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- PDB-2xct: The twinned 3.35A structure of S. aureus Gyrase complex with Cipr... -

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Basic information

Entry
Database: PDB / ID: 2xct
TitleThe twinned 3.35A structure of S. aureus Gyrase complex with Ciprofloxacin and DNA
Components
  • 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3'
  • 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3'
  • 5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3'
  • 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3'
  • DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
KeywordsISOMERASE/DNA/ANTIBIOTIC / ISOMERASE-DNA-ANTIBIOTIC COMPLEX
Function / homology
Function and homology information


DNA negative supercoiling activity / DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity / DNA topoisomerase (ATP-hydrolysing) / DNA topological change / DNA-templated DNA replication / chromosome / response to antibiotic / DNA binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily ...Rossmann fold - #670 / DNA gyrase, subunit A / DNA gyrase/topoisomerase IV, subunit A, C-terminal repeat / DNA gyrase/topoisomerase IV, subunit A, C-terminal / DNA gyrase C-terminal domain, beta-propeller / Topoisomerase (Topo) IIA-type catalytic domain profile. / DNA gyrase subunit B, TOPRIM domain / DNA gyrase, subunit B / DNA topoisomerase, type IIA, subunit B / DNA topoisomerase, type IIA, alpha-helical domain superfamily / DNA topoisomerase, type IIA, domain A / DNA topoisomerase, type IIA, domain A, alpha-beta / DNA gyrase/topoisomerase IV, subunit A / DNA Topoisomerase IV / DNA gyrase B subunit, C-terminal / DNA gyrase B subunit, carboxyl terminus / DNA topoisomerase, type IIA, subunit B, domain 2 / DNA gyrase B / DNA topoisomerase, type IIA / DNA topoisomerase, type IIA, conserved site / DNA topoisomerase II signature. / TopoisomeraseII / DNA topoisomerase, type IIA, subunit B, C-terminal / Toprim domain / DNA topoisomerase, type IIA-like domain superfamily / Toprim domain profile. / TOPRIM domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase-like ATPases / Histidine kinase/HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CPF / : / DNA / DNA (> 10) / DNA gyrase subunit B / DNA gyrase subunit A
Similarity search - Component
Biological speciesSTAPHYLOCOCCUS AUREUS (bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsBax, B.D. / Chan, P. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. ...Bax, B.D. / Chan, P. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. / Huang, J. / Jones, E. / Jones, J. / Brown, K.K. / Lewis, C.J. / May, E. / Singh, O. / Spitzfaden, C. / Shen, C. / Shillings, A. / Theobald, A. / Wohlkonig, A. / Pearson, N.D. / Gwynn, M.N.
CitationJournal: Nature / Year: 2010
Title: Type Iia Topoisomerase Inhibition by a New Class of Antibacterial Agents.
Authors: Bax, B.D. / Chan, P.F. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. / Huang, J. / Jones, E. / Jones, J. / Brown, K.K. / ...Authors: Bax, B.D. / Chan, P.F. / Eggleston, D.S. / Fosberry, A. / Gentry, D.R. / Gorrec, F. / Giordano, I. / Hann, M.M. / Hennessy, A. / Hibbs, M. / Huang, J. / Jones, E. / Jones, J. / Brown, K.K. / Lewis, C.J. / May, E.W. / Saunders, M.R. / Singh, O. / Spitzfaden, C. / Shen, C. / Shillings, A. / Theobald, A.F. / Wohlkonig, A. / Pearson, N.D. / Gwynn, M.N.
History
DepositionApr 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
D: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
E: 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3'
F: 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3'
G: 5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3'
H: 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3'
S: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
U: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
V: 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3'
W: 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3'
X: 5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3'
Y: 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)338,53124
Polymers336,76612
Non-polymers1,76512
Water0
1
B: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
D: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
E: 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3'
F: 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3'
G: 5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3'
H: 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,26512
Polymers168,3836
Non-polymers8826
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15000 Å2
ΔGint-73.9 kcal/mol
Surface area57690 Å2
MethodPISA
2
S: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
U: DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A
V: 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3'
W: 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3'
X: 5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3'
Y: 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,26512
Polymers168,3836
Non-polymers8826
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18550 Å2
ΔGint-105.3 kcal/mol
Surface area57280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.984, 123.166, 170.418
Angle α, β, γ (deg.)90.00, 90.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules BDSU

#1: Protein
DNA GYRASE SUBUNIT B, DNA GYRASE SUBUNIT A /


Mass: 78109.000 Da / Num. of mol.: 4
Fragment: GYRB- C-TERMINAL 27KDA DOMAIN, RESIDUES 410-543 AND 580-644, GYRA- N-TERMINAL 56KDA DOMAIN, RESIDUES 2-491
Mutation: YES
Source method: isolated from a genetically manipulated source
Details: C-TERMINUS GYRB (644) FUSED TO N-TERMINUS GYRA (1002). GREEK KEY DOMAIN (544-579) DELETED AND REPLACED WITH TWO RESIDUES, TG
Source: (gene. exp.) STAPHYLOCOCCUS AUREUS (bacteria) / Strain: N315 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P66937, UniProt: Q99XG5, EC: 5.99.1.3

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DNA chain , 4 types, 8 molecules EVFWGXHY

#2: DNA chain 5'-D(TP*GP*TP*GP*CP*GP*GP*T)-3'


Mass: 2473.626 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(AP*GP*CP*CP*GP*TP*AP*G)-3'


Mass: 2451.630 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#4: DNA chain 5'-D(GP*TP*AP*CP*CP*CP*AP*CP*GP*GP*CP*T)-3'


Mass: 3623.368 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#5: DNA chain 5'-D(GP*TP*AP*CP*AP*CP*CP*GP*CP*AP*CP*A)-3'


Mass: 3616.383 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 2 types, 12 molecules

#6: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn
#7: Chemical
ChemComp-CPF / 1-CYCLOPROPYL-6-FLUORO-4-OXO-7-PIPERAZIN-1-YL-1,4-DIHYDROQUINOLINE-3-CARBOXYLIC ACID / ciprofloxacin / Ciprofloxacin


Mass: 331.342 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C17H18FN3O3 / Comment: antibiotic*YM

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN B, TYR 1123 TO PHE ENGINEERED RESIDUE IN CHAIN D, TYR 1123 TO PHE ...ENGINEERED RESIDUE IN CHAIN B, TYR 1123 TO PHE ENGINEERED RESIDUE IN CHAIN D, TYR 1123 TO PHE ENGINEERED RESIDUE IN CHAIN S, TYR 1123 TO PHE ENGINEERED RESIDUE IN CHAIN U, TYR 1123 TO PHE
Sequence detailsRESIDUES 544-579 DELETED AND REPLACED WITH TWO AMINO ACIDS, TG. THE C-TERMINUS OF GYRB (6B44) IS ...RESIDUES 544-579 DELETED AND REPLACED WITH TWO AMINO ACIDS, TG. THE C-TERMINUS OF GYRB (6B44) IS FUSED TO THE N- TERMINUS OF GYRA (A2) CATALYTIC TYROSINE (A123/B1123) MUTATED TO PHENYLALANINE. DNA (8MER, 12MER ON TOP 5'-3', 12MER, 8MER UNDER 3'-5') DNA CALLED 8-3NN - FOUR STRANDS (CALLED 8-3,12-3,12-4,8-4) CAN ANNEAL TO GIVE 3 DIFFERENT DUPLEXES 5' TGTGCGGT GTAC- CTACGGCT 8-3 12-3 3' ACACGCCA-CATG GATGCCGA 12-4 8-4 5' TGTGCGGT GTAC-ACCGCACA 8-3 12-3 3' ACACGCCA-CATG TGGCGTGT 12-3 8-3 5' AGCCGTAG GTAC-CTACGGCT 8-4 12-3 3' TCGGCATC- CATG GATGCCGA 12-3 8-4

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.43 % / Description: NONE
Crystal growpH: 6.2 / Details: 11% PEG 3350, 0.15M BIS TRIS PH 6.2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.324
ReflectionResolution: 3.35→25 Å / Num. obs: 52713 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 76.3 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 11.1
Reflection shellResolution: 3.35→3.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.7 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→24.956 Å / SU ML: 0 / σ(F): 1.38 / Phase error: 37.56 / Stereochemistry target values: TWIN_LSQ_F
Details: THE DATA ARE IN P21, BUT WITH A BETA ANGLE OF 90 DEGREES.BECAUSE THE DATA ARE PSEUDO ORTHORHOMBIC. AUTHOR SELECTED THE R-FREE IN THE ABOVE MENTIONED RESOLUTION SHELLS. THIS IS NOT A STANDARD ...Details: THE DATA ARE IN P21, BUT WITH A BETA ANGLE OF 90 DEGREES.BECAUSE THE DATA ARE PSEUDO ORTHORHOMBIC. AUTHOR SELECTED THE R-FREE IN THE ABOVE MENTIONED RESOLUTION SHELLS. THIS IS NOT A STANDARD SPACE GROUP FOR A TWIN OPERATOR.
RfactorNum. reflection% reflection
Rfree0.2363 2148 4.1 %
Rwork0.1664 --
obs0.1692 52173 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.369 Å2 / ksol: 0.291 e/Å3
Displacement parametersBiso mean: 73.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.157 Å20 Å25.3898 Å2
2--15.7485 Å2-0 Å2
3----24.7844 Å2
Refinement stepCycle: LAST / Resolution: 3.35→24.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20781 1461 104 0 22346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02422861
X-RAY DIFFRACTIONf_angle_d1.44231150
X-RAY DIFFRACTIONf_dihedral_angle_d20.4728689
X-RAY DIFFRACTIONf_chiral_restr0.0823550
X-RAY DIFFRACTIONf_plane_restr0.0053859
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.35-3.40770.32881410.21142487X-RAY DIFFRACTION98
3.4077-3.46950.2875550.20052518X-RAY DIFFRACTION98
3.4695-3.5360.2556860.19842504X-RAY DIFFRACTION98
3.536-3.6080.28741410.19592444X-RAY DIFFRACTION98
3.608-3.68620.2571410.18282475X-RAY DIFFRACTION98
3.6862-3.7717000.18122558X-RAY DIFFRACTION98
3.7717-3.86570.20321410.17592494X-RAY DIFFRACTION98
3.8657-3.96980.24491410.16772417X-RAY DIFFRACTION98
3.9698-4.08610.22811410.16522475X-RAY DIFFRACTION98
4.0861-4.2174000.15442597X-RAY DIFFRACTION98
4.2174-4.36740.22141410.14972445X-RAY DIFFRACTION98
4.3674-4.54120.20451410.14242448X-RAY DIFFRACTION98
4.5412-4.74650.22741410.14392501X-RAY DIFFRACTION98
4.7465-4.9949000.1442581X-RAY DIFFRACTION98
4.9949-5.30510.22141410.14772483X-RAY DIFFRACTION98
5.3051-5.71010.28871410.16262464X-RAY DIFFRACTION98
5.7101-6.27650.29681410.16822475X-RAY DIFFRACTION98
6.2765-7.1658000.18092637X-RAY DIFFRACTION98
7.1658-8.95820.23831410.15522516X-RAY DIFFRACTION98
8.9582-24.95660.17631410.17672539X-RAY DIFFRACTION98
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)
10.9306-0.1717-0.07910.1593-0.1299-0.15280.04840.1751-0.0667-0.0529-0.0047-0.00220.0301-0.0153-0.03490.30650.0282-0.03830.3247-0.02680.359813.830330.462881.7539
20.44040.1010.35110.24-0.22180.64840.02080.16880.1346-0.00520.02150.1235-0.011-0.0769-0.0430.16510.0067-0.04150.17610.10260.32154.818262.455264.0615
30.13660.26950.1620.36240.10480.22540.15990.0612-0.0447-0.1003-0.1850.14740.04950.01550.04380.310.0751-0.06510.2625-0.04840.1751.029942.1024132.9771
40.1111-0.04090.22570.4482-0.10940.2157-0.01030.2428-0.3556-0.01950.03060.2320.0030.2067-0.0690.2531-0.0284-0.02910.43830.11310.586923.595759.800572.2793
50.2712-0.10240.23240.782-0.48330.8966-0.1512-0.10060.09150.04560.06080.0005-0.054-0.19430.06050.2475-0.0119-0.0960.4002-0.0090.3754-29.778851.911182.2621
60.4959-0.1105-0.28820.4866-0.077-0.25080.23320.2913-0.2184-0.1534-0.0536-0.07650.10830.208-0.11690.36290.1225-0.10260.2472-0.09760.2559-14.059417.03463.1686
70.25450.0336-0.13660.085-0.01240.0655-0.0895-0.0543-0.08580.1676-0.03020.0239-0.1399-0.49610.05060.34050.06110.02870.42510.03160.1678-19.154838.238131.8792
8-0.13750.66440.04170.8620.49690.937-0.00320.0319-0.1057-0.15070.2564-0.23640.087-0.2747-0.19460.2539-0.1125-0.12390.16910.03790.203-33.884320.007969.0069
90.8404-0.2442-0.6778-0.11150.03690.5083-0.25790.0373-0.26070.02670.08040.1030.12070.11640.10810.60060.03270.13630.4066-0.00870.487757.288730.0654-5.7269
100.46290.1534-0.66330.24160.04770.29250.1010.0785-0.1081-0.1572-0.0007-0.07150.0820.0171-0.05940.8043-0.00770.00770.6111-0.07730.562627.966316.737-20.8361
110.1490.03420.16220.1009-0.04440.33830.03110.0257-0.0229-0.0186-0.1480.06580.13270.30270.06910.34880.0841-0.04350.42270.00510.154850.890441.43146.6307
120.38180.1821-0.12220.0109-0.61121.13730.1293-0.01360.02160.2183-0.0331-0.1302-0.57680.17-0.09310.7044-0.130.17860.45110.01320.592767.084658.4173-15.9857
130.2732-0.0365-0.22290.47690.30360.98250.05030.00780.1025-0.0657-0.0047-0.0172-0.2148-0.1392-0.01220.21240.07630.01740.20260.02670.187413.831951.52750.0035
140.281-0.3059-0.136-0.04280.2260.33010.41610.22160.3796-0.0831-0.2045-0.174-0.6316-0.0913-0.10370.51350.11710.17710.24770.10360.380346.907162.4124-22.5056
150.7138-0.3821-0.2670.8001-0.00240.1366-0.36740.2092-0.03520.36580.20520.07020.03530.12310.07320.2821-0.02660.04280.24340.01980.169730.674837.736648.1567
160.96351.38921.39921.3542-0.24611.23180.3087-0.2344-0.31620.2435-0.0708-0.4464-0.2132-0.2522-0.13550.48050.03640.05480.46460.00610.4477.804620.7355-12.5674
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1((CHAIN B AND (RESID 1029:1374 OR RESID 1451:1491)) OR (CHAIN E) OR (CHAIN F) OR CHAIN G) OR (CHAIN H))
2X-RAY DIFFRACTION2((CHAIN B AND (RESID 417:545 OR RESID 580:606)))
3X-RAY DIFFRACTION3((CHAIN B AND (RESID 1375:1450)))
4X-RAY DIFFRACTION4((CHAIN B AND (RESID 1019:1028)) OR (CHAIN B AND (RESID 609:637)))
5X-RAY DIFFRACTION5((CHAIN D AND (RESID 1030:1374 OR RESID 1451:1491)))
6X-RAY DIFFRACTION6((CHAIN D AND (RESID 417:545 OR RESID 580:606)))
7X-RAY DIFFRACTION7((CHAIN D AND (RESID 1375:1450)))
8X-RAY DIFFRACTION8((CHAIN D AND (RESID 1010:1028)) OR (CHAIN D AND (RESID 607:639)))
9X-RAY DIFFRACTION9((CHAIN S AND (RESID 1029:1374 OR RESID 1451:1491)) OR (CHAIN V) OR (CHAIN W) OR CHAIN X) OR (CHAIN Y))
10X-RAY DIFFRACTION10((CHAIN S AND (RESID 417:545 OR RESID 580:606)))
11X-RAY DIFFRACTION11((CHAIN S AND (RESID 1375:1450)))
12X-RAY DIFFRACTION12((CHAIN S AND (RESID 1012:1028)) OR (CHAIN U AND (RESID 609:639)))
13X-RAY DIFFRACTION13((CHAIN U AND (RESID 1029:1374 OR RESID 1451:1491)))
14X-RAY DIFFRACTION14((CHAIN U AND (RESID 418:544 OR RESID 581:608)))
15X-RAY DIFFRACTION15((CHAIN U AND (RESID 1375:1450)))
16X-RAY DIFFRACTION16((CHAIN U AND (RESID 1013:1028)) OR (CHAIN S AND (RESID 609:639)))

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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

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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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