[English] 日本語
Yorodumi
- PDB-4aln: Crystal structure of S. aureus FabI (P32) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4aln
TitleCrystal structure of S. aureus FabI (P32)
ComponentsENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
KeywordsOXIDOREDUCTASE / SHORT-CHAIN DEHYDROGENASE/REDUCTASE SUPERFAMILY / FATTY ACID BIOSYNTHESIS / LIPID SYNTHESIS
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / : / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding / identical protein binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Enoyl-[acyl-carrier-protein] reductase [NADPH] / Enoyl-[acyl-carrier-protein] reductase [NADPH]
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsSchiebel, J. / Kisker, C.
CitationJournal: Structure / Year: 2012
Title: Staphylococcus Aureus Fabi: Inhibition, Substrate Recognition and Potential Implications for in Vivo Essentiality
Authors: Schiebel, J. / Chang, A. / Lu, H. / Baxter, M.V. / Tonge, P.J. / Kisker, C.
History
DepositionMar 4, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
C: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
D: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
E: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
F: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
G: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
H: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
I: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
J: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
K: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
L: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]


Theoretical massNumber of molelcules
Total (without water)373,73112
Polymers373,73112
Non-polymers00
Water4,504250
1
A: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
B: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
C: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
D: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]


Theoretical massNumber of molelcules
Total (without water)124,5774
Polymers124,5774
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9410 Å2
ΔGint-51.8 kcal/mol
Surface area36030 Å2
MethodPISA
2
E: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
F: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
G: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
H: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]


Theoretical massNumber of molelcules
Total (without water)124,5774
Polymers124,5774
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-50.8 kcal/mol
Surface area36660 Å2
MethodPISA
3
I: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
J: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
K: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]
L: ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH]


Theoretical massNumber of molelcules
Total (without water)124,5774
Polymers124,5774
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8830 Å2
ΔGint-46.7 kcal/mol
Surface area35930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.780, 123.780, 190.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

-
Components

#1: Protein
ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADPH] / ENR / ENOYL-ACP REDUCTASE


Mass: 31144.240 Da / Num. of mol.: 12 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: N315 / Plasmid: PETM-11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7A6D8, UniProt: A0A0H3JLH9*PLUS, EC: 1.3.1.10
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN B, LEU 2 TO VAL ENGINEERED ...ENGINEERED RESIDUE IN CHAIN A, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN B, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN C, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN D, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN E, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN F, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN G, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN H, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN I, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN J, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN K, LEU 2 TO VAL ENGINEERED RESIDUE IN CHAIN L, LEU 2 TO VAL

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.99 Å3/Da / Density % sol: 58.59 % / Description: NONE
Crystal growDetails: 0.61 M NH4H2PO4, 9% T-BUTANOL, 0.01 M EDTA PH 7.0

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.919
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.674
11K, H, -L20.326
ReflectionResolution: 3.05→50 Å / Num. obs: 61623 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 2.6 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 6.76
Reflection shellResolution: 3.05→3.2 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.12 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4ALL
Resolution: 3.05→44.28 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.9 / SU B: 32.195 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24554 3064 5 %RANDOM
Rwork0.20292 ---
obs0.20509 58556 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.113 Å2
Baniso -1Baniso -2Baniso -3
1-18.01 Å20 Å20 Å2
2--18.01 Å20 Å2
3----36.01 Å2
Refinement stepCycle: LAST / Resolution: 3.05→44.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19811 0 0 250 20061
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02220036
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4821.96927002
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.90852521
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46625.499911
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.079153648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.0151593
X-RAY DIFFRACTIONr_chiral_restr0.090.23160
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214731
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.391.512646
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.575220261
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.76737390
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.5954.56741
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: 3.048→3.127 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.394 168 -
Rwork0.266 4271 -
obs--96.67 %
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)
12.25250.41260.06042.0502-1.11263.779-0.0925-0.21660.19820.10620.1191-0.1632-0.6888-0.1662-0.02660.44970.07370.01550.3527-0.05120.150844.6385-10.381318.9036
24.6219-1.78520.2358-0.1743-0.32871.5475-0.3193-0.0115-0.1588-0.01120.0957-0.1134-0.0476-0.11220.22360.3-0.0255-0.01060.2720.00110.232353.0018-24.194418.815
30.1472-1.04930.46420.6396-0.15121.68980.0833-0.01290.1537-0.0233-0.0427-0.20670.07470.1553-0.04060.3575-0.0295-0.01580.3094-0.00260.229154.3301-25.031310.3122
41.31740.5801-0.85752.1383-1.06191.4805-0.06740.06620.2014-0.14270.0591-0.2283-0.20840.20010.00830.3753-0.03-0.00120.3913-0.07470.227653.9559-15.2414-0.7984
52.0011-0.23671.00822.8357-0.22594.04940.1175-0.10930.18350.24710.1435-0.1270.17910.1233-0.2610.28060.02260.0080.2136-0.02230.096977.1543-52.241217.5571
61.50581.0870.05052.87131.30622.85920.04660.12170.23560.1124-0.0378-0.0160.23850.1143-0.00880.22610.0025-0.02350.2691-0.00590.099579.6057-46.759622.6294
7-0.4937-1.31930.54631.03850.59881.4205-0.0172-0.02350.145-0.03510.038-0.05430.1282-0.089-0.02080.3066-0.0423-0.00730.3243-0.02020.237371.0062-35.213618.0649
81.13-0.3887-0.4190.99920.03731.4598-0.062-0.2177-0.0978-0.1996-0.00280.04560.1105-0.01480.06480.3055-0.0234-0.00330.33670.02470.180868.3782-36.89769.6827
90.26070.63540.28012.32830.02411.9573-0.1395-0.09380.0732-0.0982-0.04410.38650.1979-0.28140.18360.33410.00640.0140.3451-0.00390.219963.7159-50.04432.9626
102.1519-0.24611.39847.3701-4.82367.4950.29690.1938-0.29190.16510.0034-0.40750.26050.6972-0.30030.33690.11330.0480.4254-0.05060.128680.3554-50.5678-16.8031
111.5197-0.68981.2134-0.0261-0.46643.6320.16180.14330.1873-0.0868-0.0067-0.05550.19130.5302-0.15510.40290.10530.03930.4174-0.04540.178175.5173-51.9865-26.1509
120.5707-1.9340.56273.6408-1.24242.32170.1622-0.01450.03050.085-0.10480.36550.12580.2369-0.05740.3667-0.0060.02670.345-0.00540.234862.844-43.2727-20.3442
132.2848-2.50470.8379-2.36221.47552.7273-0.1215-0.01740.12230.11010.0984-0.20720.1434-0.12990.02310.3213-0.01920.01490.32890.01530.162163.6968-41.641-12.5091
140.8465-0.21670.2893.54510.88051.51170.0555-0.18850.1508-0.0799-0.1187-0.3281-0.15870.32230.06320.3026-0.0018-0.00690.41220.00050.150276.3469-36.0797-5.8147
154.6449-0.65310.9934-0.6031-0.44992.6425-0.0645-0.0087-0.0630.08160.07640.05830.1231-0.153-0.0120.29840.0110.04070.26-0.02750.140233.472-20.8779-15.6519
163.3852-0.6242-1.4751-0.00560.2812.32020.02910.2556-0.0963-0.1588-0.1454-0.00120.0135-0.31270.11630.28250.0605-0.01120.29860.01630.13535.267-21.6118-25.4695
171.6303-3.5467-0.0494.2726-0.1718-0.0675-0.03520.0236-0.07080.11980.085-0.03840.0594-0.0101-0.04980.29550.02220.02340.3109-0.00480.204549.8843-27.0155-21.7652
181.81190.3704-1.0615-2.23991.03471.7645-0.0625-0.1098-0.0060.21120.11180.04880.28480.0234-0.04930.3185-0.002-0.00740.32170.05260.189652.5727-27.5743-13.547
192.0198-0.85121.33180.02660.40864.17740.1-0.1914-0.226-0.2604-0.19060.19710.13170.01340.09050.36740.0548-0.00380.3060.00930.207342.4105-22.8982-4.7099
204.24932.69210.6761.26970.52021.5930.08990.08320.0362-0.16890.00930.1411-0.531-0.1604-0.09920.52690.1090.00510.40440.00910.2367-13.890329.5483-9.7878
212.0695-2.9151-0.13682.3683-0.84734.7502-0.15840.35280.2343-0.3572-0.14410.2885-1.4988-0.58470.30250.83430.2319-0.18510.45130.05710.3826-18.062831.2348-18.3972
223.26090.5365-0.91460.67360.8054-0.58620.14080.17310.1637-0.19480.1964-0.1167-0.1410.1132-0.33710.5657-0.00320.02280.29750.05110.1505-7.050325.1456-22.8457
230.31211.11350.3816.17190.63411.31620.0429-0.18-0.0357-0.0952-0.0051-0.1355-0.145-0.1423-0.03780.4224-0.00930.02470.3879-0.03540.1044-5.374313.9392-17.6249
24-1.7425-0.47071.41813.76292.07942.17710.07530.01690.01530.2039-0.05440.0658-0.1023-0.1308-0.02090.3791-0.01070.02310.3464-0.02610.195-2.031512.7405-9.7274
251.64470.4553-0.93110.69980.49382.1489-0.1857-0.079-0.18-0.17330.00950.18410.0633-0.27070.17620.37030.0038-0.00640.36980.00930.2939-14.004216.70342.2301
264.4696-1.64190.27981.1332-0.03434.99670.3118-0.05860.1830.30350.00730.33930.1159-0.0681-0.31910.26060.02850.03190.225-0.04990.11847.1208-20.4983-13.2824
271.8386-0.706-1.22683.3464-3.547311.94510.07350.4589-0.1405-0.1271-0.27580.03260.49760.39810.20230.17850.0818-0.02130.2982-0.09370.21838.3399-23.8622-20.0472
282.8599-0.28270.65284.2601-1.21124.34660.06110.0923-0.17750.2294-0.03860.0886-0.2209-0.1366-0.02250.2041-0.0167-0.03190.2790.02630.1017-4.1452-18.2612-21.7195
290.06791.2708-0.60095.0023-0.98892.69230.09320.0034-0.01660.1269-0.1748-0.0277-0.21490.11890.08160.2769-0.0172-0.04320.36460.00890.2364-4.5461-7.2947-16.6132
300.9208-0.5393-1.46761.4226-2.25193.712-0.01390.07450.11320.0607-0.0158-0.1265-0.01670.06630.02970.3818-0.01460.02240.3837-0.05240.1647-2.4375-3.9846-9.009
315.30183.61340.51851.8772-1.33122.7731-0.055-0.1212-0.09170.1714-0.06230.0782-0.18510.04110.11730.38370.075-0.00010.30140.0010.12415.8666-11.9729-1.3993
322.6247-0.7873-1.8914.9020.03961.06020.0894-0.0594-0.35850.32740.04310.06180.7145-0.0998-0.13250.5775-0.0021-0.11490.38210.02630.2123.1476-23.381316.6006
332.26251.42140.83182.58670.23152.56510.2289-0.0511-0.38470.3631-0.07290.2580.5126-0.1162-0.1560.50790.0857-0.02770.41460.00280.19397.2073-19.73426.7446
341.6615-1.35730.21342.88160.79970.1693-0.05270.4007-0.21920.0555-0.04850.25790.03660.18120.10120.3820.024-0.02260.39950.01510.18977.4285-5.26821.3825
35-5.58720.409-0.52370.4884-0.01373.39620.27520.26980.1076-0.063-0.2345-0.17520.0364-0.3666-0.04070.38490.0217-0.0060.4222-0.02520.24268.0434-3.762412.9969
36-0.3072-0.27810.16481.45530.05521.8928-0.0414-0.0417-0.20070.2328-0.00580.2166-0.0365-0.44950.04720.4217-0.00660.00460.46190.02130.1926-6.7047-12.70727.1898
374.8541-2.04420.76283.0615-1.47963.07340.17970.1743-0.12460.0905-0.0805-0.0361-0.21880.0242-0.09920.35640.00220.02850.204-0.02480.11412.032232.063817.0899
383.90441.5192-1.28862.3856-1.43722.97030.0968-0.1016-0.08420.3035-0.156-0.0174-0.3760.08690.05920.36410.0264-0.04470.1775-0.01820.08381.571330.041426.7934
392.5365-3.95640.97274.8593-1.46683.06960.1259-0.0609-0.1666-0.18730.03150.04240.02970.2284-0.15740.3552-0.0436-0.00540.2629-0.00030.2438-0.225114.637522.6178
40-0.2621-0.0416-0.35442.2680.73760.23270.21050.1171-0.2776-0.2563-0.2058-0.2413-0.12320.1383-0.00470.42710.01930.00180.4997-0.02590.2057-0.926412.494214.3366
411.94280.7287-0.52582.1103-0.65752.3302-0.17950.3432-0.1784-0.4025-0.0051-0.32210.11530.3020.18450.4612-0.03980.04490.4412-0.02190.26655.945820.93722.9191
42-0.74831.29090.97424.9755-1.01124.17080.0580.25950.17020.53040.1027-0.4298-0.35250.7287-0.16070.5947-0.12360.02790.7112-0.00110.444128.3421-56.291616.5908
43-0.1299-0.3304-0.64710.20870.97872.31160.1126-0.2329-0.0712-0.0389-0.0537-0.21-0.20890.2953-0.05890.7674-0.1437-0.06450.69020.04410.473325.8244-57.508528.0907
440.93231.377-0.4422.4814-0.62640.53690.1766-0.2931-0.05620.0862-0.1604-0.1748-0.27350.0541-0.01620.5913-0.03580.0170.5253-0.03010.425211.259-62.74224.4004
451.75741.2288-0.43242.74510.0281-0.25820.24760.0603-0.24650.0013-0.24180.0675-0.12230.0062-0.00580.6142-0.0103-0.03580.419-0.00820.46658.3455-62.874916.3172
46-0.20650.8551-0.7082-0.3789-1.1590.59710.08580.14480.11060.1004-0.2105-0.0940.0894-0.06090.12470.4957-0.0429-0.04140.5584-0.03140.455520.7583-67.20424.6122
473.1455-0.11170.28923.11114.18717.24120.2494-0.2440.1819-0.16970.32990.05520.1676-0.424-0.57940.4527-0.0839-0.03940.48940.14690.3771-19.7086-85.958119.3607
485.4066-1.1863-0.27444.33780.33921.27850.0654-0.293-0.05320.15240.12150.38580.0548-0.4124-0.18680.5579-0.1003-0.01750.52030.05410.3958-15.3056-87.322628.9742
492.3012.69090.86781.44111.26060.60140.1882-0.01990.12350.0367-0.1056-0.0823-0.05210.0431-0.08260.579-0.0121-0.06270.47960.04010.3811-1.7563-80.914223.3919
50-0.84310.51070.0482-3.85520.54734.1017-0.06480.0754-0.015-0.08730.00630.0813-0.10370.13550.05840.53570.0028-0.03740.459-0.03540.4438-0.8072-80.194214.6488
512.1401-1.22371.2402-0.64160.74722.70170.09430.0165-0.0137-0.0367-0.07280.0701-0.3355-0.1954-0.02150.5698-0.0070.08220.5660.00820.4632-15.0988-72.54967.8199
520.8797-1.4041-0.0809-0.7582-0.35563.39920.1150.2422-0.2818-0.18750.01040.13650.4642-0.211-0.12540.7001-0.0986-0.09020.7348-0.06430.5303-16.5339-89.1871-16.7581
53-0.523-0.6577-1.68084.7852-1.55772.1015-0.07420.0188-0.1101-0.2290.221-0.00640.2836-0.1537-0.14680.3609-0.101-0.08530.76530.07430.3428-19.6625-77.1609-19.6174
541.05491.10631.3062-0.04410.68790.2831-0.0499-0.0671-0.0619-0.16830.1426-0.10230.1595-0.2346-0.09270.5713-0.0305-0.01360.70930.06230.4692-8.7646-72.6538-15.1457
554.8033-1.3171-2.65920.94291.07141.60210.1824-0.00950.22560.09-0.036-0.0947-0.1597-0.0984-0.14640.4047-0.00340.0120.5142-0.00310.3844-7.0195-71.2511-7.3359
56-0.4848-0.83440.71771.4377-1.46651.1387-0.07690.10630.16570.0301-0.0695-0.19170.32160.09120.14640.57770.0155-0.01340.6291-0.05810.4655-2.6149-86.4884-0.1941
577.6152-5.08772.39984.15672.01554.21660.1635-0.1225-0.0151-0.00240.0423-0.1117-0.1871-0.2096-0.20580.5925-0.05530.04180.44670.10110.347918.3695-46.0179-8.7724
583.71670.35647.06082.24442.61397.20130.2210.27840.3929-0.2365-0.44090.0348-0.12020.32720.21980.557-0.10830.11260.56130.03270.472517.9582-41.8686-17.5651
592.2637-0.5877-0.27540.7347-1.04383.0949-0.2790.33510.0442-0.2149-0.05580.19320.0070.13620.33480.4703-0.048-0.03270.4776-0.05070.423318.3237-54.5551-21.5284
602.3785-1.0336-0.30181.0776-1.54560.9002-0.1351-0.3907-0.0531-0.15370.1007-0.02050.1087-0.12260.03440.456-0.02150.03550.4196-0.1150.33339.7591-61.8469-16.3784
61-1.55991.6128-0.23422.4889-0.4958-0.1069-0.0685-0.0389-0.1944-0.09220.17180.07-0.1032-0.1022-0.10320.3920.04-0.01130.4519-0.02510.449111.5956-65.2133-8.314
620.5593-0.4353-0.16692.7247-1.34862.1848-0.3198-0.22980.0340.41270.31640.0775-0.1792-0.2720.00340.5035-0.02780.05330.4791-0.00080.421214.4303-54.80860.6971
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 98
2X-RAY DIFFRACTION2A107 - 147
3X-RAY DIFFRACTION3A154 - 194
4X-RAY DIFFRACTION4A205 - 255
5X-RAY DIFFRACTION5B3 - 46
6X-RAY DIFFRACTION6B47 - 96
7X-RAY DIFFRACTION7B109 - 146
8X-RAY DIFFRACTION8B158 - 194
9X-RAY DIFFRACTION9B205 - 255
10X-RAY DIFFRACTION10C3 - 39
11X-RAY DIFFRACTION11C40 - 94
12X-RAY DIFFRACTION12C107 - 148
13X-RAY DIFFRACTION13C157 - 194
14X-RAY DIFFRACTION14C203 - 255
15X-RAY DIFFRACTION15D3 - 40
16X-RAY DIFFRACTION16D41 - 94
17X-RAY DIFFRACTION17D109 - 146
18X-RAY DIFFRACTION18D156 - 190
19X-RAY DIFFRACTION19D222 - 251
20X-RAY DIFFRACTION20E3 - 30
21X-RAY DIFFRACTION21E31 - 61
22X-RAY DIFFRACTION22E62 - 94
23X-RAY DIFFRACTION23E107 - 147
24X-RAY DIFFRACTION24E157 - 190
25X-RAY DIFFRACTION25E203 - 256
26X-RAY DIFFRACTION26F3 - 25
27X-RAY DIFFRACTION27F26 - 61
28X-RAY DIFFRACTION28F62 - 94
29X-RAY DIFFRACTION29F109 - 147
30X-RAY DIFFRACTION30F154 - 191
31X-RAY DIFFRACTION31F222 - 255
32X-RAY DIFFRACTION32G3 - 32
33X-RAY DIFFRACTION33G33 - 97
34X-RAY DIFFRACTION34G109 - 148
35X-RAY DIFFRACTION35G159 - 189
36X-RAY DIFFRACTION36G203 - 255
37X-RAY DIFFRACTION37H3 - 40
38X-RAY DIFFRACTION38H41 - 94
39X-RAY DIFFRACTION39H108 - 147
40X-RAY DIFFRACTION40H156 - 193
41X-RAY DIFFRACTION41H206 - 255
42X-RAY DIFFRACTION42I3 - 34
43X-RAY DIFFRACTION43I35 - 94
44X-RAY DIFFRACTION44I109 - 146
45X-RAY DIFFRACTION45I157 - 189
46X-RAY DIFFRACTION46I205 - 255
47X-RAY DIFFRACTION47J3 - 39
48X-RAY DIFFRACTION48J40 - 93
49X-RAY DIFFRACTION49J109 - 146
50X-RAY DIFFRACTION50J159 - 190
51X-RAY DIFFRACTION51J205 - 253
52X-RAY DIFFRACTION52K3 - 68
53X-RAY DIFFRACTION53K69 - 94
54X-RAY DIFFRACTION54K109 - 148
55X-RAY DIFFRACTION55K157 - 190
56X-RAY DIFFRACTION56K204 - 255
57X-RAY DIFFRACTION57L3 - 30
58X-RAY DIFFRACTION58L31 - 61
59X-RAY DIFFRACTION59L62 - 94
60X-RAY DIFFRACTION60L108 - 146
61X-RAY DIFFRACTION61L159 - 189
62X-RAY DIFFRACTION62L222 - 252

+
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://pdbjlvh1.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