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- PDB-5ux9: The crystal structure of chloramphenicol acetyltransferase from V... -

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Basic information

Entry
Database: PDB / ID: 5ux9
TitleThe crystal structure of chloramphenicol acetyltransferase from Vibrio fischeri ES114
ComponentsChloramphenicol acetyltransferase
KeywordsTRANSFERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


chloramphenicol O-acetyltransferase / chloramphenicol O-acetyltransferase activity
Similarity search - Function
Hexapeptide transferase, conserved site / Hexapeptide-repeat containing-transferases signature. / Hexapeptide repeat proteins / UDP N-Acetylglucosamine Acyltransferase; domain 1 / Hexapeptide repeat / Bacterial transferase hexapeptide (six repeats) / Trimeric LpxA-like superfamily / 3 Solenoid / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / FORMIC ACID / Chloramphenicol acetyltransferase
Similarity search - Component
Biological speciesVibrio fischeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.7 Å
AuthorsTan, K. / Zhou, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: The crystal structure of chloramphenicol acetyltransferase from Vibrio fischeri ES114
Authors: Tan, K. / Zhou, M. / Anderson, W.F. / Joachimiak, A.
History
DepositionFeb 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chloramphenicol acetyltransferase
B: Chloramphenicol acetyltransferase
C: Chloramphenicol acetyltransferase
D: Chloramphenicol acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,99127
Polymers100,1094
Non-polymers1,88223
Water1,54986
1
A: Chloramphenicol acetyltransferase
B: Chloramphenicol acetyltransferase
C: Chloramphenicol acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,40820
Polymers75,0823
Non-polymers1,32617
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13480 Å2
ΔGint-123 kcal/mol
Surface area25920 Å2
MethodPISA
2
D: Chloramphenicol acetyltransferase
hetero molecules

D: Chloramphenicol acetyltransferase
hetero molecules

D: Chloramphenicol acetyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,74821
Polymers75,0823
Non-polymers1,66618
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area15190 Å2
ΔGint-91 kcal/mol
Surface area25640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)147.426, 147.426, 101.211
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Chloramphenicol acetyltransferase /


Mass: 25027.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio fischeri (strain ATCC 700601 / ES114) (bacteria)
Strain: ATCC 700601 / ES114 / Gene: VF_A0790 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic
References: UniProt: Q5DZD6, chloramphenicol O-acetyltransferase

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Non-polymers , 6 types, 109 molecules

#2: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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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: 3.21 Å3/Da / Density % sol: 61.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Magnesium Chloride, 0.1 M MES:NaOH, 10% (w/v) PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97919 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 34158 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 38.1 Å2 / Rmerge(I) obs: 0.055 / Rpim(I) all: 0.027 / Χ2: 0.672 / Net I/σ(I): 21.6
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1724 / CC1/2: 0.705 / Rpim(I) all: 0.4 / Χ2: 0.82 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.7→47.045 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.7
RfactorNum. reflection% reflectionSelection details
Rfree0.2397 1625 4.82 %random
Rwork0.2 ---
obs0.2018 33713 97.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.7→47.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6715 0 109 86 6910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036982
X-RAY DIFFRACTIONf_angle_d0.5689455
X-RAY DIFFRACTIONf_dihedral_angle_d6.9633998
X-RAY DIFFRACTIONf_chiral_restr0.05990
X-RAY DIFFRACTIONf_plane_restr0.0051210
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7003-2.77970.35451120.29222349X-RAY DIFFRACTION86
2.7797-2.86940.341610.2912618X-RAY DIFFRACTION98
2.8694-2.9720.31311570.27922690X-RAY DIFFRACTION99
2.972-3.0910.37931430.2752697X-RAY DIFFRACTION99
3.091-3.23160.27271470.25352683X-RAY DIFFRACTION99
3.2316-3.40190.27831370.21542709X-RAY DIFFRACTION100
3.4019-3.6150.25591230.21062736X-RAY DIFFRACTION99
3.615-3.8940.25091410.19662704X-RAY DIFFRACTION99
3.894-4.28560.2061970.17062738X-RAY DIFFRACTION99
4.2856-4.90520.16521250.14552702X-RAY DIFFRACTION98
4.9052-6.17780.18911380.16392738X-RAY DIFFRACTION99
6.1778-47.05190.17111440.16562724X-RAY DIFFRACTION97
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)
14.01121.3741-4.10360.5785-1.88587.27750.22320.08470.49490.08840.08030.4934-0.96350.0119-0.17680.50650.03380.26380.2648-0.05430.823663.93287.086187.2209
23.0132-1.4856-0.47480.89810.552.0020.2577-0.17340.8897-0.13650.03680.1016-0.30320.5648-0.26350.5093-0.05740.2140.363-0.18070.718371.760985.727688.8758
37.3242-0.43860.96672.14530.83291.69650.03560.69590.2128-0.28170.1654-0.4186-0.65110.5567-0.19360.4523-0.09270.20330.5289-0.13190.549374.843182.728678.8674
44.5812-0.01760.85470.6023-0.04680.64710.09310.19070.1609-0.0840.0184-0.1203-0.15360.2396-0.12950.3098-0.02890.10760.3148-0.13820.410379.035873.091685.2993
57.2198-4.93094.38646.0637-5.03274.27020.96960.8255-1.1526-0.11480.40650.36130.46590.6181-1.06460.31070.15620.03280.3711-0.19050.426562.888360.559283.0292
63.49753.6629-1.28226.47150.26754.38070.32780.6794-0.1657-0.5777-0.1260.14470.13610.6085-0.18350.26990.1311-0.05680.4856-0.07930.383655.883870.019270.1803
73.582-4.54130.30146.5083-1.84176.6530.16860.1611-0.2562-0.24940.35141.5686-0.5313-0.8285-0.4810.36620.15830.01140.45370.03420.687545.969475.565275.3706
86.5899-3.78674.77617.55-3.88028.32220.20810.3605-0.2987-0.29280.16111.04450.1066-0.6086-0.44070.41290.1677-0.10380.5035-0.08770.645546.473770.708666.4865
92.0163-0.42262.19120.1433-0.85662.7857-0.5042-0.01051.15950.38630.4143-0.7133-0.52670.7950.07950.8465-0.1330.20140.7709-0.43530.841389.54985.224299.8557
100.04670.23690.12381.3931-0.79564.44830.1727-0.193-0.18551.1503-0.1459-0.42660.19720.6531-0.16260.621-0.08760.06960.7752-0.36760.595895.155276.9362109.5793
117.0456-1.4260.65673.9228-1.16970.2706-0.4867-0.77390.96720.67330.2987-0.1594-0.12820.07220.12420.5219-0.05210.05720.5624-0.25960.509483.345281.2159102.2722
121.82880.0108-0.78041.45121.17123.788-0.1478-1.53330.83241.00110.04270.19910.15370.03790.15660.8794-0.04870.07390.9139-0.32940.612484.737774.958120.5246
130.77221.1243-1.44371.4288-1.01011.94880.3151-0.57640.32060.6575-0.06870.0277-0.34390.2482-0.20970.5519-0.02540.05650.6739-0.21520.376179.279866.3907114.9634
144.9003-0.2656-5.84131.5237-1.39379.0762-0.0029-0.80030.53540.9906-0.3998-0.47390.64520.23980.01060.6988-0.11780.07470.981-0.23870.384279.977861.8182124.4598
151.9838-0.18071.3372.5086-0.36763.5175-0.38230.0538-0.14460.18850.3198-0.00870.3483-0.20460.06560.431-0.08030.08510.4553-0.2270.345386.81967.9452101.9377
164.5543-1.209-0.81042.11580.02762.41070.09510.1092-0.12530.3781-0.14350.0330.2682-0.10150.02330.2838-0.03090.02140.3608-0.18530.339687.764362.346298.7202
176.92421.1431-0.24651.6195-0.082.6973-0.15830.1966-0.59210.10520.1071-0.34620.27930.48670.03770.29960.06110.01730.4216-0.18020.415998.9261.377993.9707
184.72340.87180.8551.3816-1.2321.5772-0.14690.3727-0.3345-0.06010.207-0.6873-0.71560.34470.05890.3346-0.17920.06620.7188-0.2540.7037107.288673.766288.5524
196.85362.1623-1.37465.3321-3.20362.5499-0.35210.1488-0.5927-0.69950.292-1.92660.68171.14250.38030.2291-0.0590.11950.9993-0.33580.8968113.209965.149789.5155
206.8432-0.955-1.3044-0.05180.32970.3611-0.3066-1.17591.31750.3050.12440.1539-0.03490.15660.09470.66240.01840.21120.649-0.27160.666361.756676.149117.3172
211.8135-0.40981.60150.0106-0.14921.4366-0.1024-0.61420.71620.16220.1885-0.0496-0.0870.0572-0.03440.52280.05310.17830.4353-0.16960.573259.643477.7948109.7963
224.6774-3.67255.88685.2777-5.21578.31330.1745-0.3502-0.2550.16960.49960.80920.0237-0.2796-0.68340.39030.02320.17510.3595-0.05790.527351.02670.6829109.0127
230.27540.34591.20240.1816-0.40642.16290.0793-0.0709-0.05870.13690.17570.1128-0.2003-0.1177-0.14150.30760.08830.11240.3592-0.0940.54456.785469.983396.2121
241.3061-0.08191.10550.16610.21141.44660.21450.08370.28310.45670.12910.4253-0.6256-0.6755-0.2970.47650.13060.15460.4193-0.10980.836547.874575.456287.7524
252.13870.56561.57412.8133-1.0181.5230.1474-0.25460.30640.20340.17420.2106-0.0030.2817-0.32130.41140.0420.13360.3533-0.160.316863.41660.957107.5648
266.08021.0523-2.34986.0362-7.15038.78260.0143-0.3593-0.1803-0.5869-0.17740.0691.23190.54080.12390.44290.02830.07530.3188-0.1150.288768.201851.7228108.3643
276.3635-5.53572.4332.0942-3.56711.2510.0552-0.4243-0.1034-0.8257-0.10050.1165-0.1601-0.43030.09760.49860.00350.02810.4410.00110.289659.308146.803119.6331
283.2462-0.3513-2.76233.82434.29636.675-0.032-1.3197-0.06431.222-0.14610.275-0.1237-0.06070.13890.8243-0.01140.13530.6992-0.01880.312762.336656.6298129.7546
295.55791.0645-5.07184.41810.03318.49870.0793-0.7349-0.43530.55940.01930.1690.3491-0.3042-0.03630.7468-0.03110.15240.9683-0.08170.301859.269147.8809131.8197
302.34573.16811.67332.6020.78370.9352-0.46670.49450.1388-1.29110.6760.2170.209-0.3429-0.18350.47330.0232-0.04920.5257-0.0340.269856.27240.96346.9529
314.3961.3233-0.73122.1909-1.37671.53260.0239-0.1271-0.2120.0023-0.0718-0.0962-0.22940.17040.0090.39490.0431-0.04130.3633-0.05190.114459.574442.188650.1527
326.48933.31790.15535.03771.83376.0947-0.551.2637-0.7093-1.10150.54790.13750.27360.22120.04280.4412-0.0508-0.03090.3732-0.10050.300962.944925.4547.9091
334.7948-1.7686-0.41577.30631.93615.334-0.30540.1106-0.8991-0.29390.4730.19310.8988-0.1737-0.08910.4459-0.09080.00010.2873-0.00080.248255.571327.524155.7429
341.0531-1.6671.30482.3282-1.14771.25890.26120.0838-0.2422-0.4704-0.0910.09330.4186-0.1438-0.16170.3047-0.0261-0.04680.2102-0.05070.233868.81427.16560.8104
351.8432-1.84841.183.9603-0.63950.71810.10.6172-0.7343-0.23360.03990.2340.0448-0.1025-0.13490.44510.045-0.07320.3663-0.1080.314873.815714.827458.0975
362.07260.1459-0.80293.65830.31021.8062-0.0472-0.1782-0.11580.18340.1334-0.1769-0.0691-0.1779-0.12730.22940.0149-0.05680.27330.00730.110659.583239.052565.8748
373.8276-1.0803-0.74541.833-0.13382.1557-0.0555-0.3828-0.09580.26070.26950.2414-0.126-0.3893-0.20160.27150.047-0.02950.31540.08170.208444.745545.997768.1354
382.1548-0.24843.84931.62410.81534.91650.3498-0.88890.63940.74570.04530.8865-0.0434-1.8095-0.20230.32910.18730.17540.71450.25940.50233.382247.538969.7925
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 24 )
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 58 )
3X-RAY DIFFRACTION3chain 'A' and (resid 59 through 75 )
4X-RAY DIFFRACTION4chain 'A' and (resid 76 through 162 )
5X-RAY DIFFRACTION5chain 'A' and (resid 163 through 173 )
6X-RAY DIFFRACTION6chain 'A' and (resid 174 through 189 )
7X-RAY DIFFRACTION7chain 'A' and (resid 190 through 204 )
8X-RAY DIFFRACTION8chain 'A' and (resid 205 through 217 )
9X-RAY DIFFRACTION9chain 'B' and (resid 3 through 16 )
10X-RAY DIFFRACTION10chain 'B' and (resid 17 through 28 )
11X-RAY DIFFRACTION11chain 'B' and (resid 29 through 42 )
12X-RAY DIFFRACTION12chain 'B' and (resid 43 through 67 )
13X-RAY DIFFRACTION13chain 'B' and (resid 68 through 105 )
14X-RAY DIFFRACTION14chain 'B' and (resid 106 through 118 )
15X-RAY DIFFRACTION15chain 'B' and (resid 119 through 136 )
16X-RAY DIFFRACTION16chain 'B' and (resid 137 through 162 )
17X-RAY DIFFRACTION17chain 'B' and (resid 163 through 189 )
18X-RAY DIFFRACTION18chain 'B' and (resid 190 through 204 )
19X-RAY DIFFRACTION19chain 'B' and (resid 205 through 217 )
20X-RAY DIFFRACTION20chain 'C' and (resid 3 through 24 )
21X-RAY DIFFRACTION21chain 'C' and (resid 25 through 58 )
22X-RAY DIFFRACTION22chain 'C' and (resid 59 through 75 )
23X-RAY DIFFRACTION23chain 'C' and (resid 76 through 95 )
24X-RAY DIFFRACTION24chain 'C' and (resid 96 through 118 )
25X-RAY DIFFRACTION25chain 'C' and (resid 119 through 162 )
26X-RAY DIFFRACTION26chain 'C' and (resid 163 through 173 )
27X-RAY DIFFRACTION27chain 'C' and (resid 174 through 183 )
28X-RAY DIFFRACTION28chain 'C' and (resid 184 through 204 )
29X-RAY DIFFRACTION29chain 'C' and (resid 205 through 217 )
30X-RAY DIFFRACTION30chain 'D' and (resid 1 through 24 )
31X-RAY DIFFRACTION31chain 'D' and (resid 25 through 42 )
32X-RAY DIFFRACTION32chain 'D' and (resid 43 through 58 )
33X-RAY DIFFRACTION33chain 'D' and (resid 59 through 75 )
34X-RAY DIFFRACTION34chain 'D' and (resid 76 through 95 )
35X-RAY DIFFRACTION35chain 'D' and (resid 96 through 118 )
36X-RAY DIFFRACTION36chain 'D' and (resid 119 through 162 )
37X-RAY DIFFRACTION37chain 'D' and (resid 163 through 204 )
38X-RAY DIFFRACTION38chain 'D' and (resid 205 through 217 )

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