.12471936X-RAY DIFFRACTION100
5.01-6.30.16552160.17161954X-RAY DIFFRACTION100
6.31-49.640.19972270.19322034X-RAY DIFFRACTION99.78
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)
14.13919610240.799920437234-1.009359330912.18987283089-0.3770028123840.2513217341930.00238128804083-0.01953059432940.0970565996097-0.368392623133-0.04976647231460.139630610058-0.0634612871513-0.0358964105430.01024476839070.2226451641290.02070338911940.004687630190920.2053283705550.005555262404140.15491821755525.50411.9820.295
22.064418645931.928673198113.74096800373.539103519361.591402494023.807325751630.227444307519-0.142320937107-0.175339748389-0.0270114677282-0.0529544659293-0.2337439625010.1612714511840.149056849882-0.2278742466440.2342142803320.0001254360418010.0307927630040.190748172523-0.01657679400090.22403916190237.9216.2266.114
34.35332934766-1.006296384940.8157522370522.654470786930.7377596985782.856703128060.1632647451-0.06962129828790.0856181722765-0.1025084857520.00230780652911-0.137988564092-0.05420780403440.1227266505-0.1470242151990.1576316585450.009456742128630.02288450029070.106042380668-0.01015827246430.12465017887231.3215.0377.579
49.553822640842.827755212990.5120485010222.026142244586.414714028676.586215357840.3089252607010.4381679406360.221374770297-0.7326777957760.140162971985-0.702662657559-0.1952308556270.176593196852-0.365240160150.3145827209770.04211378664320.09100877915470.2473390468230.00122483232830.29595784494844.55312.606-0.458
58.291437449052.476697426665.484120964262.6019496831-1.245828525128.121385313310.2432084453990.511909817546-0.272704806881-0.611202109526-0.0589926334274-0.1600335675710.5128935381720.408398872701-0.1774023921740.2967982813870.02570810810930.0145381675570.147821241562-0.01947226868220.18492225933832.9326.108-5.275
62.93492013741.87734171142.514524931713.788875784563.006336692565.48963018411-0.0991158022758-0.111357039356-0.0254242929905-0.3315418658470.241217020285-0.312412379357-0.5345151749420.246273186611-0.09539088562780.238716376159-0.004714124031730.05969985293180.225094773294-0.002705531244670.23365743778935.37923.1025.235
72.182001652681.2479006036-0.2404046749693.71961198082-1.611576457923.17896946509-0.0147543673916-0.03904181486430.313394148438-0.225322412265-0.06369312247810.086961686224-0.3129150084160.1201752001930.09135025980920.23964817338-0.0009247985471830.02177417659110.19939124456-0.03699097451570.21407722103130.87334.62911.485
81.442077458910.0842283749347-0.5509242638243.599103528-0.1915108209373.2547473380.0215504561941-0.1835070666050.09387816845360.1571674203570.00416893208646-0.0683233385658-0.1147859855820.303964319778-0.01562892078350.1916260509360.0162178405141-0.02779454520220.243150715692-0.02730836224650.187686075333.83328.16919.333
93.074698116761.46372887208-1.39348979126.79754400697-2.330815126294.72280155466-0.0730372059624-0.182150124432-0.07654030880390.191817201290.0666214892438-0.132931508487-0.0672877773044-0.08828271010040.04184617525120.1717704211050.0118826851374-0.01198729309140.19668116467-0.03539137880710.13216579035128.14424.77915.71
101.111399387330.602206847663-0.1272329247972.14943060614-0.2355765064021.9167844703-0.023858742527-0.2296739228240.08782863987190.2777357334890.04114776655370.266845249432-0.125857389862-0.0993877119802-0.00878442128220.1848088651480.0273525651440.01418173472160.225622862839-0.006290780791480.17557984608223.94128.69218.335
111.03623209055-0.803334101049-0.05928554918294.25273266942-1.539295027082.28750798532-0.00682876816080.1465857048060.0300672982376-0.30954177467-0.00691344392449-0.00013622865270.1679957145170.01376733809930.01322525039230.191581124197-0.041084235204-0.02659301486260.2303905517640.009533865246760.16596950612823.67624.815-22.125
121.86786448148-0.4089272646620.5284796059852.9896023127-1.984578059863.58877384859-0.05974811224680.0851689185285-0.0835957250704-0.159193591826-0.0319514461035-0.08170828884880.143702106530.2604038497660.1112782727640.232496971897-0.00524420227198-0.02102584703530.2213031292980.003553532917810.15302237789628.1525.292-16.797
130.9104982621070.503326340691-0.2974962038057.84972416005-3.128921868441.79700093292-0.05151165719930.240745217144-0.0571483016366-0.5077318866320.2289107785920.5225327627640.327182338105-0.275806168108-0.1937258232710.257812573423-0.0393886964876-0.05939042665240.283628704827-0.01045345000340.22824456246815.07324.183-24.206
142.334847075461.471336982361.215298218415.666546529460.5801487637421.02860436775-0.1714590679740.2972910327670.214937852941-0.4123548792520.1216138048160.118177275739-0.08053774452440.1526103398080.08144674386420.210253980719-0.004122483565860.009408145444930.2394050632250.01623395586570.21875003368423.16835.104-14.307
152.97854422899-0.2261025882180.2721750398742.063518633780.2714788187161.7121184193-0.1077767323710.08153402595270.382874813709-0.01131237146140.0868322399943-0.163056311584-0.2799748629420.1876217752250.004284973702880.243825806652-0.0547992305827-0.04858703039410.2364958507720.004751780706060.22144054216836.2742.852-9.565
164.94492185415-0.594026215025-0.9016984291722.047543031680.4280478619772.45059208606-0.06278287277930.4159076663060.0317515382494-0.006468482252120.00147971755462-0.0769486258-0.1020400668760.009825301843250.02681002728940.189627199475-0.0275767962548-0.03184167824740.2072763313540.004349374826930.16974315033130.86238.663-11.725
177.85395257763.269703940022.902682234372.023527853384.17650743943.089239321720.0196893530610.25035110894-0.3914197646730.2652010870870.17374545729-0.7111244436820.02823206642590.593202772804-0.1575704892480.201907471884-0.00908841186619-0.02038030959350.3591016697060.02973148800170.26906420340646.99435.529-8.451
182.2047557117-0.385104947269-0.7902071236972.665873962320.08074019075171.646002173190.106381126081-0.4371225533860.2303636684710.44307140224-0.104569994274-0.306651879057-0.1299722188070.25246157535-0.006805745863820.186009812236-0.0149415907724-0.04523408786730.274308704834-0.02145950799250.20010623196337.39341.052-2.291
196.662909683992.58719906374.550554493377.50057520522.227262790422.0057667675-0.1035010810240.700721699611-0.707274348012-0.4699915002150.0946339177987-0.5948230550631.032015680910.8554424282220.2327112366790.2732781064930.04693182597630.06839155970.331681453201-0.01507829211340.29645109330835.64523.255-19.168
202.0464137895-0.592010512221-1.268749159391.550951784942.05282916184.70794863167-0.08492955581090.0483986617149-0.073383768047-0.005249396222330.1155256540280.3280790388240.1764287806470.00394584835568-0.01355523623420.16676701038-0.00889686594983-0.01409946301190.1437103504570.03901074835910.19498659143210.09219.306-2.061
211.32337634883-0.491696496019-0.5032616036021.2920430410.4367591829212.21135352423-0.0779634911910.0286600389793-0.1243372222550.017565225030.03633862063310.2834849463360.0199554298842-0.3072469280450.03231602992260.19041516581-0.0225695245459-0.01905411892470.2752771558650.01897403501440.2927287689121.18320.350.543
222.7098112109-0.506499380977-2.327810109431.767625609951.190622992368.54541691739-0.2271390734280.0557412671381-0.1652425259510.0215613731337-0.124865949470.294866160342-0.165850025634-0.5419595697350.1858087566440.16799886040.001742465031810.002070104075290.1944402199680.008351595290120.2418509719657.37322.9050.853
231.526918150820.4605480816942.481251873222.02940219089.943281196232.017190930280.123761658489-0.274560481068-0.2787387755020.254666845302-0.0368380345886-0.3147147826190.4770020215820.297731650801-0.09307779815930.31026384614-0.02086776750940.05184364231490.3256552689960.08669251404320.3454281133534.35615.30613.147
247.78976466706-4.72377802511-3.119976208434.977276556143.741196774272.014469158560.0601237780167-0.293349808127-0.7223800609110.4733648970670.04658433658260.4139883964980.555997989169-0.1599739967920.007504688371070.277728131069-0.0359394081506-0.01705263833680.216848712970.04341978772170.3053088200918.0058.7671.411
251.438737829970.9443012709141.192321235686.640466554532.657021538521.56621057841-0.027147748678-0.098396714803-0.1156323868570.1455432141130.02261004916810.2296588646870.0502165495648-0.050882412065-0.03000668216770.1548780790190.003550531469230.03176677139650.1622127408330.02291754272530.18302645260414.55221.6592.959
266.41138288098-0.997938109571-1.133914297128.399579803641.436611225739.18119142362-0.436369362973-0.4615753339790.3111853507540.555446283799-0.00282078673031.20465055157-0.0992122921413-0.9122097105380.3549557350460.14060407179-0.002635519931280.00469087648950.31856351192-0.06868573025580.3599308981925.73636.00911.493
270.8699225922721.246132723250.2526262975322.162453290760.9838237302341.97481533341-0.117277462305-0.05838684824560.712091328394-0.116691861362-0.165959845880.909140706052-0.200493416466-0.2842540568770.254821708090.2238306059580.0249408444826-0.04604167649970.202000720865-0.007289996963940.493354061127.99343.9142.661
282.147075330351.950035653310.181158912092.576555206311.028655005250.762002018411-0.255168931240.182858794680.550522094964-0.4129901437820.08125024059760.640405663904-0.283116019194-0.1709681175460.167912261360.2191633491740.0354214446731-0.08064604329990.2268839906530.03870573095480.3452497995999.72541.346-0.806
291.69865248579-1.595112360940.5667764538854.026115988913.280950539215.93835869699-0.04535958777030.548837018303-0.7139536359930.00962992236816-0.0284700015930.3444616290470.17763347161-0.734417828243-0.07746102111620.174233329028-0.0102533491283-0.1013388450890.3773984200690.04858623561450.3725382886791.76126.269-7.639
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 5:16 )A5 - 16
2X-RAY DIFFRACTION2( CHAIN A AND RESID 17:37 )A17 - 37
3X-RAY DIFFRACTION3( CHAIN A AND RESID 38:62 )A38 - 62
4X-RAY DIFFRACTION4( CHAIN A AND RESID 63:74 )A63 - 74
5X-RAY DIFFRACTION5( CHAIN A AND RESID 75:84 )A75 - 84
6X-RAY DIFFRACTION6( CHAIN A AND ( RESID 85:98 OR RESID 101:102 ) )A85 - 98
7X-RAY DIFFRACTION6( CHAIN A AND ( RESID 85:98 OR RESID 101:102 ) )A101 - 102
8X-RAY DIFFRACTION7( CHAIN B AND RESID 4:16 )B4 - 16
9X-RAY DIFFRACTION8( CHAIN B AND RESID 17:48 )B17 - 48
10X-RAY DIFFRACTION9( CHAIN B AND RESID 49:64 )B49 - 64
11X-RAY DIFFRACTION10( CHAIN B AND ( RESID 65:98 OR RESID 101:102 ) )B65 - 98
12X-RAY DIFFRACTION10( CHAIN B AND ( RESID 65:98 OR RESID 101:102 ) )B101 - 102
13X-RAY DIFFRACTION11( CHAIN C AND RESID 1:37 )C1 - 37
14X-RAY DIFFRACTION12( CHAIN C AND RESID 38:62 )C38 - 62
15X-RAY DIFFRACTION13( CHAIN C AND RESID 63:84 )C63 - 84
16X-RAY DIFFRACTION14( CHAIN C AND ( RESID 85:98 OR RESID 101:102 ) )C85 - 98
17X-RAY DIFFRACTION14( CHAIN C AND ( RESID 85:98 OR RESID 101:102 ) )C101 - 102
18X-RAY DIFFRACTION15( CHAIN D AND RESID 4:37 )D4 - 37
19X-RAY DIFFRACTION16( CHAIN D AND RESID 38:62 )D38 - 62
20X-RAY DIFFRACTION17( CHAIN D AND RESID 63:74 )D63 - 74
21X-RAY DIFFRACTION18( CHAIN D AND RESID 75:91 )D75 - 91
22X-RAY DIFFRACTION19( CHAIN D AND ( RESID 92:98 OR RESID 101:101 ) )D92 - 98
23X-RAY DIFFRACTION19( CHAIN D AND ( RESID 92:98 OR RESID 101:101 ) )D101
24X-RAY DIFFRACTION20( CHAIN E AND RESID 3:16 )E3 - 16
25X-RAY DIFFRACTION21( CHAIN E AND RESID 17:48 )E17 - 48
26X-RAY DIFFRACTION22( CHAIN E AND RESID 49:64 )E49 - 64
27X-RAY DIFFRACTION23( CHAIN E AND RESID 65:74 )E65 - 74
28X-RAY DIFFRACTION24( CHAIN E AND RESID 75:84 )E75 - 84
29X-RAY DIFFRACTION25( CHAIN E AND RESID 85:91 )E85 - 91
30X-RAY DIFFRACTION26( CHAIN E AND ( RESID 92:98 OR RESID 101:102 ) )E92 - 98
31X-RAY DIFFRACTION26( CHAIN E AND ( RESID 92:98 OR RESID 101:102 ) )E101 - 102
32X-RAY DIFFRACTION27( CHAIN F AND RESID 4:37 )F4 - 37
33X-RAY DIFFRACTION28( CHAIN F AND RESID 38:91 )F38 - 91
34X-RAY DIFFRACTION29( CHAIN F AND ( RESID 92:98 OR RESID 101:102 ) )F92 - 98
35X-RAY DIFFRACTION29( CHAIN F AND ( RESID 92:98 OR RESID 101:102 ) )F101 - 102

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • 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

-
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

Read more