[English] 日本語
Yorodumi
- PDB-4fw3: Crystal Structure of the LpxC in complex with N-[(2S)-3-AMINO-1-(... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fw3
TitleCrystal Structure of the LpxC in complex with N-[(2S)-3-AMINO-1-(HYDROXYAMINO)-1-OXOPROPAN-2-YL]-4-(4-PHENYLBUTA-1,3-DIYN-1-YL)BENZAMIDE inhibitor
ComponentsUDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
KeywordsHydrolase/Hydrolase Inhibitor / Hydrolase / Hydrolase-Hydrolase Inhibitor complex
Function / homology
Function and homology information


UDP-3-O-acyl-N-acetylglucosamine deacetylase / UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase activity / UDP-3-O-acyl-N-acetylglucosamine deacetylase activity / lipid A biosynthetic process / metal ion binding
Similarity search - Function
lpxc deacetylase, domain 1 / lpxc deacetylase, domain 2 / lpxc deacetylase, domain 1 / UDP-3-O-acyl N-acetylglucosamine deacetylase / UDP-3-O-acyl N-acetylglucosamine deacetylase, C-terminal / UDP-3-O-acyl N-acetylglucosamine deacetylase, N-terminal / UDP-3-O-acyl N-acetylglycosamine deacetylase / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-L52 / UDP-3-O-acyl-N-acetylglucosamine deacetylase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKang, Y.N. / Stuckey, J.A.
CitationJournal: to be published
Title: Crystal Structure of the LpxC
Authors: Kang, Y.N. / Stuckey, J.A.
History
DepositionJun 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
C: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
D: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,51114
Polymers133,6764
Non-polymers1,83510
Water5,891327
1
A: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9244
Polymers33,4191
Non-polymers5053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8323
Polymers33,4191
Non-polymers4132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8323
Polymers33,4191
Non-polymers4132
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9244
Polymers33,4191
Non-polymers5053
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.599, 170.903, 89.853
Angle α, β, γ (deg.)90.000, 90.010, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine deacetylase / Protein envA / UDP-3-O-acyl-GlcNAc deacetylase


Mass: 33418.875 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: envA, lpxC, PA4406 / Plasmid: pMOCR / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 AI
References: UniProt: P47205, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-L52 / N-[(2S)-3-amino-1-(hydroxyamino)-1-oxopropan-2-yl]-4-(4-phenylbuta-1,3-diyn-1-yl)benzamide


Mass: 347.367 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H17N3O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.85 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.9
Details: 24-30% PEG8000, 0.2M Sodium Acetate, 0.1M Sodium acetate pH 4.9, vapor diffusion, sitting drop, temperature 293.15K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 3, 2011
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→50 Å / Num. obs: 44503 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.116 / Χ2: 1.058 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.35-2.393.80.45222250.7141100
2.39-2.433.80.41822000.7321100
2.43-2.483.80.39422330.7581100
2.48-2.533.90.3822390.7691100
2.53-2.593.80.33921780.7981100
2.59-2.653.80.29422290.7921100
2.65-2.713.80.26622370.8061100
2.71-2.793.80.24321970.8421100
2.79-2.873.80.21622060.8951100
2.87-2.963.80.1922780.927199.8
2.96-3.073.80.16521800.9411100
3.07-3.193.80.13622301.0071100
3.19-3.333.80.12622351.091100
3.33-3.513.80.11222231.377199.9
3.51-3.733.80.10522161.593199.8
3.73-4.023.80.09922442.041199.9
4.02-4.423.70.08922332.136199.6
4.42-5.063.60.06222241.367199.5
5.06-6.373.80.04722140.742199.9
6.37-503.80.0422820.923199.8

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.11.1refinement
PDB_EXTRACT3.11data extraction
MD2data collection
HKL-2000data reduction
PHASERphasing
BUSTER2.11.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P3E
Resolution: 2.35→42.73 Å / Cor.coef. Fo:Fc: 0.9333 / Cor.coef. Fo:Fc free: 0.8974 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.638 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2466 2239 5.04 %RANDOM
Rwork0.1966 ---
obs0.199 44467 99.78 %-
Displacement parametersBiso max: 115.9 Å2 / Biso mean: 35.5905 Å2 / Biso min: 12.41 Å2
Baniso -1Baniso -2Baniso -3
1-2.2139 Å20 Å2-0.928 Å2
2---3.3698 Å20 Å2
3---1.1559 Å2
Refine analyzeLuzzati coordinate error obs: 0.307 Å
Refinement stepCycle: LAST / Resolution: 2.35→42.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9290 0 120 327 9737
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4520SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes244HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1536HARMONIC5
X-RAY DIFFRACTIONt_it9672HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1256SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact11170SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d9672HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg13121HARMONIC20.94
X-RAY DIFFRACTIONt_omega_torsion2.43
X-RAY DIFFRACTIONt_other_torsion2.7
LS refinement shellResolution: 2.35→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2372 180 5.56 %
Rwork0.2057 3056 -
all0.2075 3236 -
obs--99.78 %
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)
11.22860.79671.18992.1042-0.29160.0082-0.03490.0304-0.09320.0920.0242-0.2962-0.03930.04550.0108-0.09260.0645-0.0422-0.0077-0.019-0.01321.4441-0.1020.7788
22.4183-0.008-1.19933.27360.4832.4247-0.0063-0.1347-0.19440.0268-0.09560.06850.1070.05290.1018-0.06140.0336-0.0068-0.03780.0073-0.02214.0456-4.73856.9297
30.159-0.44710.17210.5053-0.58210.96870.0109-0.07730.02170.02420.01240.0267-0.05510.0332-0.02330.15540.0279-0.05410.00720.0955-0.02695.88679.09812.7522
40.3363-1.6342-0.27471.0582-0.4273-0.0001-0.021-0.0697-0.08730.0919-0.00080.07880.03280.01580.0218-0.0330.0270.0290.0227-0.0188-0.12869.44783.257812.1448
53.18570.33690.96240.43480.24480.00030.015-0.0685-0.00920.03720.1255-0.0519-0.02510.0705-0.14060.01210.0309-0.0548-0.0202-0.00050.001521.49383.45883.4687
60.29821.33691.15580.8887-1.89031.9503-0.00230.0134-0.0258-0.0392-0.0208-0.0291-0.0651-0.02260.0231-0.00180.0115-0.0414-0.0151-0.0287-0.01118.97015.1036-12.9057
73.7082-0.5660.61274.5555-1.36090.0653-0.012-0.16010.15930.03140.08560.0651-0.0441-0.0249-0.0736-0.13360.0599-0.0011-0.01620.06440.02338.00224.5052.2138
82.49260.3861.19490.9509-1.29440.0238-0.01970.10120.1056-0.16460.0404-0.1023-0.01960.0708-0.0207-0.06280.02430.0202-0.13780.01240.021721.200921.2185-1.1631
90.11890.1253-0.12530.17351.36481.1549-0.0005-0.0668-0.01650.0632-0.00880.0666-0.0004-0.02850.00930.2148-0.0775-0.03390.0223-0.1059-0.074715.478918.792422.7979
100.92051.12022.780.280.10251.46150.0153-0.04270.10610.04850.02640.0198-0.0510.0129-0.04170.07050.006-0.1451-0.1196-0.06920.010723.384121.200419.0909
110.91830.63570.32753.45741.22391.99090.0307-0.0197-0.0018-0.0989-0.05920.1763-0.05070.04250.0285-0.10520.05370.0048-0.02010.0395-0.077710.641516.38171.5733
120.24161.2802-1.30650.0048-1.3012-0.0005-0.0053-0.01270.0243-0.04530.0069-0.0413-0.02060.0812-0.0016-0.0167-0.0489-0.07890.01180.0160.018816.4877.1247-17.1798
131.5177-0.5265-0.35050.69890.3552.4060.01330.19450.0374-0.1021-0.0671-0.0044-0.0181-0.02010.0537-0.0390.0287-0.00830.0230.0454-0.0624-4.899857.94-10.4645
141.46590.8882-1.67972.24111.83820.82380.00090.10270.0494-0.0171-0.0129-0.0191-0.09850.07660.012-0.0405-0.00710.01420.04070.0348-0.06686.438964.206-8.2388
151.2229-0.3993-0.70220.0006-0.46521.725-0.02040.03120.0235-0.2048-0.0516-0.0647-0.19250.11940.072-0.02370.01650.00660.02640.0153-0.0402-1.246758.3152-3.1061
160.7432-0.56561.14280.0516-0.71270.77850.00270.0021-0.02450.0119-0.00570.02250.0179-0.01010.0031-0.03070.10130.03280.1284-0.0239-0.0729-6.15848.6313-19.8983
171.5604-1.0602-1.33270.0313-1.54510.01-0.0033-0.02330.01050.026-0.0031-0.03870.02140.02980.00650.06360.07390.0005-0.02440.065-0.034512.598840.0304-6.1982
181.5558-0.61-1.98891.36540.19051.16530.0658-0.1112-0.18970.0858-0.11470.04040.02340.02290.0488-0.01390.02780.0176-0.00140.0316-0.07464.123240.776210.0269
191.2164-1.35591.75040-1.08482.2502-0.00730.0187-0.0591-0.0170.03870.06190.0901-0.0248-0.0314-0.089-0.03940.03990.03480.0047-0.0418-6.880347.63396.5835
200.71710.05710.54591.51941.77160.9371-0.01190.0320.0247-0.0411-0.00150.0133-0.06330.01330.0134-0.00470.0131-0.010.1009-0.01830.00351.651964.877119.4115
210.3912.5479-0.59872.2394-0.38790.78440.0139-0.0653-0.0190.1072-0.03840.1286-0.0434-0.03890.0244-0.0260.02410.0460.0835-0.0072-0.0392-8.688757.683117.7826
220.0448-0.7956-0.03210.795-0.03720.42990.0221-0.0669-0.0599-0.1726-0.0632-0.01140.17330.02340.0411-0.04530.0276-0.02070.01-0.014-0.03562.456846.07424.6162
230.3211.6478-0.0250.0156-0.93681.10050.0118-0.01820.0387-0.0348-0.0313-0.02920.03920.07510.0195-0.08040.02620.00810.048-0.00380.019417.340645.525-4.6688
240.78651.07891.48220-1.1110.3234-0.0050.007-0.0024-0.038-0.01730.07560.0267-0.03870.02220.00310.02740.06860.041-0.0391-0.0243-0.323436.7153-15.5517
250.78560.71570.017501.01280.4957-0.00090.03450.0499-0.02210.0163-0.0478-0.04320.0133-0.01530.06220.00890.07680.02820.0451-0.04321.86027.225624.7244
260.12290.17720.68370.50690.25710.71190.03830.15580.0112-0.0111-0.0999-0.02070.0505-0.02790.0616-0.0680.0430.03340.0559-0.0054-0.05115.5969-13.502736.7556
273.4940.27672.43931.5443-0.93230.81760.01940.0866-0.0533-0.0760.0209-0.00720.0662-0.0566-0.0403-0.0552-0.02150.01680.0496-0.0251-0.0531-6.3957-15.850336.6822
280.9187-0.97510.57690.14510.18081.87040.01470.063-0.1389-0.155-0.11460.0370.2033-0.06730.0999-0.04760.00970.00430.0189-0.0269-0.01921.5685-9.63441.2078
290.7168-0.74471.41231.99490.0330.00690.00390.10650.00440.0190.0009-0.0156-0.0260.0607-0.00480.05670.06760.0018-0.0034-0.0179-0.1051-5.13516.073829.3764
301.76840.3849-0.63580.2525-0.7074-0.00020.0218-0.0040.03550.0259-0.0243-0.02460.0011-0.01960.0026-0.0195-0.0255-0.06960.0881-0.08810.0165-17.10785.646851.8581
310.6534-0.9550.54551.48360.40130.51620.0052-0.12160.16120.07310.0238-0.1432-0.21620.0355-0.029-0.0586-0.003-0.00210.00430.0138-0.0813-0.18756.113253.6645
320.8377-0.41130.07661.8032-2.10751.5098-0.00680.027-0.0305-0.02730.0064-0.01560.04420.00340.00040.02590.00120.00240.0960.0079-0.0309-1.6771-16.554664.3166
330.20251.3533-0.32882.04181.57722.00770.0087-0.0389-0.00330.1292-0.0106-0.14770.02490.00530.0019-0.01790.0229-0.02880.13250.0284-0.06968.5403-9.49362.7473
340.425-1.2923-1.2040.9670.0448-0.00040.0034-0.02580.1042-0.1062-0.0581-0.0311-0.0993-0.09970.0547-0.06710.00390.00860.01120.0063-0.0386-2.26172.219349.6921
351.29741.258-0.84360-0.36240.80940.012-0.0174-0.0291-0.043-0.0340.0465-0.0679-0.06350.0219-0.08510.0422-0.0060.0734-0.02650.0063-17.3482.828140.2722
361.1890.9076-1.6790.00711.86840.5484-0.00720.02460.0084-0.0451-0.0089-0.083-0.01190.05190.0161-0.04130.0213-0.06040.08190.0334-0.03160.319511.619629.4943
37-0.0001-0.57620.22590.4864-0.03820.0001-0.0020.0148-0.0699-0.08820.02510.0530.0369-0.0626-0.0231-0.01960.01980.0426-0.01210.0499-0.021815.184550.47133.3649
380.56580.36230.86362.53761.15951.31160.0087-0.07540.18590.1598-0.03010.09350.0899-0.08290.0214-0.08490.1150.07950.0541-0.00830.035115.687549.532853.5397
392.4671.44190.47710-0.64182.7827-0.0165-0.05410.08230.0165-0.0384-0.0924-0.03540.0320.0549-0.00840.00050.0066-0.0657-0.0026-0.009126.507151.809554.7397
401.6105-0.39142.02020.05411.30071.2864-0.0014-0.01550.01290.058-0.002-0.04260.0674-0.03870.00340.0810.0083-0.0135-0.0269-0.0395-0.093928.411141.584157.53
413.64250.1324-1.75262.1273-1.00240.1997-0.0034-0.13730.00480.10780.07410.0296-0.0769-0.0357-0.0707-0.01020.0320.049-0.0208-0.0118-0.024116.556444.485751.0747
420.0223-1.3798-0.090.06720.16551.3177-0.00790.0634-0.0019-0.06150.03030.02560.00240.0257-0.0224-0.00530.03830.0417-0.07010.0107-0.018721.561446.329732.9573
432.0639-0.42230.95590.40411.17840.16420.00190.0208-0.0462-0.028-0.0026-0.04230.01060.03540.0006-0.00160.050.0537-0.0689-0.02470.101336.357927.070644.3739
443.23560.596-0.18333.47831.8524-0.0001-0.0015-0.0924-0.1190.08990.02020.04630.08280.0142-0.0186-0.10290.09450.0143-0.0254-0.0273-0.022522.612522.329947.2023
453.25940.5443-2.15295.4661-0.69060.60680.0263-0.0005-0.15570.1013-0.07630.15290.03440.00970.0501-0.0590.02880.0443-0.0962-0.0109-0.063715.660729.104452.3351
462.4421-0.2757-2.13720.8033-0.50152.92780.0124-0.0837-0.09550.09070.033-0.04230.03460.0735-0.04540.10350.05640.1402-0.09650.02670.002714.375529.109765.6095
470.5045-0.32920.18832.2728-0.55321.1384-0.0055-0.05770.0004-0.09430.0174-0.1670.1082-0.0133-0.0119-0.0890.05050.0144-0.0102-0.0373-0.06925.158432.019146.3405
480.37651.67921.11480.07621.10870.0004-0.00230.0035-0.0106-0.05340.00130.05570.0271-0.05560.00090.0557-0.01820.12620.0293-0.0045-0.063419.117641.211727.6991
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|-2 - 22}A-2 - 22
2X-RAY DIFFRACTION2{A|23 - 55}A23 - 55
3X-RAY DIFFRACTION3{A|56 - 63}A56 - 63
4X-RAY DIFFRACTION4{A|64 - 78}A64 - 78
5X-RAY DIFFRACTION5{A|79 - 120}A79 - 120
6X-RAY DIFFRACTION6{A|121 - 133}A121 - 133
7X-RAY DIFFRACTION7{A|134 - 167}A134 - 167
8X-RAY DIFFRACTION8{A|168 - 189}A168 - 189
9X-RAY DIFFRACTION9{A|190 - 205}A190 - 205
10X-RAY DIFFRACTION10{A|206 - 222}A206 - 222
11X-RAY DIFFRACTION11{A|223 - 282}A223 - 282
12X-RAY DIFFRACTION12{A|283 - 299}A283 - 299
13X-RAY DIFFRACTION13{B|-1 - 36}B-1 - 36
14X-RAY DIFFRACTION14{B|37 - 59}B37 - 59
15X-RAY DIFFRACTION15{B|60 - 116}B60 - 116
16X-RAY DIFFRACTION16{B|117 - 124}B117 - 124
17X-RAY DIFFRACTION17{B|125 - 138}B125 - 138
18X-RAY DIFFRACTION18{B|139 - 178}B139 - 178
19X-RAY DIFFRACTION19{B|179 - 193}B179 - 193
20X-RAY DIFFRACTION20{B|194 - 204}B194 - 204
21X-RAY DIFFRACTION21{B|205 - 227}B205 - 227
22X-RAY DIFFRACTION22{B|228 - 267}B228 - 267
23X-RAY DIFFRACTION23{B|268 - 282}B268 - 282
24X-RAY DIFFRACTION24{B|283 - 299}B283 - 299
25X-RAY DIFFRACTION25{C|-1 - 5}C-1 - 5
26X-RAY DIFFRACTION26{C|6 - 36}C6 - 36
27X-RAY DIFFRACTION27{C|37 - 59}C37 - 59
28X-RAY DIFFRACTION28{C|60 - 120}C60 - 120
29X-RAY DIFFRACTION29{C|121 - 132}C121 - 132
30X-RAY DIFFRACTION30{C|133 - 142}C133 - 142
31X-RAY DIFFRACTION31{C|143 - 193}C143 - 193
32X-RAY DIFFRACTION32{C|194 - 204}C194 - 204
33X-RAY DIFFRACTION33{C|205 - 226}C205 - 226
34X-RAY DIFFRACTION34{C|227 - 267}C227 - 267
35X-RAY DIFFRACTION35{C|268 - 282}C268 - 282
36X-RAY DIFFRACTION36{C|283 - 299}C283 - 299
37X-RAY DIFFRACTION37{D|-2 - 10}D-2 - 10
38X-RAY DIFFRACTION38{D|11 - 38}D11 - 38
39X-RAY DIFFRACTION39{D|39 - 59}D39 - 59
40X-RAY DIFFRACTION40{D|60 - 68}D60 - 68
41X-RAY DIFFRACTION41{D|69 - 117}D69 - 117
42X-RAY DIFFRACTION42{D|118 - 131}D118 - 131
43X-RAY DIFFRACTION43{D|132 - 145}D132 - 145
44X-RAY DIFFRACTION44{D|146 - 172}D146 - 172
45X-RAY DIFFRACTION45{D|173 - 201}D173 - 201
46X-RAY DIFFRACTION46{D|202 - 222}D202 - 222
47X-RAY DIFFRACTION47{D|223 - 282}D223 - 282
48X-RAY DIFFRACTION48{D|283 - 299}D283 - 299

+
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