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- PDB-5j92: Crystal structure of a putative alpha-ketoglutarate dependent 2,4... -

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Basic information

Entry
Database: PDB / ID: 5j92
TitleCrystal structure of a putative alpha-ketoglutarate dependent 2,4-D dioxygenase from Burkholderia xenovorans
ComponentsPutative alpha KG dependent 2,4-D dioxygenase
KeywordsOXIDOREDUCTASE / SSGCID / alpha-ketoglutarate dependent dioxygenase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor / dioxygenase activity
Similarity search - Function
Clavaminate synthase-like / Double-stranded beta-helix / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / : / Putative alpha KG dependent 2,4-D dioxygenase
Similarity search - Component
Biological speciesBurkholderia xenovorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of a putative alpha-ketoglutarate dependent 2,4-D dioxygenase from Burkholderia xenovorans
Authors: Conrady, D.G. / Dranow, D.M. / Lorimer, D. / Edwards, T.E.
History
DepositionApr 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_prerelease_seq / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative alpha KG dependent 2,4-D dioxygenase
B: Putative alpha KG dependent 2,4-D dioxygenase
C: Putative alpha KG dependent 2,4-D dioxygenase
D: Putative alpha KG dependent 2,4-D dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,3419
Polymers141,0594
Non-polymers2825
Water20,0871115
1
A: Putative alpha KG dependent 2,4-D dioxygenase
D: Putative alpha KG dependent 2,4-D dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,6414
Polymers70,5292
Non-polymers1122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative alpha KG dependent 2,4-D dioxygenase
C: Putative alpha KG dependent 2,4-D dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7005
Polymers70,5292
Non-polymers1713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.700, 77.880, 92.140
Angle α, β, γ (deg.)90.000, 92.110, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 2 and (name N or name...
21(chain B and ((resid 2 and (name N or name...
31(chain C and (resid 2:31 or resid 33:46 or resid...
41(chain D and (resid 2:22 or (resid 23 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 2 and (name N or name...A2
121(chain A and ((resid 2 and (name N or name...A1 - 291
131(chain A and ((resid 2 and (name N or name...A1 - 291
141(chain A and ((resid 2 and (name N or name...A1 - 291
151(chain A and ((resid 2 and (name N or name...A1 - 291
211(chain B and ((resid 2 and (name N or name...B2
221(chain B and ((resid 2 and (name N or name...B2 - 291
231(chain B and ((resid 2 and (name N or name...B2 - 291
241(chain B and ((resid 2 and (name N or name...B2 - 291
251(chain B and ((resid 2 and (name N or name...B2 - 291
311(chain C and (resid 2:31 or resid 33:46 or resid...C2 - 31
321(chain C and (resid 2:31 or resid 33:46 or resid...C33 - 46
331(chain C and (resid 2:31 or resid 33:46 or resid...C48 - 66
341(chain C and (resid 2:31 or resid 33:46 or resid...C102 - 103
351(chain C and (resid 2:31 or resid 33:46 or resid...C2 - 301
361(chain C and (resid 2:31 or resid 33:46 or resid...C2 - 301
371(chain C and (resid 2:31 or resid 33:46 or resid...C2 - 301
381(chain C and (resid 2:31 or resid 33:46 or resid...C2 - 301
411(chain D and (resid 2:22 or (resid 23 and (name...D2 - 22
421(chain D and (resid 2:22 or (resid 23 and (name...D23
431(chain D and (resid 2:22 or (resid 23 and (name...D2 - 290
441(chain D and (resid 2:22 or (resid 23 and (name...D2 - 290
451(chain D and (resid 2:22 or (resid 23 and (name...D2 - 290
461(chain D and (resid 2:22 or (resid 23 and (name...D2 - 290

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Components

#1: Protein
Putative alpha KG dependent 2,4-D dioxygenase


Mass: 35264.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia xenovorans (strain LB400) (bacteria)
Strain: LB400 / Gene: Bxe_B2152 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q13Q05, Oxidoreductases; Acting on paired donors, with incorporation or reduction of molecular oxygen; With 2-oxoglutarate as one donor, and incorporation of one atom of oxygen into each donor
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1115 / 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: 2.15 Å3/Da / Density % sol: 42.87 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Rigaku Reagents MCSG1 screen h3: 20% PEG 3350, 200mM LiCl; BuxeA.00024.e.B1 PS02518 at 19.1mg/ml, cryo protected in 80% mother liquor-20% ethylene glycol mix

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Mar 16, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→48.121 Å / Num. obs: 85505 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.22 % / Biso Wilson estimate: 20.23 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.17
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.95-20.5112.79198.8
2-2.060.3594.03199.1
2.06-2.120.2924.93199.1
2.12-2.180.2565.56199.2
2.18-2.250.1728.58187.8
2.25-2.330.2236.68187
2.33-2.420.1638.41199.4
2.42-2.520.13110.2199.2
2.52-2.630.11211.87199.5
2.63-2.760.09314.12199.7
2.76-2.910.07317.12199.6
2.91-3.080.05820.91199.8
3.08-3.30.04625.49199.8
3.3-3.560.04128.44199.7
3.56-3.90.04130.9198.6
3.9-4.360.03236.36199.6
4.36-5.030.0337.82199.8
5.03-6.170.03134.991100
6.17-8.720.02837.441100
8.720.02243.5198

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXdev_2356refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PVJ

3pvj


Resolution: 1.95→48.121 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.98
RfactorNum. reflection% reflection
Rfree0.2149 4153 4.86 %
Rwork0.1764 --
obs0.1782 85485 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.15 Å2 / Biso mean: 25.3388 Å2 / Biso min: 7.74 Å2
Refinement stepCycle: final / Resolution: 1.95→48.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8167 0 8 1136 9311
Biso mean--39 31.82 -
Num. residues----1032
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068515
X-RAY DIFFRACTIONf_angle_d0.82211614
X-RAY DIFFRACTIONf_chiral_restr0.0541251
X-RAY DIFFRACTIONf_plane_restr0.0061527
X-RAY DIFFRACTIONf_dihedral_angle_d13.9115125
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4524X-RAY DIFFRACTION9.315TORSIONAL
12B4524X-RAY DIFFRACTION9.315TORSIONAL
13C4524X-RAY DIFFRACTION9.315TORSIONAL
14D4524X-RAY DIFFRACTION9.315TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-1.97210.34681540.28532704285899
1.9721-1.99530.27051500.22322694284498
1.9953-2.01960.24061430.203427652908100
2.0196-2.04520.26321370.19462734287199
2.0452-2.07210.22221370.18122704284199
2.0721-2.10050.2351410.17972709285099
2.1005-2.13050.23141490.1772756290599
2.1305-2.16230.25751460.17842734288099
2.1623-2.19610.23411420.199327272869100
2.1961-2.23210.50591200.36992136225677
2.2321-2.27060.50981320.45872427255989
2.2706-2.31190.37091300.2872352248285
2.3119-2.35630.24671520.18612748290099
2.3563-2.40440.24481420.173127202862100
2.4044-2.45670.20691380.16042750288899
2.4567-2.51380.20081510.16112745289699
2.5138-2.57670.27071090.164927752884100
2.5767-2.64640.20911360.16282756289299
2.6464-2.72420.22091210.169327752896100
2.7242-2.81220.22081230.171327912914100
2.8122-2.91260.2371070.171727812888100
2.9126-3.02920.20531330.160627862919100
3.0292-3.16710.18851220.154927912913100
3.1671-3.3340.16171460.156527442890100
3.334-3.54290.17091520.15227992951100
3.5429-3.81630.22861510.17592698284998
3.8163-4.20010.1481920.132715290799
4.2001-4.80740.12531330.117428192952100
4.8074-6.0550.16331290.135928442973100
6.055-48.13530.14781350.14992853298899
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)
15.6888-1.13341.04761.813-2.37528.2443-0.2482-0.17880.3190.2014-0.2250.0127-0.29090.2610.42130.10740.0025-0.01560.15020.01410.190828.493511.435574.1496
22.9254-0.4186-0.9592.3097-0.81573.1892-0.1364-0.6136-0.01170.42990.1610.0272-0.0067-0.31020.01440.19630.001-0.01710.33570.00010.145420.48369.663583.8898
31.76650.29120.02870.68090.10961.63390.0187-0.2966-0.16840.11410.01750.08710.19-0.1882-0.04110.14050.01940.02680.19640.02310.178810.22445.866769.8569
43.002-0.1766-0.27731.79650.3732.15-0.0270.12080.29960.0842-0.00840.27780.0159-0.25180.0030.11190.0339-0.00440.1539-0.01980.16132.963114.548558.5068
51.8215-0.48630.57930.8547-0.06240.872-0.0205-0.1419-0.00970.07580.00910.171-0.0598-0.1140.01950.10450.01080.01660.12090.00430.15488.547713.318763.0904
62.4668-0.26650.21680.0407-0.16352.2460.1241-0.1326-0.39150.1891-0.15960.2370.5183-0.15550.00870.2611-0.0181-0.00660.23190.03220.231413.371-0.898566.9066
74.12130.22141.43611.5535-0.7014.8379-0.2255-0.67180.02570.4964-0.00780.1637-0.3787-0.78240.28380.24790.02760.06430.4261-0.01090.19888.970912.879881.1379
82.8195-0.7886-0.89332.30351.6022.91140.01230.21130.0683-0.2434-0.0350.0258-0.0541-0.05770.02720.1132-0.0054-0.01220.08640.01860.114734.46276.703242.9278
91.23530.20770.6981.5921-2.11613.77760.04520.0551-0.0374-0.1073-0.057-0.1770.23530.28470.02880.16490.03290.02820.1555-0.01820.202452.77626.56553.9329
100.70480.36930.332510.25730.9890.0323-0.0105-0.0550.0213-0.0403-0.08470.07170.10760.02680.10270.01240.01010.11070.01430.141147.163611.852660.0409
112.29311.4877-0.06447.6483-0.01011.3071-0.16750.20750.0555-0.61440.1967-0.1677-0.06190.0943-0.03650.1776-0.01730.02760.23120.00540.182747.914610.439842.8125
121.3803-0.671-0.22741.92840.48563.49790.0484-0.38480.00060.3037-0.01430.26680.1209-0.5204-0.05770.2878-0.01310.03580.3407-0.0240.120833.28527.745997.3614
130.8860.06460.05251.38670.12991.45040.0491-0.482-0.08920.6519-0.0018-0.06160.2172-0.1277-0.0230.3870.00140.00590.41170.02590.114241.72425.8702107.4176
141.90660.08310.21122.57860.57842.4529-0.162-0.34350.18230.4450.1985-0.0863-0.27660.0052-0.01920.31940.04290.00980.3031-0.02470.118544.805314.6726102.9745
150.0180.1822-0.29252.5265-4.53278.04270.1207-0.34270.13010.4294-0.2044-0.2145-0.40240.67010.17980.2685-0.0137-0.03520.3241-0.03560.198557.429415.654789.5487
161.6202-1.1406-0.29622.57880.13171.3980.0567-0.110.12060.0833-0.0419-0.2043-0.02750.15780.00120.2109-0.012-0.00570.2350.00420.144950.122412.797990.2323
171.6834-0.5953-0.86852.44030.89112.714-0.05640.0963-0.2647-0.0076-0.11380.1470.3231-0.23420.16050.2361-0.01470.00370.19090.01460.140742.4317-3.83780.8149
181.1365-0.78890.7663.24180.24432.7076-0.0241-0.03720.02730.28850.0496-0.4005-0.04690.4439-0.05850.20360.0324-0.0080.33280.04040.221163.72596.923180.5419
191.3654-0.325-0.2661.01420.02681.304-0.0044-0.098-0.07430.1117-0.0613-0.21320.15890.17310.04710.2490.0373-0.01150.20460.04070.195353.956-3.315884.423
205.7897-1.2896-2.8642.91380.48514.53850.07430.3363-0.0579-0.2322-0.2341-0.19830.16180.03580.13490.19090.02930.0130.19470.03760.164650.8738-0.840772.0517
211.0002-0.16420.04291.50650.00451.87790.0417-0.04260.09840.1253-0.07950.017-0.2052-0.02750.03150.2030.01290.0020.21930.00580.138743.165314.877587.7282
223.15430.5203-1.04032.02170.15665.6777-0.0403-0.4524-0.26210.55190.2679-0.25080.21590.3548-0.18250.2645-0.0083-0.09450.35630.00470.218253.78947.168999.9927
231.72640.31890.72082.2168-0.18832.9883-0.03440.43970.107-0.43140.05190.0585-0.18810.083-0.01020.18480.00850.00090.19940.02760.161216.60260.892821.3248
241.28850.1078-0.15141.50160.15541.93970.01220.13770.11-0.105-0.04440.1403-0.2347-0.10890.02960.11860.0048-0.0050.1357-0.00160.20476.48764.374134.8111
256.2541-0.131.31513.2945-0.8923.13940.1113-0.1942-0.70930.1445-0.11410.16170.36490.2129-0.00570.1784-0.01310.00410.16270.01070.17189.4638-12.111449.3585
261.08240.0044-0.37461.15980.00631.18370.052-0.01920.0982-0.0041-0.04020.1946-0.0951-0.0678-0.00280.11740.0001-0.00190.112-0.01180.21175.92590.835941.652
275.94255.18360.1517.84040.7452.5892-0.01940.3320.1031-0.4785-0.0410.5247-0.09870.04420.05840.18730.0439-0.09320.26370.00760.2143.5628-2.542525.1953
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 17 )A1 - 17
2X-RAY DIFFRACTION2chain 'A' and (resid 18 through 61 )A18 - 61
3X-RAY DIFFRACTION3chain 'A' and (resid 62 through 151 )A62 - 151
4X-RAY DIFFRACTION4chain 'A' and (resid 152 through 183 )A152 - 183
5X-RAY DIFFRACTION5chain 'A' and (resid 184 through 257 )A184 - 257
6X-RAY DIFFRACTION6chain 'A' and (resid 258 through 275 )A258 - 275
7X-RAY DIFFRACTION7chain 'A' and (resid 276 through 291 )A276 - 291
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 61 )B2 - 61
9X-RAY DIFFRACTION9chain 'B' and (resid 62 through 125 )B62 - 125
10X-RAY DIFFRACTION10chain 'B' and (resid 126 through 275 )B126 - 275
11X-RAY DIFFRACTION11chain 'B' and (resid 276 through 291 )B276 - 291
12X-RAY DIFFRACTION12chain 'C' and (resid 2 through 17 )C2 - 17
13X-RAY DIFFRACTION13chain 'C' and (resid 18 through 39 )C18 - 39
14X-RAY DIFFRACTION14chain 'C' and (resid 40 through 61 )C40 - 61
15X-RAY DIFFRACTION15chain 'C' and (resid 62 through 111 )C62 - 111
16X-RAY DIFFRACTION16chain 'C' and (resid 112 through 140 )C112 - 140
17X-RAY DIFFRACTION17chain 'C' and (resid 141 through 161 )C141 - 161
18X-RAY DIFFRACTION18chain 'C' and (resid 162 through 189 )C162 - 189
19X-RAY DIFFRACTION19chain 'C' and (resid 190 through 222 )C190 - 222
20X-RAY DIFFRACTION20chain 'C' and (resid 223 through 237 )C223 - 237
21X-RAY DIFFRACTION21chain 'C' and (resid 238 through 275 )C238 - 275
22X-RAY DIFFRACTION22chain 'C' and (resid 276 through 290 )C276 - 290
23X-RAY DIFFRACTION23chain 'D' and (resid 2 through 61 )D2 - 61
24X-RAY DIFFRACTION24chain 'D' and (resid 62 through 151 )D62 - 151
25X-RAY DIFFRACTION25chain 'D' and (resid 152 through 169 )D152 - 169
26X-RAY DIFFRACTION26chain 'D' and (resid 170 through 275 )D170 - 275
27X-RAY DIFFRACTION27chain 'D' and (resid 276 through 290 )D276 - 290

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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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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